ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Models, Molecular  (484)
  • Chemistry
  • EARTH RESOURCES AND REMOTE SENSING
  • Nature Publishing Group (NPG)  (495)
  • Freshwater Biological Association  (39)
  • 2020-2022  (39)
  • 2010-2014  (495)
  • 1995-1999
  • 1980-1984
  • 1945-1949
  • 1925-1929
Collection
Keywords
Years
Year
  • 1
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4839 | 1256 | 2011-09-29 15:49:48 | 4839 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: The purpose of this work is a contribution to the quantitative record of the use of iron by planktonic algae. Preliminary experiments with Chlorella to determine the rate of iron intake in the presence of inorganic sources of iron did not produce the desired result. The crucial point of this work is the investigation of the influence of various external factors on the stability of FeEDTA (FeEDTA = Ferric(III)-compound of ethylene-diamine tetra-acetic acid), since this compound appears to be particularly well-suited as a source of iron for planktonic algae (e.g. TAMIYA et al. 1953). Cultures of Chlorella fusca in a light thermostat were used in experimental research. Methods and results are discussed.
    Description: Translated from German into English
    Keywords: Chemistry ; Ecology ; Limnology ; Biometrics ; Biological sampling ; Geographical distribution ; Population density ; Population characteristics ; Population number ; Freshwater crustaceans ; Population dynamics
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 2
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4843 | 1256 | 2011-09-29 15:49:28 | 4843 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: The reaction of Mn(II) with water-dissolved oxygen, to a higher manganese hydroxide in an alkaline medium, as with the longstanding classic Winkler method, is the first step in the method described here. The assumption for faultless results by the conventional and modified Winkler method is clean water, which contains no organic substances by Mn(III) or Mn(IV). In many cases, however, eg. in river and lake-water tests, it can be seen with the naked eye that after some time the originally brown-coloured precipitate of manganese hydroxide becomes more and more colourless. Oxygen content was analysed in the water samples and evaluated by raising the amount of the leuko-base and giving the corresponding dilution of the colouring matter solution formed still higher oxygen contents can be measured.
    Description: Translated from German into English
    Keywords: Chemistry ; Ecology ; Limnology ; Methodology ; Experimental research ; Dissolved oxygen ; Analytical techniques ; Water analysis
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 3
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4848 | 1256 | 2011-09-29 15:49:18 | 4848 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: When dissolved in water, compounds of nitrogen and phosphorus ought to contain the basic assimilated food requirements for autotrophic plants and therefore autotrophic algae. This article summarises the occurrence of nitrogen in water, how species of algae utilize nitrogen and phosphorus forms for growth and the capacities of algae to adapt to environments of different nutrient wealth. This topic has unquestionable importance not only for the purpose of survival of a species but also in deciding indirectly about the stability of ecosystems.
    Description: Translated from Polish into English
    Keywords: Biology ; Chemistry ; Limnology ; Algae ; Nitrogen fixation ; Nitrogen ; Phosphorus ; Nutritional requirements ; Bacteria ; Organic compounds
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 4
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4856 | 1256 | 2011-09-29 15:48:26 | 4856 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: Pseudomonas aeruginosa has for some time been known as a denitrifier. Pseudomonas aeruginosa was chosen for further studies, because P. aeruginosa occurs abundantly in Plusssee and moreover there are contradictory assertions on the gas products of denitrification by this bacteria. In experimental research the pattern of growth and gas production of Pseudomonas aeruginosa on nutrient broth was studied.
    Description: Translated from German into English
    Keywords: Chemistry ; Ecology ; Limnology ; Experimental research ; Bacteria ; Freshwater lakes ; Growth ; Microbiological culture ; Plusssee
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 5
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4857 | 1256 | 2011-09-29 15:48:28 | 4857 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: There is no doubt that determination of the biomass of zooplankton (primarily of crustaceans) will be taken into consideration in practice and limnological works, especially after the recent publication of fairly comprehensive tables of weights of a whole range of species of freshwater copepods and cladocerans. The usefulness of applying formulae of determining the biomass of marine crustaceans for freshwater copepods is discussed.
    Description: Translated from Russian into English
    Keywords: Chemistry ; Ecology ; Limnology ; Freshwater crustaceans ; Zooplankton ; Biomass ; Formulae
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 6
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4877 | 1256 | 2011-09-29 15:47:02 | 4877 | Freshwater Biological Association
    Publication Date: 2021-07-06
    Description: The determination of bi- and trivalent iron in proximity, in mineral waters has gained in significance, on biological and technical grounds. This short paper describes the procedure of the determination of bivalent iron and total iron in a water sample.
    Description: Translated from German into English
    Keywords: Chemistry ; Limnology ; Iron ; Acids ; Analytical techniques ; Minerals ; Water analysis
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 7
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4964 | 1256 | 2011-09-29 15:39:04 | 4964 | Freshwater Biological Association
    Publication Date: 2021-07-07
    Description: The nitrification in the ocean is influenced by several environmental factors and the importance of these is more or less known. There are very likely many more to be discovered in the study of the interaction of nitrification bacteria and other micro-organisms in the ocean. Some of the factors to be considered will briefly be dealt with in this paper. Then the authors give the results of an incubation experiment in the Baltic Sea and from a detailed study in Gullmarn.
    Description: Translated from Swedish into English
    Keywords: Chemistry ; Ecology ; Oceanography ; Marine ecology ; Nitrification ; Experimental research ; Sediment analysis ; Bacteria ; Carbon fixation ; Nitrosococcus oceanus ; Nitrococcus mobilis
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 8
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4967 | 1256 | 2011-09-29 15:36:52 | 4967 | Freshwater Biological Association
    Publication Date: 2021-07-07
    Description: Utilization of the heavy isotope of nitrogen as a tracer has found numerous applications in soil biology. It allows better definition of different stages of the nitrogen cycle, in particular the immobilization-mineralization cycle. In this work, the authors report the results of calculations of natural isotope ratios of nitrogen in samples of water, soil and vegetation prevailing in Dombes and discuss the possibilities of errors and coefficients of fractionation.
    Description: Translated from French into English
    Keywords: Chemistry ; Ecology ; Limnology ; Nitrogen isotopes ; Soils ; Tracers ; Bacteria ; Nitrogen compounds ; France ; Dombes
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 9
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4963 | 1256 | 2011-09-29 15:39:01 | 4963 | Freshwater Biological Association
    Publication Date: 2021-07-07
    Description: This short translation summarises experiments on the production of a highly dispersible precipitate of calcium carbonate. The translation covers the 'Experimental section' (of the original larger paper) only.
    Description: Translated from Polish into English
    Keywords: Chemistry ; Limnology ; Experimental research ; Calcium carbonates ; Magnetic fields ; Ultrasonic devices
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 10
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4988 | 1256 | 2011-09-29 15:36:31 | 4988 | Freshwater Biological Association
    Publication Date: 2021-07-07
    Description: This abbreviated translation summarises the chemical composition of Iraq water resources. Among the described water bodies are the River Euphrates, Shatt al Arab River and a number of standing waters.
    Description: Translated from Russian into English
    Keywords: Chemistry ; Ecology ; Limnology ; Inland water environment ; Inland waters ; Water analysis ; Iraq
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 11
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/4980 | 1256 | 2011-09-29 15:38:06 | 4980 | Freshwater Biological Association
    Publication Date: 2021-07-07
    Description: This partial translation of the original paper provides the summary of this study of the mechanism of mass transfer in the formation of hydrothermal deposits of sulphides. For determining the solubility of sulphides of iron, the radioactive isotope Fe59 was used. The solubility of two sulphides was determined.
    Description: Translated from Russian into English
    Keywords: Chemistry ; Ecology ; Limnology ; Sulphide deposits ; Sulphides ; Hydrothermal deposits ; Iron isotopes ; Solubility
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 12
    facet.materialart.
    Unknown
    Freshwater Biological Association | Windermere, UK
    In:  http://aquaticcommons.org/id/eprint/5054 | 1256 | 2011-09-29 15:29:08 | 5054 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: Observations are reported on the content of organic matter in the Moscow region in 1941. Some data is given on alkalinity, oxygen content and colourisation of the rivers.
    Description: Translated from Russian into English
    Keywords: Biology ; Chemistry ; Limnology ; Rivers ; Organic matter ; Alkalinity ; Dissolved oxygen ; Colour
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 13
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5238 | 1256 | 2011-09-29 15:13:42 | 5238 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: This report presents five batches of data which have been despatched to the Joint Research Centre, Ispra. The data as been allocated to various ECDIN (Environmental Chemicals Data and Information Network) files. The data comprises environmental chemicals in the freshwater environment, taking in paricular consideration: aquatic toxicity, bioaccumulation, metabolism and elimination biodegradation.
    Keywords: Chemistry ; Ecology ; Limnology ; Data ; Data processing ; Data collections ; Chemical compounds ; Toxicity ; Bioaccumulation ; Biodegradation ; Metabolism
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 8
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 14
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5293 | 1256 | 2011-09-29 15:08:09 | 5293 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Esthwaite Water is the most productive or eutrophic lake in the English Lake District. Since 1945 its water quality has been determined from weekly or biweekly measurements of temperature, oxygen, plant nutrients and phytoplankton abundance. The lake receives phosphorus from its largely lowland-pasture catchment, sewage effluent from the villages of Hawkshead and Near Sawrey, and from a cage-culture fish farm. From 1986 phosphorus has been removed from the sewage effluent of Hawkshead which was considered to contribute between 47% and 67% of the total phosphorus loading to the lake. At the commencement of phosphorus removal regular measurements of phosphorus in the superficial 0-4 cm layer of lake sediment were made from cores collected at random sites. Since 1986 the mean annual concentration of alkali-extractable sediment phosphorus has decreased by 23%. This change is not significant at the 5% level but nearly so. There has been no marked change in water quality over this period. Summer dominance of blue-green algae which arose in the early 1980s after decline of the previous summer forms, Ceratium spp., has been maintained. Improvement in water quality is unlikely to be achieved at the present phosphorus loading.
    Keywords: Chemistry ; Limnology ; Pollution ; Eutrophication ; Freshwater lakes ; Limnological surveys ; Phosphorus ; Phytoplankton ; Primary production ; Sediment analysis ; Water quality ; England ; Esthwaite Water
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 119-131
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 15
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5157 | 3949 | 2011-09-29 15:19:58 | 5157 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: The area studied was the River Frome system below Dorchester. The main river has its origins mainly in chalk springs, although some of its tributaries have surface run-off from farm lands and heath-lands. Thus the chemistry of the river is affected by changes in land practice and differences in the geology of the catchment area. Regular chemical analysis of chalk waters started at the River Laboratory in 1964, Regular weekly analyses have been carried out since 1965 at Bere Stream (a small chalk stream) and the River Frome (a large chalk stream); also single samples have been analysed to provide preliminary information. In 1970-71 an attempt was made to discover the contribution each main source made to the flow and chemical composition of the River Frome. Results of these investigations are presented in the paper.
    Keywords: Chemistry ; Environment ; Chemical analysis ; Chemical composition ; Rivers ; Stream flow ; Annual report ; England ; Dorset
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 16
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5171 | 3949 | 2011-09-29 15:18:48 | 5171 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An explanation of the basic premises of the subject and its terminology is given. The article then outlines aspects of research on the organic material found in lacustrine sediments, and the analytical methods involved.
    Keywords: Chemistry ; Earth Sciences ; Diagenesis ; Freshwater lakes ; Geochemistry ; Lipids ; Sediment analysis ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 45-56
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 17
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5225 | 1256 | 2011-09-29 15:12:36 | 5225 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The overall goal of the joint research project is to relate the chemical reactions involved in the formation of organo-aluminium complexes under acid conditions to their toxic effects on the physiology of aquatic organisms. Finally, this research is intended to predict toxic effects arising from acidity and aluminium under varying environmental conditions. This interim report examines the chemical modelling of ion-binding by humic substances where a computer model has been developed and is being tested using field data, and conditions required for the precipitation of aluminium in surface waters.
    Keywords: Chemistry ; Limnology ; Pollution ; Modelling ; Models ; Humic acids ; Surface water ; Aluminium compounds ; Aluminium ; Ions ; Toxicity ; England ; Duddon River
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 26
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 18
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5239 | 3949 | 2011-09-29 15:13:47 | 5239 | Freshwater Biological Association
    Publication Date: 2021-06-24
    Description: This review discusses the processes involved in the decomposition of organic carbon derived initially from structural components of algae and other primary producers. It describes how groups of bacteria interact in time and space in a eutrophic lake. The relative importance of anaerobic and aerobic processes are discussed. The bulk of decomposition occurs within the sediment. The role of bacteria in the nitrogen cycle and the iron cycle, and in sulphate reduction and methanogenesis as the terminal metabolism of organic carbon are described.
    Keywords: Biology ; Chemistry ; Anaerobic bacteria ; Bacteria ; Biodegradation ; Carbon cycle ; Eutrophic lakes ; Fresh water ; Geochemical cycle ; Iron ; Manganese ; Nitrates ; Nitrogen cycle ; Organic carbon ; Oxygen consumption ; Partical size ; Sedimentation ; Sulphates ; Sulphur ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 31-44
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 19
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5247 | 3949 | 2011-09-29 15:08:19 | 5247 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The dace, Leuciscus leuciscus (L.) is an important cyprinid in terms of population biomass in chalk streams of southern England. Dace recruitment has been shown to vary widely from year to year and it is thought that this variation is largely as a result of the influence of abiotic factors, chiefly water temperature. From 1968 to 1981 there was a thirteen-fold difference in the year class structure index between the minimum index (0.25 in 1972) and the maximum (3.21 in 1976). The problems of such variation, especially those that could ensue from a succession of poor year-classes, are offset by the spread of reproductive effort by each female over several years.
    Keywords: Biology ; Chemistry ; Fisheries ; Abiotic factors ; Age composition ; Annual variations ; Climate ; Fecundity ; Fish eggs ; Fish larvae ; Freshwater fish ; Life history ; Mortality ; Population dynamics ; Predation ; Recruitment ; Sexual reproduction ; Survivial ; Water temperature ; Cyprinidae ; Leuciscus leuciscus ; England ; Dorset ; Chalk streams ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 83-96
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 20
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5257 | 1256 | 2011-09-29 15:09:23 | 5257 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Phosalone is a non systematic, wide spectrum organophosphate pesticide which was discovered in 1961 in the laboratories of the Societe des Usines Chimique Rhone-Poulenc in France. It has been approved for commercial use since 1964 in France, in Australia since 1966, in the United Kingdom in 1967 and in many other countries including Japan, Egypt, USSR and the USA. This study provides a full literature review on all aspects of phosalone including its physical, biological and chemical characteristics, and analytical methods of analysis with particular reference to soils/sediments. Furthermore, it aims to develop a method for the determintion of phosalone in aquatic sediments and to determine the adsorption of phosalone onto kaolinite.
    Keywords: Chemistry ; Limnology ; Pollution ; Insecticides ; Metabolism ; Toxicity ; Biodegradation ; Adsorption
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 54
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 21
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5278 | 1256 | 2011-09-29 15:11:09 | 5278 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: A literature survey was carried out into the effects of petroleum hydrocarbons in freshwater, from the toxicity, biodegradability and concentration aspects. It was supplemented by a selective search on hydrocarbons in the marine environment for comparison. The aim was to determine the major inputs of these hydrocarbons, their accumulation, effects and fate in freshwaters. The search was confined to the period 1965-1978. The bibliography contains 390 references, divided by subject.
    Keywords: Chemistry ; Limnology ; Pollution ; literature reviews ; petroleum ; toxicity ; biodegradation
    Repository Name: AquaDocs
    Type: book , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 52
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 22
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5349 | 1256 | 2011-05-13 11:55:43 | 5349 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of some major ions in the stream water of the River Duddon in Cumbria. Measurements of sodium, calcium, potassium, magnesium and chloride ions and pH were taken at 5 stations in the River Duddon between January 1970 and August 1974.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of Major Ions in Streams on Catchments of the River Duddon (1971-1974) and Windermere (1975-1978), English Lake District. Freshwater Biological Association, Ambleside, UK, 1983 (FBA Occasional Publications 22)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: text/html
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 23
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5351 | 1256 | 2011-05-13 11:55:21 | 5351 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of some major ions in the stream water of the catchment of Lake Windermere in Cumbria. Measurements of sodium, calcium, potassium, magnesium, chloride ions and pH were taken at 37 stations in the catchment between 1975 and 1978.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of major ions in streams on catchments of the River Duddon (1971-1974) and Windermere (1975-1978), English Lake District. Freshwater Biological Association, Ambleside, UK, 1983 (FBA Occasional Publications 22)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; England ; Lake Windermere ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: text/html
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 24
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5354 | 1256 | 2011-09-16 12:01:28 | 5354 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of 182 tarns in the English Lake District, Cumbria. Measurements of sodium, calcium, potassium, magnesium, pH, chloride ions, alkalinity, sulphite, strong acids and nitrate were taken between 1953 and 1978.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of major ions in lakes and tarns on the English Lake District (1953-1978). Freshwater Biological Association, Ambleside, UK, 1982 (FBA Occasional Publications 16)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; alkalinity ; England ; Lake District ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: application/vnd.ms-excel
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 25
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5352 | 1256 | 2012-07-04 19:32:47 | 5352 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of treated sewage effluent from Grasmere Treatment Unit in Cumbria. Measurements of sodium, calcium, potassium, magnesium and chloride ions were taken between 1974 and 1976.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of major ions in streams on catchments of the River Duddon (1971-1974) and Windermere (1975-1978), English Lake District. Freshwater Biological Association, Ambleside, UK, 1983 (FBA Occasional Publications 22)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; England ; Grasmere ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: application/vnd.ms-excel
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 26
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5350 | 1256 | 2011-05-13 11:56:03 | 5350 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of some major ions in the stream water of the upper basin of the River Duddon in Cumbria. Measurements of sodium, calcium, potassium, magnesium and chloride ions and pH were taken at 26 stations in the River Duddon basin between 1972 and 1974.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of Major Ions in Streams on Catchments of the River Duddon (1971-1974) and Windermere (1975-1978), English Lake District. Freshwater Biological Association, Ambleside, UK, 1983 (FBA Occasional Publications 22)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; England ; River Duddon ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: text/html
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 27
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5353 | 1256 | 2012-07-04 19:33:33 | 5353 | Freshwater Biological Association
    Publication Date: 2021-07-10
    Description: This dataset provides raw data of chemical analyses made during studies on seasonal variations of 25 frequently sampled tarns in Cumbria. Measurements of sodium, calcium, potassium, magnesium, pH, chloride ions, alkalinity, sulphite, strong acids and nitrate were taken between 1954 and 1956 and between 1974-1976.
    Description: This data was used in the publication: Carrick, T.R. & Sutcliffe, D.W.: Concentrations of major ions in streams on catchments of the River Duddon (1971-1974) and Windermere (1975-1978), English Lake District. Freshwater Biological Association, Ambleside, UK, 1983 (FBA Occasional Publications 22)
    Keywords: Chemistry ; Limnology ; Calcium ; chlorides ; fresh water ; ions ; magnesium ; potassium ; seasonal variations ; sodium ; water analysis ; alkalinity ; England ; Lake District ; dataset
    Repository Name: AquaDocs
    Type: other
    Format: application/vnd.ms-excel
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 28
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5111 | 3949 | 2011-09-29 15:23:22 | 5111 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article discussing changes observed in phytoplankton of the Lake District. An overview is given of previous phytoplankton studies undertaken in the area, detailing some changes found in various waterbodies. Water quality changes in Lake Windermere are mentioned, including the gradual increase of dissolved organic matter (DOM), believed to be caused by the increase of sewage to the lake. The lakes in the Alps are given as an example of a similar anthropogenic pollution scenario. The treatment of a Lake District tarn with bone meal is described. The article goes on to discuss the composition of plankton throughout the year under a variety of climatic conditions. A figure shows seasonal variation in the consistuents of phytoplankton in Windermere (north basin).
    Keywords: Biology ; Chemistry ; Limnology ; Phytoplankton ; Limnology ; Dissolved organic matter ; Seasonal variations ; Sewage ; Water quality ; Annual reports ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 42-45
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 29
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5107 | 3949 | 2011-09-29 15:23:50 | 5107 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: A progress report on research undertaken on the chemical budget of a lake, outlining the importance of nitrogen and phosphorus in governing the production of life in freshwater. The report uses the Rivers Brathay and Leven, which flow into Windermere, as examples. The report also refers to the Rivers Rothay, Troutbeck and Cunsey. A table is including which shows the monthly average nitrate content (mg per litre) of the River Brathey and River Leven for 1937 into 1938. The report also includes a figure showing Windermere lake levels, discharge and rainfall during 1937. It also briefly considers possible anthropogenic influences on water quality.
    Keywords: Chemistry ; Ecology ; Limnology ; Phosphorus ; Organic compounds ; Sewage ; Diatoms ; Algae ; Sediment chemistry ; Seasonal variations ; Annual reports ; Nitrates ; River discharge ; England
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 38-42
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 30
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5114 | 3949 | 2011-09-29 15:21:32 | 5114 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article looking at the numerical distribution of bacteria in lakes, the types most commonly present and the nitrogen-cycle, in Lake Windermere. The methodology is explained, including the sampling frequency and depths, and bacteria culturing techniques. Water bodies other than Lake Windermere were also sampled and these are detailed, including a water reservoir. A summary of the work into horizontal of bacteria is given, including a table showing the number of bacteria per millilitre at different distances from inflow into Windermere. A summary of the work into vertical distribution is also given, including two figures, one showing seasonal variation during 1938-9 in numbers of bacteria at different depths in Winderemere, and the other showing the relationship between the numbers of bacteria at 10 metres depth in Windermere and the rainfull during the previous 7 days. A summary of the types of bacteria found, as well as work on the nitrogen cycle in Esthwaite Water, Lake Windermere and Blelham Tarn are given.
    Keywords: Biology ; Chemistry ; Limnology ; Nitrogen cycle ; Bacteria ; Freshwater ecology ; Limnology ; Seasonal variations ; Water column ; Water reservoirs ; Annual reports ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 51-57
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 31
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5112 | 3949 | 2011-09-29 15:23:20 | 5112 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article reviewing the work undertaken looking at the seasonal variation of chemical conditions in water at various depths in lakes. The laboratory tests undertaken for the research is outlined, as well as details of the sampling locations and the staff involved with the work. One figure shows the seasonal variation in the amounts of dissolved substances in the surface water of Windermere during 1936. Another figure shows seasonal varation inthe dry weight of phyto- and zooplankton in Windermere. Seasonal changes are discussed further and a table is included showing chemical conditions in winter and summer for Windermere.
    Keywords: Biology ; Chemistry ; Limnology ; Limnology ; Chemistry ; Seasonal variations ; Diatoms ; Phytoplankton ; Zooplankton ; Water column ; Surface water ; Annual reports ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 46-51
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 32
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5122 | 3949 | 2011-09-29 15:22:47 | 5122 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article reviewing the methods of biological surveillance of chalk-streams developed and commonly used at that time, with a focus on their application to the River Frome catchment in Dorset. In evaluating the surveillance methods, the author looks at sampling methods (including cores and kick-sampling), the level of identification of macroinvertebrates, and temporal and spatial variations. Responses of indices to organic pollution are also discussed. A number of accompanying figures are also included.
    Keywords: Biology ; Chemistry ; Ecology ; Environment ; Chalk ; Water management ; Cores ; Aquatic communities ; Freshwater ecology ; Invertebrate larvae ; Biological surveys ; Temporal variations ; Spatial variations ; Annual reports ; England
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 81-92
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 33
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5123 | 3949 | 2011-09-29 15:22:51 | 5123 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: A review article detailing the background, development and functionality of the Windermere Profiler, a multi parameter environmental monitoring instrument for use in lakes, reservoirs and rivers. The article explains the requirement for regular data collection by the Freshwater Biological Association at Windermere. The article covers the requirements of a profiling instrument, the design considerations, the electronic circuitry, the computer program, the operation of the computer software, the profiler in use and further developments to the design. A number of figures and images accompany the article.
    Keywords: Chemistry ; Environment ; Limnology ; Profilers ; Inland water environment ; Water reservoirs ; Lakes ; Rivers ; Temperature data ; Electrical conductivity ; Dissolved oxygen ; Depth measurement ; Light attenuation ; Annual reports ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 93-106
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 34
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5117 | 3949 | 2011-09-29 15:22:21 | 5117 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article discussing the factors affecting the rate of growth of brown trout, detailing the research udnertaken at Wray Castle, designed to clarify the influencing factors in different waters and investigate what would be required to increase their size. The article considers factors such as alkalinity, total hardness, the presence of coarse fish in the waterbodies and competition for food. Previous work undertaken on brown trout in Ireland by other authors is reviewed. A figure showing average growth rate of brown trout in five lakes, as determined from their scales (Lough Derg, Windermere, Loch Leven, Ullswater, Haweswater).
    Keywords: Biology ; Chemistry ; Limnology ; Coarse fish ; pH effects ; Water hardness ; Food availability ; Limnology ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 66-71
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 35
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5189 | 3949 | 2011-09-29 15:16:49 | 5189 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: There is no evidence of an increase in the acidity (lower pH or alkalinity) of water-bodies in the Lake District over the last 50 years. Brown trout occur in acid streams and upland tarns where pH is 4.5-5.2 throughout the year. Their occurrence in such waters in Britain and Ireland has been known for most of this century and there is no previous evidence of harmful effects on salmonid fisheries, though numbers of fish are naturally low. However, many benthic invertebrates that are common in hill-streams where pH is above 5.7 do not occur in more acid streams. This phenomenon occurs in the headwaters of several western rivers in Cumbria. It is not a recent response to "acid rain". Harmful effects of pH are undoubtedly more pronounced in waters that are poor in other dissolved ions. Low concentrations of sodium, potassium, calcium and chloride are especially important and may limit the distributions of some aquatic animals even where pH is above 5.7. The concentration of sulphate ions is usually relatively high but this is not important to the fauna; concentrations are at least two times higher in productive alkaline water-bodies than they are in unproductive acid waters.
    Keywords: Chemistry ; Ecology ; Limnology ; Acid rain ; Acidification ; Alkalinity ; Freshwater pollution ; pH ; Pollution effects ; Invertebrata ; Salmonidae ; England ; Lake District ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 30-62
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 36
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5181 | 3949 | 2011-09-29 15:17:17 | 5181 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The chemical speciation of both metals and non-metals, the use of polarographic techniques, and application to the study of the chemistry of anoxic waters are considered. In the first part of the paper unfamiliar terminology is explained and then an example of simple lake chemistry is presented to illustrate why the concept of speciation is necessary.
    Keywords: Chemistry ; Limnology ; Chemical speciation ; Anoxic basins ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 53-59
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 37
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5195 | 3949 | 2011-09-29 15:15:06 | 5195 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: This review is concerned with the kinetics of calcium carbonate formation and related processes which are important in many hard waters.
    Keywords: Chemistry ; Calcite ; Calcium carbonates ; Chemical precipitation ; Fresh water ; Geochemical cycle ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 75-90
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 38
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5193 | 3949 | 2011-09-29 15:15:03 | 5193 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: A study of the geochemical cycling of iron and manganese in a seasonally stratified lake, Esthwaite water is described. This work is based on speculative ideas on environmental redox chemistry of iron which were proposed by C.H. Mortimer in the 1940's. These observations have been verified and some speculations confirmed, along with a new understanding of the manganese cycle, and detailed information on the particulate forms of both iron and manganese. Details on the mechanisms and transformations of iron have also emerged.
    Keywords: Biology ; Chemistry ; Chemical precipitation ; Freshwater lakes ; Iron ; Manganese ; Oxidation ; Redox potential ; Reduction ; Stratification ; England ; Esthwaite Lake ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 91-101
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 39
    facet.materialart.
    Unknown
    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5197 | 3949 | 2011-09-29 15:15:33 | 5197 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Studies by the Freshwater Biological Association over the last 25 years have supplied data relevant to the levels of acidity in local soils and water before the onset of industrial pollution and current interest in acid rain. This article reviews published analysis from cores of lake sediments, in or near the catchment of the River Duddon. Electron spin resonance spectra of humic acids and iodine values confirm evidence from pollen analysis for a history of progressive acidification of the source material of lake sediments since before 5000 radiocarbon years, in upland catchments of the Lake District. Processes involved included: removal of basic ions from soils by rainfall, the effects of which were intensified by removal by man of deciduous forest; acidification of soils and waters by decomposition products of Calluna and further acidification of waters by Sphagnum species which colonized habitats where drainage became impeded by paludification processes.
    Keywords: Biology ; Chemistry ; Earth Sciences ; Acid rain ; Acidification ; Freshwater lakes ; Lake Basins ; Lake deposits ; pH ; Palnology ; England ; Cumbria ; Annual report
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 28-46
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 40
    Publication Date: 2010-10-15
    Description: The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR beta-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent alphabeta T-cell lineage differentiation. Whereas alphabetaTCR ligation by the peptide-loaded major histocompatibility complex initiates T-cell signalling, pre-TCR-induced signalling occurs by means of a ligand-independent dimerization event. The pre-TCR comprises an invariant alpha-chain (pre-Talpha) that pairs with any TCR beta-chain (TCRbeta) following successful TCR beta-gene rearrangement. Here we provide the basis of pre-Talpha-TCRbeta assembly and pre-TCR dimerization. The pre-Talpha chain comprised a single immunoglobulin-like domain that is structurally distinct from the constant (C) domain of the TCR alpha-chain; nevertheless, the mode of association between pre-Talpha and TCRbeta mirrored that mediated by the Calpha-Cbeta domains of the alphabetaTCR. The pre-TCR had a propensity to dimerize in solution, and the molecular envelope of the pre-TCR dimer correlated well with the observed head-to-tail pre-TCR dimer. This mode of pre-TCR dimerization enabled the pre-Talpha domain to interact with the variable (V) beta domain through residues that are highly conserved across the Vbeta and joining (J) beta gene families, thus mimicking the interactions at the core of the alphabetaTCR's Valpha-Vbeta interface. Disruption of this pre-Talpha-Vbeta dimer interface abrogated pre-TCR dimerization in solution and impaired pre-TCR expression on the cell surface. Accordingly, we provide a mechanism of pre-TCR self-association that allows the pre-Talpha chain to simultaneously 'sample' the correct folding of both the V and C domains of any TCR beta-chain, regardless of its ultimate specificity, which represents a critical checkpoint in T-cell development. This unusual dual-chaperone-like sensing function of pre-Talpha represents a unique mechanism in nature whereby developmental quality control regulates the expression and signalling of an integral membrane receptor complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pang, Siew Siew -- Berry, Richard -- Chen, Zhenjun -- Kjer-Nielsen, Lars -- Perugini, Matthew A -- King, Glenn F -- Wang, Christina -- Chew, Sock Hui -- La Gruta, Nicole L -- Williams, Neal K -- Beddoe, Travis -- Tiganis, Tony -- Cowieson, Nathan P -- Godfrey, Dale I -- Purcell, Anthony W -- Wilce, Matthew C J -- McCluskey, James -- Rossjohn, Jamie -- England -- Nature. 2010 Oct 14;467(7317):844-8. doi: 10.1038/nature09448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944746" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Gene Rearrangement, T-Lymphocyte/genetics ; Humans ; Models, Molecular ; Mutation ; Protein Folding ; *Protein Multimerization ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/*chemistry/genetics/*metabolism ; Receptors, Antigen, T-Cell, alpha-beta/chemistry/metabolism ; Signal Transduction ; Solutions ; T-Lymphocytes/cytology/immunology/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 41
    Publication Date: 2010-02-19
    Description: E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866016/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866016/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Shaun K -- Capili, Allan D -- Lu, Xuequan -- Tan, Derek S -- Lima, Christopher D -- F32 GM075695/GM/NIGMS NIH HHS/ -- F32 GM075695-03/GM/NIGMS NIH HHS/ -- R01 AI068038/AI/NIAID NIH HHS/ -- R01 AI068038-02/AI/NIAID NIH HHS/ -- R01 AI068038-03/AI/NIAID NIH HHS/ -- R01 GM065872/GM/NIGMS NIH HHS/ -- R01 GM065872-09/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Feb 18;463(7283):906-12. doi: 10.1038/nature08765.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology, Sloan-Kettering Institute, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164921" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; *Biocatalysis ; Catalytic Domain/*physiology ; Conserved Sequence ; Crystallography, X-Ray ; Cysteine/chemistry/metabolism ; Humans ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; SUMO-1 Protein/*chemistry/*metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Sulfides/*metabolism ; Ubiquitin/metabolism ; Ubiquitin-Activating Enzymes/*chemistry/*metabolism ; Ubiquitins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 42
    Publication Date: 2010-05-21
    Description: Type II topoisomerases are required for the management of DNA tangles and supercoils, and are targets of clinical antibiotics and anti-cancer agents. These enzymes catalyse the ATP-dependent passage of one DNA duplex (the transport or T-segment) through a transient, double-stranded break in another (the gate or G-segment), navigating DNA through the protein using a set of dissociable internal interfaces, or 'gates'. For more than 20 years, it has been established that a pair of dimer-related tyrosines, together with divalent cations, catalyse G-segment cleavage. Recent efforts have proposed that strand scission relies on a 'two-metal mechanism', a ubiquitous biochemical strategy that supports vital cellular processes ranging from DNA synthesis to RNA self-splicing. Here we present the structure of the DNA-binding and cleavage core of Saccharomyces cerevisiae topoisomerase II covalently linked to DNA through its active-site tyrosine at 2.5A resolution, revealing for the first time the organization of a cleavage-competent type II topoisomerase configuration. Unexpectedly, metal-soaking experiments indicate that cleavage is catalysed by a novel variation of the classic two-metal approach. Comparative analyses extend this scheme to explain how distantly-related type IA topoisomerases cleave single-stranded DNA, unifying the cleavage mechanisms for these two essential enzyme families. The structure also highlights a hitherto undiscovered allosteric relay that actuates a molecular 'trapdoor' to prevent subunit dissociation during cleavage. This connection illustrates how an indispensable chromosome-disentangling machine auto-regulates DNA breakage to prevent the aberrant formation of mutagenic and cytotoxic genomic lesions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882514/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882514/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Bryan H -- Burgin, Alex B -- Deweese, Joseph E -- Osheroff, Neil -- Berger, James M -- CA077373/CA/NCI NIH HHS/ -- GM033944/GM/NIGMS NIH HHS/ -- GM053960/GM/NIGMS NIH HHS/ -- GM08295/GM/NIGMS NIH HHS/ -- R01 CA077373/CA/NCI NIH HHS/ -- R01 CA077373-11S1/CA/NCI NIH HHS/ -- R01 CA077373-12/CA/NCI NIH HHS/ -- R01 GM033944/GM/NIGMS NIH HHS/ -- T32 CA009592/CA/NCI NIH HHS/ -- T32CA09592/CA/NCI NIH HHS/ -- England -- Nature. 2010 Jun 3;465(7298):641-4. doi: 10.1038/nature08974.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485342" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; DNA/*chemistry/genetics/*metabolism ; DNA Topoisomerases, Type I/*chemistry/*metabolism ; DNA Topoisomerases, Type II/*chemistry/*metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Saccharomyces cerevisiae/*enzymology ; Tyrosine
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 43
    Publication Date: 2010-01-16
    Description: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Cuimin -- Young, Anna L -- Starling-Windhof, Amanda -- Bracher, Andreas -- Saschenbrecker, Sandra -- Rao, Bharathi Vasudeva -- Rao, Karnam Vasudeva -- Berninghausen, Otto -- Mielke, Thorsten -- Hartl, F Ulrich -- Beckmann, Roland -- Hayer-Hartl, Manajit -- England -- Nature. 2010 Jan 14;463(7278):197-202. doi: 10.1038/nature08651.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075914" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Chaperonin 10/metabolism ; Chaperonin 60/metabolism ; Cryoelectron Microscopy ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Protein Binding ; *Protein Folding ; *Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Ribulose-Bisphosphate Carboxylase/*chemistry/*metabolism/ultrastructure ; Synechococcus/*chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 44
    Publication Date: 2010-05-25
    Description: The three-dimensional structures of proteins often show a modular architecture comprised of discrete structural regions or domains. Cooperative communication between these regions is important for catalysis, regulation and efficient folding; lack of coupling has been implicated in the formation of fibrils and other misfolding pathologies. How different structural regions of a protein communicate and contribute to a protein's overall energetics and folding, however, is still poorly understood. Here we use a single-molecule optical tweezers approach to induce the selective unfolding of particular regions of T4 lysozyme and monitor the effect on other regions not directly acted on by force. We investigate how the topological organization of a protein (the order of structural elements along the sequence) affects the coupling and folding cooperativity between its domains. To probe the status of the regions not directly subjected to force, we determine the free energy changes during mechanical unfolding using Crooks' fluctuation theorem. We pull on topological variants (circular permutants) and find that the topological organization of the polypeptide chain critically determines the folding cooperativity between domains and thus what parts of the folding/unfolding landscape are explored. We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911970/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911970/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shank, Elizabeth A -- Cecconi, Ciro -- Dill, Jesse W -- Marqusee, Susan -- Bustamante, Carlos -- GM 32543/GM/NIGMS NIH HHS/ -- GM 50945/GM/NIGMS NIH HHS/ -- R01 GM050945/GM/NIGMS NIH HHS/ -- R01 GM050945-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jun 3;465(7298):637-40. doi: 10.1038/nature09021. Epub 2010 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20495548" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacteriophage T4/*enzymology ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism ; Optical Tweezers ; Probability ; Protein Denaturation ; *Protein Folding ; Protein Structure, Tertiary ; Viral Proteins/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 45
    Publication Date: 2010-10-12
    Description: Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved alpha-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988090/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sheard, Laura B -- Tan, Xu -- Mao, Haibin -- Withers, John -- Ben-Nissan, Gili -- Hinds, Thomas R -- Kobayashi, Yuichi -- Hsu, Fong-Fu -- Sharon, Michal -- Browse, John -- He, Sheng Yang -- Rizo, Josep -- Howe, Gregg A -- Zheng, Ning -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-10/DK/NIDDK NIH HHS/ -- R01 AI068718/AI/NIAID NIH HHS/ -- R01 AI068718-04/AI/NIAID NIH HHS/ -- R01 CA107134/CA/NCI NIH HHS/ -- R01 CA107134-07/CA/NCI NIH HHS/ -- R01 GM057795/GM/NIGMS NIH HHS/ -- R01 GM057795-12/GM/NIGMS NIH HHS/ -- R01AI068718/AI/NIAID NIH HHS/ -- R01GM57795/GM/NIGMS NIH HHS/ -- T32 GM07270/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Nov 18;468(7322):400-5. doi: 10.1038/nature09430. Epub 2010 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Box 357280, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927106" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis/chemistry/metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry/*metabolism ; F-Box Proteins/chemistry/metabolism ; Indenes/chemistry/metabolism ; Inositol Phosphates/*metabolism ; Isoleucine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxylipins/chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Plant Growth Regulators/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 46
    Publication Date: 2010-02-05
    Description: Photosynthesis makes use of sunlight to convert carbon dioxide into useful biomass and is vital for life on Earth. Crucial components for the photosynthetic process are antenna proteins, which absorb light and transmit the resultant excitation energy between molecules to a reaction centre. The efficiency of these electronic energy transfers has inspired much work on antenna proteins isolated from photosynthetic organisms to uncover the basic mechanisms at play. Intriguingly, recent work has documented that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws at temperatures up to 180 K. This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures. Here we present two-dimensional photon echo spectroscopy measurements on two evolutionarily related light-harvesting proteins isolated from marine cryptophyte algae, which reveal exceptionally long-lasting excitation oscillations with distinct correlations and anti-correlations even at ambient temperature. These observations provide compelling evidence for quantum-coherent sharing of electronic excitation across the 5-nm-wide proteins under biologically relevant conditions, suggesting that distant molecules within the photosynthetic proteins are 'wired' together by quantum coherence for more efficient light-harvesting in cryptophyte marine algae.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collini, Elisabetta -- Wong, Cathy Y -- Wilk, Krystyna E -- Curmi, Paul M G -- Brumer, Paul -- Scholes, Gregory D -- England -- Nature. 2010 Feb 4;463(7281):644-7. doi: 10.1038/nature08811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St George Street, Toronto, Ontario, M5S 3H6 Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130647" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/chemistry/metabolism ; Cryptophyta/*metabolism/*radiation effects ; *Light ; Light-Harvesting Protein Complexes/chemistry/metabolism ; Models, Molecular ; Photons ; Photosynthesis/physiology/*radiation effects ; Protein Conformation ; Quantum Theory ; *Temperature
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 47
    Publication Date: 2010-06-26
    Description: DNA polymerase eta (Poleta) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of Poleta (also known as POLH) in humans causes the variant form of xeroderma pigmentosum (XPV). We present the crystal structures of Saccharomyces cerevisiae Poleta (also known as RAD30) in ternary complex with a cis-syn thymine-thymine (T-T) dimer and with undamaged DNA. The structures reveal that the ability of Poleta to replicate efficiently through the ultraviolet-induced lesion derives from a simple and yet elegant mechanism, wherein the two Ts of the T-T dimer are accommodated in an active site cleft that is much more open than in other polymerases. We also show by structural, biochemical and genetic analysis that the two Ts are maintained in a stable configuration in the active site via interactions with Gln 55, Arg 73 and Met 74. Together, these features define the basis for Poleta's action on ultraviolet-damaged DNA that is crucial in suppressing the mutagenic and carcinogenic consequences of sun exposure, thereby reducing the incidence of skin cancers in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030469/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030469/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Silverstein, Timothy D -- Johnson, Robert E -- Jain, Rinku -- Prakash, Louise -- Prakash, Satya -- Aggarwal, Aneel K -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 CA107650/CA/NCI NIH HHS/ -- R01 CA107650-39/CA/NCI NIH HHS/ -- R01 ES017767/ES/NIEHS NIH HHS/ -- R01 ES017767-01/ES/NIEHS NIH HHS/ -- England -- Nature. 2010 Jun 24;465(7301):1039-43. doi: 10.1038/nature09104.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577207" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Damage ; DNA-Directed DNA Polymerase/*chemistry/genetics/*metabolism ; Humans ; Kinetics ; Models, Molecular ; Mutation, Missense ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; Pyrimidine Dimers/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Skin Neoplasms/*enzymology/genetics ; Structure-Activity Relationship ; Xeroderma Pigmentosum/enzymology/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 48
    Publication Date: 2010-10-12
    Description: Blood pressure is critically controlled by angiotensins, which are vasopressor peptides specifically released by the enzyme renin from the tail of angiotensinogen-a non-inhibitory member of the serpin family of protease inhibitors. Although angiotensinogen has long been regarded as a passive substrate, the crystal structures solved here to 2.1 A resolution show that the angiotensin cleavage site is inaccessibly buried in its amino-terminal tail. The conformational rearrangement that makes this site accessible for proteolysis is revealed in our 4.4 A structure of the complex of human angiotensinogen with renin. The co-ordinated changes involved are seen to be critically linked by a conserved but labile disulphide bridge. Here we show that the reduced unbridged form of angiotensinogen is present in the circulation in a near 40:60 ratio with the oxidized sulphydryl-bridged form, which preferentially interacts with receptor-bound renin. We propose that this redox-responsive transition of angiotensinogen to a form that will more effectively release angiotensin at a cellular level contributes to the modulation of blood pressure. Specifically, we demonstrate the oxidative switch of angiotensinogen to its more active sulphydryl-bridged form in the maternal circulation in pre-eclampsia-the hypertensive crisis of pregnancy that threatens the health and survival of both mother and child.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024006/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024006/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Aiwu -- Carrell, Robin W -- Murphy, Michael P -- Wei, Zhenquan -- Yan, Yahui -- Stanley, Peter L D -- Stein, Penelope E -- Broughton Pipkin, Fiona -- Read, Randy J -- 082961/Wellcome Trust/United Kingdom -- BS/05/002/18361/British Heart Foundation/United Kingdom -- MC_U105663142/Medical Research Council/United Kingdom -- PG/08/041/24818/British Heart Foundation/United Kingdom -- PG/09/072/27945/British Heart Foundation/United Kingdom -- British Heart Foundation/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Nov 4;468(7320):108-11. doi: 10.1038/nature09505. Epub 2010 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. awz20@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927107" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensinogen/blood/*chemistry/*metabolism ; Angiotensins/chemistry/*metabolism/secretion ; Blood Pressure ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Female ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Pre-Eclampsia/blood/metabolism ; Pregnancy ; Protein Conformation ; *Protein Processing, Post-Translational ; Renin/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 49
    Publication Date: 2010-09-25
    Description: Gram-negative bacteria, such as Escherichia coli, frequently use tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel various toxic compounds from the cell. The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. No previous structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner-membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide new structural information about the HME subfamily of RND efflux pumps. The structures suggest that the metal-binding sites, formed by a three-methionine cluster, are located within the cleft region of the periplasmic domain. This cleft is closed in the apo-CusA form but open in the CusA-Cu(I) and CusA-Ag(I) structures, which directly suggests a plausible pathway for ion export. Binding of Cu(I) and Ag(I) triggers significant conformational changes in both the periplasmic and transmembrane domains. The crystal structure indicates that CusA has, in addition to the three-methionine metal-binding site, four methionine pairs-three located in the transmembrane region and one in the periplasmic domain. Genetic analysis and transport assays suggest that CusA is capable of actively picking up metal ions from the cytosol, using these methionine pairs or clusters to bind and export metal ions. These structures suggest a stepwise shuttle mechanism for transport between these sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946090/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Feng -- Su, Chih-Chia -- Zimmermann, Michael T -- Boyken, Scott E -- Rajashankar, Kanagalaghatta R -- Jernigan, Robert L -- Yu, Edward W -- GM 072014/GM/NIGMS NIH HHS/ -- GM 074027/GM/NIGMS NIH HHS/ -- GM 081680/GM/NIGMS NIH HHS/ -- GM 086431/GM/NIGMS NIH HHS/ -- R01 GM072014/GM/NIGMS NIH HHS/ -- R01 GM074027/GM/NIGMS NIH HHS/ -- R01 GM074027-05/GM/NIGMS NIH HHS/ -- R01 GM086431/GM/NIGMS NIH HHS/ -- R01 GM086431-01A2/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Sep 23;467(7314):484-8. doi: 10.1038/nature09395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Iowa 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20865003" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry/metabolism ; Binding Sites ; Cell Membrane/metabolism ; Copper/chemistry/*metabolism ; Crystallography, X-Ray ; Cytosol/metabolism ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Ion Transport ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Biological ; Models, Molecular ; Periplasm/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Silver/chemistry/*metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 50
    Publication Date: 2010-09-30
    Description: Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes (4 and 6) that are capable of direct signalling through members of the two largest plexin classes, B and A, respectively. In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. Here we present crystal structures of cognate complexes of the semaphorin-binding regions of plexins B1 and A2 with semaphorin ectodomains (human PLXNB1(1-2)-SEMA4D(ecto) and murine PlxnA2(1-4)-Sema6A(ecto)), plus unliganded structures of PlxnA2(1-4) and Sema6A(ecto). These structures, together with biophysical and cellular assays of wild-type and mutant proteins, reveal that semaphorin dimers independently bind two plexin molecules and that signalling is critically dependent on the avidity of the resulting bivalent 2:2 complex (monomeric semaphorin binds plexin but fails to trigger signalling). In combination, our data favour a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data. Furthermore, the shared generic architecture of the complexes, formed through conserved contacts of the amino-terminal seven-bladed beta-propeller (sema) domains of both semaphorin and plexin, suggests that a common mode of interaction triggers all semaphorin-plexin based signalling, while distinct insertions within or between blades of the sema domains determine binding specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587840/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587840/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janssen, Bert J C -- Robinson, Ross A -- Perez-Branguli, Francesc -- Bell, Christian H -- Mitchell, Kevin J -- Siebold, Christian -- Jones, E Yvonne -- 082301/Wellcome Trust/United Kingdom -- 083111/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- A10976/Cancer Research UK/United Kingdom -- A3964/Cancer Research UK/United Kingdom -- A5261/Cancer Research UK/United Kingdom -- G0700232/Medical Research Council/United Kingdom -- G0700232(82098)/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- G9900061(69203)/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Oct 28;467(7319):1118-22. doi: 10.1038/nature09468. Epub 2010 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20877282" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD/chemistry/genetics/metabolism ; Binding Sites ; Cell Adhesion Molecules/*chemistry/genetics/*metabolism ; Cell Communication ; Crystallography, X-Ray ; Humans ; Ligands ; Mice ; Mice, Inbred C57BL ; Models, Molecular ; NIH 3T3 Cells ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Semaphorins/*chemistry/genetics/*metabolism ; *Signal Transduction ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 51
    Publication Date: 2010-04-16
    Description: Tumour metastasis is the primary cause of death of cancer patients. Development of new therapeutics preventing tumour metastasis is urgently needed. Migrastatin is a natural product secreted by Streptomyces, and synthesized migrastatin analogues such as macroketone are potent inhibitors of metastatic tumour cell migration, invasion and metastasis. Here we show that these migrastatin analogues target the actin-bundling protein fascin to inhibit its activity. X-ray crystal structural studies reveal that migrastatin analogues bind to one of the actin-binding sites on fascin. Our data demonstrate that actin cytoskeletal proteins such as fascin can be explored as new molecular targets for cancer treatment, in a similar manner to the microtubule protein tubulin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857318/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lin -- Yang, Shengyu -- Jakoncic, Jean -- Zhang, J Jillian -- Huang, Xin-Yun -- CA136837/CA/NCI NIH HHS/ -- R01 CA136837/CA/NCI NIH HHS/ -- R01 CA136837-01A1/CA/NCI NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):1062-6. doi: 10.1038/nature08978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Cornell University Weill Medical College, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393565" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Antineoplastic Agents/chemistry/metabolism/pharmacology/therapeutic use ; Binding Sites/drug effects ; Breast Neoplasms/drug therapy/pathology ; Carrier Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Cell Line, Tumor ; Cell Movement/drug effects ; Crystallography, X-Ray ; Drug Resistance, Neoplasm/genetics ; Female ; Humans ; Lung Neoplasms/prevention & control/secondary ; Macrolides/*chemistry/metabolism/*pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Mice, Inbred NOD ; Mice, SCID ; Microfilament Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Models, Molecular ; Mutation/genetics ; Neoplasm Invasiveness/pathology/prevention & control ; Neoplasm Metastasis/drug therapy/pathology/*prevention & control ; Piperidones/*chemistry/metabolism/*pharmacology/therapeutic use ; Protein Conformation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 52
    Publication Date: 2010-12-24
    Description: Neurotransmitter/sodium symporters (NSSs) couple the uptake of neurotransmitter with one or more sodium ions, removing neurotransmitter from the synaptic cleft. NSSs are essential to the function of chemical synapses, are associated with multiple neurological diseases and disorders, and are the targets of therapeutic and illicit drugs. LeuT, a prokaryotic orthologue of the NSS family, is a model transporter for understanding the relationships between molecular mechanism and atomic structure in a broad range of sodium-dependent and sodium-independent secondary transporters. At present there is a controversy over whether there are one or two high-affinity substrate binding sites in LeuT. The first-reported crystal structure of LeuT, together with subsequent functional and structural studies, provided direct evidence for a single, high-affinity, centrally located substrate-binding site, defined as the S1 site. Recent binding, flux and molecular simulation studies, however, have been interpreted in terms of a model where there are two high-affinity binding sites: the central, S1, site and a second, the S2 site, located within the extracellular vestibule. Furthermore, it was proposed that the S1 and S2 sites are allosterically coupled such that occupancy of the S2 site is required for the cytoplasmic release of substrate from the S1 site. Here we address this controversy by performing direct measurement of substrate binding to wild-type LeuT and to S2 site mutants using isothermal titration calorimetry, equilibrium dialysis and scintillation proximity assays. In addition, we perform uptake experiments to determine whether the proposed allosteric coupling between the putative S2 site and the S1 site manifests itself in the kinetics of substrate flux. We conclude that LeuT harbours a single, centrally located, high-affinity substrate-binding site and that transport is well described by a simple, single-substrate kinetic mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079577/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079577/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piscitelli, Chayne L -- Krishnamurthy, Harini -- Gouaux, Eric -- R37 MH070039/MH/NIMH NIH HHS/ -- R37 MH070039-07/MH/NIMH NIH HHS/ -- R37 MH070039-08/MH/NIMH NIH HHS/ -- T32 DK007680/DK/NIDDK NIH HHS/ -- T32 DK007680-17/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Dec 23;468(7327):1129-32. doi: 10.1038/nature09581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179170" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Humans ; Ionophores/pharmacology ; Kinetics ; Leucine/genetics ; Models, Molecular ; Mutation ; Plasma Membrane Neurotransmitter Transport ; Proteins/*chemistry/genetics/*metabolism ; Protein Transport/drug effects ; Valinomycin/pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 53
    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 54
    Publication Date: 2010-07-09
    Description: Interconversion between conductive and non-conductive forms of the K(+) channel selectivity filter underlies a variety of gating events, from flicker transitions (at the microsecond timescale) to C-type inactivation (millisecond to second timescale). Here we report the crystal structure of the Streptomyces lividans K(+) channel KcsA in its open-inactivated conformation and investigate the mechanism of C-type inactivation gating at the selectivity filter from channels 'trapped' in a series of partially open conformations. Five conformer classes were identified with openings ranging from 12 A in closed KcsA (Calpha-Calpha distances at Thr 112) to 32 A when fully open. They revealed a remarkable correlation between the degree of gate opening and the conformation and ion occupancy of the selectivity filter. We show that a gradual filter backbone reorientation leads first to a loss of the S2 ion binding site and a subsequent loss of the S3 binding site, presumably abrogating ion conduction. These structures indicate a molecular basis for C-type inactivation in K(+) channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033749/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuello, Luis G -- Jogini, Vishwanath -- Cortes, D Marien -- Perozo, Eduardo -- R01 GM057846/GM/NIGMS NIH HHS/ -- R01 GM057846-15/GM/NIGMS NIH HHS/ -- R01-GM57846/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 8;466(7303):203-8. doi: 10.1038/nature09153.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20613835" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Electrons ; *Ion Channel Gating ; Kinetics ; Models, Biological ; Models, Molecular ; Potassium/metabolism ; Potassium Channels/*chemistry/metabolism ; Protein Conformation ; Streptomyces lividans/*chemistry ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 55
    Publication Date: 2010-10-01
    Description: In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Takuhiro -- Yokoyama, Shigeyuki -- England -- Nature. 2010 Sep 30;467(7315):612-6. doi: 10.1038/nature09411.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20882017" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/genetics ; Biocatalysis ; Crystallography, X-Ray ; Electrophoretic Mobility Shift Assay ; Glutamate-tRNA Ligase/*chemistry/*metabolism ; Models, Molecular ; Molecular Conformation ; Nitrogenous Group Transferases/*chemistry/*metabolism ; Protein Binding ; RNA, Transfer, Gln/biosynthesis/*chemistry/*metabolism ; RNA, Transfer, Glu/chemistry/metabolism ; Staphylococcus aureus/enzymology ; Substrate Specificity ; Thermotoga maritima/*enzymology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 56
    Publication Date: 2010-04-30
    Description: The interferon-inducible dynamin-like myxovirus resistance protein 1 (MxA; also called MX1) GTPase is a key mediator of cell-autonomous innate immunity against pathogens such as influenza viruses. MxA partially localizes to COPI-positive membranes of the smooth endoplasmic reticulum-Golgi intermediate compartment. At the point of infection, it redistributes to sites of viral replication and promotes missorting of essential viral constituents. It has been proposed that the middle domain and the GTPase effector domain of dynamin-like GTPases constitute a stalk that mediates oligomerization and transmits conformational changes from the G domain to the target structure; however, the molecular architecture of this stalk has remained elusive. Here we report the crystal structure of the stalk of human MxA, which folds into a four-helical bundle. This structure tightly oligomerizes in the crystal in a criss-cross pattern involving three distinct interfaces and one loop. Mutations in each of these interaction sites interfere with native assembly, oligomerization, membrane binding and antiviral activity of MxA. On the basis of these results, we propose a structural model for dynamin oligomerization and stimulated GTP hydrolysis that is consistent with previous structural predictions and has functional implications for all members of the dynamin family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Song -- von der Malsburg, Alexander -- Paeschke, Susann -- Behlke, Joachim -- Haller, Otto -- Kochs, Georg -- Daumke, Oliver -- England -- Nature. 2010 May 27;465(7297):502-6. doi: 10.1038/nature08972. Epub 2010 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Delbruck-Centrum for Molecular Medicine, Crystallography, Robert-Rossle-Strasse 10, 13125 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428112" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents/chemistry/metabolism/pharmacology ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Dynamins/*chemistry/metabolism ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/*chemistry/genetics/*metabolism/pharmacology ; Guanosine Triphosphate/metabolism ; Humans ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Influenza A Virus, H5N1 Subtype/drug effects/physiology ; Models, Molecular ; Myxovirus Resistance Proteins ; Protein Conformation ; *Protein Multimerization ; Virus Replication/drug effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 57
    Publication Date: 2010-07-30
    Description: The post-translational methylation of alpha-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L33 (refs 1, 2), but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be alpha-N-methylated. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of alpha-N-methylation has been identified. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating that they may be targets of the same, unknown enzyme. The initiating Met is cleaved, and the exposed alpha-amino group is mono-, di- or trimethylated. Here we report the discovery of the first alpha-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET (also known as TAF-I or PHAPII) and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939154/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939154/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tooley, Christine E Schaner -- Petkowski, Janusz J -- Muratore-Schroeder, Tara L -- Balsbaugh, Jeremy L -- Shabanowitz, Jeffrey -- Sabat, Michal -- Minor, Wladek -- Hunt, Donald F -- Macara, Ian G -- R01 GM050526/GM/NIGMS NIH HHS/ -- R01 GM050526-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 26;466(7310):1125-8. doi: 10.1038/nature09343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA. ces5g@virginia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20668449" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/*metabolism ; Cell Line ; Chromosome Segregation ; Gene Knockdown Techniques ; Guanine Nucleotide Exchange Factors/*metabolism ; HeLa Cells ; Histone Chaperones/metabolism ; Humans ; Methyltransferases/chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Retinoblastoma Protein/*metabolism ; Spindle Apparatus/metabolism ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 58
    Publication Date: 2010-01-16
    Description: Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB'. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the D ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intradomain and interdomain contact sites within the phytochrome dimer. On the basis of our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807988/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ulijasz, Andrew T -- Cornilescu, Gabriel -- Cornilescu, Claudia C -- Zhang, Junrui -- Rivera, Mario -- Markley, John L -- Vierstra, Richard D -- P41 RR002301/RR/NCRR NIH HHS/ -- P41 RR002301-237748/RR/NCRR NIH HHS/ -- U54 GM074901/GM/NIGMS NIH HHS/ -- U54 GM074901-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 14;463(7278):250-4. doi: 10.1038/nature08671.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075921" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry/metabolism/radiation effects ; Bacterial Proteins/*chemistry/genetics/metabolism/*radiation effects ; Bile Pigments/chemistry/metabolism/radiation effects ; Binding Sites ; *Light ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Phytochrome/*chemistry/genetics/metabolism/*radiation effects ; Protein Kinases/*chemistry/genetics/metabolism/*radiation effects ; Protein Structure, Tertiary/radiation effects ; Rotation ; Synechococcus/*chemistry/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 59
    Publication Date: 2010-08-20
    Description: The Na(+)/K(+)-ATPase pumps three sodium ions out of and two potassium ions into the cell for each ATP molecule that is split, thereby generating the chemical and electrical gradients across the plasma membrane that are essential in, for example, signalling, secondary transport and volume regulation in animal cells. Crystal structures of the potassium-bound form of the pump revealed an intimate docking of the alpha-subunit carboxy terminus at the transmembrane domain. Here we show that this element is a key regulator of a previously unrecognized ion pathway. Current models of P-type ATPases operate with a single ion conduit through the pump, but our data suggest an additional pathway in the Na(+)/K(+)-ATPase between the ion-binding sites and the cytoplasm. The C-terminal pathway allows a cytoplasmic proton to enter and stabilize site III when empty in the potassium-bound state, and when potassium is released the proton will also return to the cytoplasm, thus allowing an overall asymmetric stoichiometry of the transported ions. The C terminus controls the gate to the pathway. Its structure is crucial for pump function, as demonstrated by at least eight mutations in the region that cause severe neurological diseases. This novel model for ion transport by the Na(+)/K(+)-ATPase is established by electrophysiological studies of C-terminal mutations in familial hemiplegic migraine 2 (FHM2) and is further substantiated by molecular dynamics simulations. A similar ion regulation is likely to apply to the H(+)/K(+)-ATPase and the Ca(2+)-ATPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poulsen, Hanne -- Khandelia, Himanshu -- Morth, J Preben -- Bublitz, Maike -- Mouritsen, Ole G -- Egebjerg, Jan -- Nissen, Poul -- England -- Nature. 2010 Sep 2;467(7311):99-102. doi: 10.1038/nature09309. Epub 2010 Aug 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉PUMPKIN - Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Department of Molecular Biology, Aarhus University, DK-8000 Aarhus C, Denmark. hp@mb.au.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20720542" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; Humans ; *Ion Transport ; Migraine with Aura/genetics/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Oocytes/metabolism ; Potassium/metabolism ; Protons ; Sodium-Potassium-Exchanging ATPase/*chemistry/*metabolism ; Squalus acanthias/metabolism ; Sus scrofa/metabolism ; Xenopus
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 60
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-09-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lok, Corie -- England -- Nature. 2010 Sep 2;467(7311):18-21. doi: 10.1038/467018a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811430" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry ; Financing, Government/legislation & jurisprudence ; Nanostructures/chemistry ; *Nanotechnology/economics ; *Research Support as Topic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 61
    Publication Date: 2010-04-09
    Description: X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to subnanometre resolution, it can use similar tools.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859093/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859093/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schroder, Gunnar F -- Levitt, Michael -- Brunger, Axel T -- EY016525/EY/NEI NIH HHS/ -- GM63718/GM/NIGMS NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- U54 GM072970/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Apr 22;464(7292):1218-22. doi: 10.1038/nature08892. Epub 2010 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Strukturbiologie und Biophysik (ISB-3), Forschungszentrum Julich, 52425 Julich, Germany. gu.schroeder@fz-juelich.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20376006" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray/*methods ; Databases, Protein ; Electrons ; Likelihood Functions ; Models, Molecular ; Oligopeptides/chemistry ; Protein Conformation ; Software ; Static Electricity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 62
    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharya, Ananyo -- England -- Nature. 2010 Feb 4;463(7281):605-6. doi: 10.1038/463605a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130626" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Child ; Crystallization ; Crystallography, X-Ray ; Diacylglycerol Kinase/chemistry ; Humans ; Magnetic Resonance Spectroscopy/*instrumentation/*methods ; Metabolomics/instrumentation/methods ; Models, Molecular ; Protein Conformation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 63
    Publication Date: 2010-05-14
    Description: A huge variety of proteins are able to form fibrillar structures, especially at high protein concentrations. Hence, it is surprising that spider silk proteins can be stored in a soluble form at high concentrations and transformed into extremely stable fibres on demand. Silk proteins are reminiscent of amphiphilic block copolymers containing stretches of polyalanine and glycine-rich polar elements forming a repetitive core flanked by highly conserved non-repetitive amino-terminal and carboxy-terminal domains. The N-terminal domain comprises a secretion signal, but further functions remain unassigned. The C-terminal domain was implicated in the control of solubility and fibre formation initiated by changes in ionic composition and mechanical stimuli known to align the repetitive sequence elements and promote beta-sheet formation. However, despite recent structural data, little is known about this remarkable behaviour in molecular detail. Here we present the solution structure of the C-terminal domain of a spider dragline silk protein and provide evidence that the structural state of this domain is essential for controlled switching between the storage and assembly forms of silk proteins. In addition, the C-terminal domain also has a role in the alignment of secondary structural features formed by the repetitive elements in the backbone of spider silk proteins, which is known to be important for the mechanical properties of the fibre.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagn, Franz -- Eisoldt, Lukas -- Hardy, John G -- Vendrely, Charlotte -- Coles, Murray -- Scheibel, Thomas -- Kessler, Horst -- England -- Nature. 2010 May 13;465(7295):239-42. doi: 10.1038/nature08936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Integrated Protein Science (CIPSM), Technische Universitat Munchen, 85747 Garching, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463741" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calorimetry, Differential Scanning ; Circular Dichroism ; *Conserved Sequence ; Hydrophobic and Hydrophilic Interactions ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Protein Structure, Tertiary ; Silk/*chemistry/*metabolism ; Spectrometry, Fluorescence ; Spectroscopy, Fourier Transform Infrared ; Spiders/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 64
    Publication Date: 2010-01-08
    Description: G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the beta(2) adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805469/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805469/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bokoch, Michael P -- Zou, Yaozhong -- Rasmussen, Soren G F -- Liu, Corey W -- Nygaard, Rie -- Rosenbaum, Daniel M -- Fung, Juan Jose -- Choi, Hee-Jung -- Thian, Foon Sun -- Kobilka, Tong Sun -- Puglisi, Joseph D -- Weis, William I -- Pardo, Leonardo -- Prosser, R Scott -- Mueller, Luciano -- Kobilka, Brian K -- GM56169/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R01 GM056169-13/GM/NIGMS NIH HHS/ -- R21 MH082313/MH/NIMH NIH HHS/ -- R21 MH082313-01A1/MH/NIMH NIH HHS/ -- R37 NS028471/NS/NINDS NIH HHS/ -- R37 NS028471-19/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Jan 7;463(7277):108-12. doi: 10.1038/nature08650.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054398" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-2 Receptor Agonists ; Adrenergic beta-2 Receptor Antagonists ; Allosteric Regulation/drug effects ; Binding Sites ; Crystallography, X-Ray ; Drug Inverse Agonism ; Ethanolamines/pharmacology ; Formoterol Fumarate ; Humans ; Ligands ; Lysine/analogs & derivatives/metabolism ; Methylation ; Models, Molecular ; Mutant Proteins ; Nuclear Magnetic Resonance, Biomolecular ; Propanolamines/metabolism/pharmacology ; Protein Structure, Tertiary/drug effects ; Receptors, Adrenergic, beta-2/*chemistry/*metabolism ; Static Electricity ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 65
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-05-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 May 13;465(7295):145. doi: 10.1038/465145a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463710" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Methylation ; Epigenesis, Genetic/*genetics ; Genome, Human/genetics ; Genomics/*methods ; Humans ; Models, Molecular ; Neoplasms/genetics ; Sequence Analysis, DNA/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 66
    Publication Date: 2010-08-06
    Description: People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, Seth -- Khatib, Firas -- Treuille, Adrien -- Barbero, Janos -- Lee, Jeehyung -- Beenen, Michael -- Leaver-Fay, Andrew -- Baker, David -- Popovic, Zoran -- Players, Foldit -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 5;466(7307):756-60. doi: 10.1038/nature09304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686574" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology/*methods ; Computer Graphics ; Computer Simulation ; Cooperative Behavior ; Cues ; *Games, Experimental ; *Group Processes ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Imaging, Three-Dimensional ; *Internet ; Leisure Activities ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Photic Stimulation ; *Problem Solving ; Protein Conformation ; *Protein Folding ; Proteins/*chemistry/metabolism ; Stochastic Processes ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 67
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agre, Peter -- England -- Nature. 2010 Oct 14;467(7317):S11. doi: 10.1038/467S11a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944611" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/metabolism ; Chemistry ; Happiness ; Interdisciplinary Communication ; Mentors ; Neurosciences/trends ; *Nobel Prize ; Peer Review, Research ; Politics ; Public Policy ; Research/standards/trends ; *Research Personnel/psychology/standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 68
    Publication Date: 2010-09-24
    Description: Symplekin (Pta1 in yeast) is a scaffold in the large protein complex that is required for 3'-end cleavage and polyadenylation of eukaryotic messenger RNA precursors (pre-mRNAs); it also participates in transcription initiation and termination by RNA polymerase II (Pol II). Symplekin mediates interactions between many different proteins in this machinery, although the molecular basis for its function is not known. Here we report the crystal structure at 2.4 A resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser 5 phosphatase Ssu72 (refs 7, 10-17) and a CTD Ser 5 phosphopeptide. The N-terminal domain of symplekin has the ARM or HEAT fold, with seven pairs of antiparallel alpha-helices arranged in the shape of an arc. The structure of Ssu72 has some similarity to that of low-molecular-mass phosphotyrosine protein phosphatase, although Ssu72 has a unique active-site landscape as well as extra structural features at the C terminus that are important for interaction with symplekin. Ssu72 is bound to the concave face of symplekin, and engineered mutations in this interface can abolish interactions between the two proteins. The CTD peptide is bound in the active site of Ssu72, with the pSer 5-Pro 6 peptide bond in the cis configuration, which contrasts with all other known CTD peptide conformations. Although the active site of Ssu72 is about 25 A from the interface with symplekin, we found that the symplekin N-terminal domain stimulates Ssu72 CTD phosphatase activity in vitro. Furthermore, the N-terminal domain of symplekin inhibits polyadenylation in vitro, but only when coupled to transcription. Because catalytically active Ssu72 overcomes this inhibition, our results show a role for mammalian Ssu72 in transcription-coupled pre-mRNA 3'-end processing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038789/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038789/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiang, Kehui -- Nagaike, Takashi -- Xiang, Song -- Kilic, Turgay -- Beh, Maia M -- Manley, James L -- Tong, Liang -- GM028983/GM/NIGMS NIH HHS/ -- GM077175/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM028983/GM/NIGMS NIH HHS/ -- R01 GM028983-31/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- R01 GM077175-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 7;467(7316):729-33. doi: 10.1038/nature09391. Epub 2010 Sep 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20861839" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Carrier Proteins/*chemistry/genetics/*metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Drosophila Proteins/chemistry ; Humans ; Models, Molecular ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Phosphopeptides/chemistry/*metabolism ; Phosphoprotein Phosphatases/chemistry/genetics/metabolism ; Polyadenylation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Substrate Specificity ; mRNA Cleavage and Polyadenylation Factors/chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 69
    Publication Date: 2010-11-03
    Description: Natural killer cells and cytotoxic T lymphocytes accomplish the critically important function of killing virus-infected and neoplastic cells. They do this by releasing the pore-forming protein perforin and granzyme proteases from cytoplasmic granules into the cleft formed between the abutting killer and target cell membranes. Perforin, a 67-kilodalton multidomain protein, oligomerizes to form pores that deliver the pro-apoptopic granzymes into the cytosol of the target cell. The importance of perforin is highlighted by the fatal consequences of congenital perforin deficiency, with more than 50 different perforin mutations linked to familial haemophagocytic lymphohistiocytosis (type 2 FHL). Here we elucidate the mechanism of perforin pore formation by determining the X-ray crystal structure of monomeric murine perforin, together with a cryo-electron microscopy reconstruction of the entire perforin pore. Perforin is a thin 'key-shaped' molecule, comprising an amino-terminal membrane attack complex perforin-like (MACPF)/cholesterol dependent cytolysin (CDC) domain followed by an epidermal growth factor (EGF) domain that, together with the extreme carboxy-terminal sequence, forms a central shelf-like structure. A C-terminal C2 domain mediates initial, Ca(2+)-dependent membrane binding. Most unexpectedly, however, electron microscopy reveals that the orientation of the perforin MACPF domain in the pore is inside-out relative to the subunit arrangement in CDCs. These data reveal remarkable flexibility in the mechanism of action of the conserved MACPF/CDC fold and provide new insights into how related immune defence molecules such as complement proteins assemble into pores.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Law, Ruby H P -- Lukoyanova, Natalya -- Voskoboinik, Ilia -- Caradoc-Davies, Tom T -- Baran, Katherine -- Dunstone, Michelle A -- D'Angelo, Michael E -- Orlova, Elena V -- Coulibaly, Fasseli -- Verschoor, Sandra -- Browne, Kylie A -- Ciccone, Annette -- Kuiper, Michael J -- Bird, Phillip I -- Trapani, Joseph A -- Saibil, Helen R -- Whisstock, James C -- 079605/Wellcome Trust/United Kingdom -- BB/D008573/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Arthritis Research UK/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Nov 18;468(7322):447-51. doi: 10.1038/nature09518. Epub 2010 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21037563" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Membrane/*metabolism ; Cholesterol/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Epidermal Growth Factor/chemistry ; Granzymes/metabolism ; Humans ; Lymphocytes/*metabolism ; Mice ; Models, Molecular ; Pore Forming Cytotoxic Proteins/*chemistry/genetics/*metabolism/ultrastructure ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 70
    Publication Date: 2010-09-24
    Description: Transporter proteins from the MATE (multidrug and toxic compound extrusion) family are vital in metabolite transport in plants, directly affecting crop yields worldwide. MATE transporters also mediate multiple-drug resistance (MDR) in bacteria and mammals, modulating the efficacy of many pharmaceutical drugs used in the treatment of a variety of diseases. MATE transporters couple substrate transport to electrochemical gradients and are the only remaining class of MDR transporters whose structure has not been determined. Here we report the X-ray structure of the MATE transporter NorM from Vibrio cholerae determined to 3.65 A, revealing an outward-facing conformation with two portals open to the outer leaflet of the membrane and a unique topology of the predicted 12 transmembrane helices distinct from any other known MDR transporter. We also report a cation-binding site in close proximity to residues previously deemed critical for transport. This conformation probably represents a stage of the transport cycle with high affinity for monovalent cations and low affinity for substrates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152480/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152480/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Xiao -- Szewczyk, Paul -- Karyakin, Andrey -- Evin, Mariah -- Hong, Wen-Xu -- Zhang, Qinghai -- Chang, Geoffrey -- GM70480/GM/NIGMS NIH HHS/ -- GM73197/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-07/GM/NIGMS NIH HHS/ -- R01 GM070480/GM/NIGMS NIH HHS/ -- R01 GM070480-01A1/GM/NIGMS NIH HHS/ -- R01 GM070480-02/GM/NIGMS NIH HHS/ -- R01 GM070480-03/GM/NIGMS NIH HHS/ -- R01 GM070480-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 21;467(7318):991-4. doi: 10.1038/nature09408. Epub 2010 Sep 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CB105, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20861838" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/*metabolism ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Cations/chemistry/metabolism ; Crystallography, X-Ray ; Cysteine/genetics/metabolism ; Ion Transport ; Models, Molecular ; Protein Conformation ; Reproducibility of Results ; Static Electricity ; Substrate Specificity ; Vibrio cholerae/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 71
    Publication Date: 2010-10-12
    Description: DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160814/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160814/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubinson, Emily H -- Gowda, A S Prakasha -- Spratt, Thomas E -- Gold, Barry -- Eichman, Brandt F -- P30 CA068485/CA/NCI NIH HHS/ -- P30 ES000267/ES/NIEHS NIH HHS/ -- R01 CA029088/CA/NCI NIH HHS/ -- R01 CA29088/CA/NCI NIH HHS/ -- T32 ES007028/ES/NIEHS NIH HHS/ -- England -- Nature. 2010 Nov 18;468(7322):406-11. doi: 10.1038/nature09428. Epub 2010 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927102" target="_blank"〉PubMed〈/a〉
    Keywords: Alkylation ; Bacillus cereus/*enzymology ; Base Sequence ; Biocatalysis ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; *DNA Damage ; DNA Glycosylases/*metabolism ; DNA Repair/*physiology ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Solvents/chemistry ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 72
    Publication Date: 2010-02-05
    Description: The M2 protein of influenza A virus is a membrane-spanning tetrameric proton channel targeted by the antiviral drugs amantadine and rimantadine. Resistance to these drugs has compromised their effectiveness against many influenza strains, including pandemic H1N1. A recent crystal structure of M2(22-46) showed electron densities attributed to a single amantadine in the amino-terminal half of the pore, indicating a physical occlusion mechanism for inhibition. However, a solution NMR structure of M2(18-60) showed four rimantadines bound to the carboxy-terminal lipid-facing surface of the helices, suggesting an allosteric mechanism. Here we show by solid-state NMR spectroscopy that two amantadine-binding sites exist in M2 in phospholipid bilayers. The high-affinity site, occupied by a single amantadine, is located in the N-terminal channel lumen, surrounded by residues mutated in amantadine-resistant viruses. Quantification of the protein-amantadine distances resulted in a 0.3 A-resolution structure of the high-affinity binding site. The second, low-affinity, site was observed on the C-terminal protein surface, but only when the drug reaches high concentrations in the bilayer. The orientation and dynamics of the drug are distinct in the two sites, as shown by (2)H NMR. These results indicate that amantadine physically occludes the M2 channel, thus paving the way for developing new antiviral drugs against influenza viruses. The study demonstrates the ability of solid-state NMR to elucidate small-molecule interactions with membrane proteins and determine high-resolution structures of their complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818718/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818718/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cady, Sarah D -- Schmidt-Rohr, Klaus -- Wang, Jun -- Soto, Cinque S -- Degrado, William F -- Hong, Mei -- AI74571/AI/NIAID NIH HHS/ -- GM088204/GM/NIGMS NIH HHS/ -- GM56423/GM/NIGMS NIH HHS/ -- R01 GM056423/GM/NIGMS NIH HHS/ -- R01 GM056423-12/GM/NIGMS NIH HHS/ -- R01 GM088204/GM/NIGMS NIH HHS/ -- R01 GM088204-01/GM/NIGMS NIH HHS/ -- U01 AI074571/AI/NIAID NIH HHS/ -- U01 AI074571-02/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Feb 4;463(7281):689-92. doi: 10.1038/nature08722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Iowa State University, Ames, Iowa 50011 2, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130653" target="_blank"〉PubMed〈/a〉
    Keywords: Amantadine/chemistry/*metabolism/pharmacology ; Amino Acid Sequence ; Antiviral Agents/chemistry/*metabolism/pharmacology ; Binding Sites ; Crystallography, X-Ray ; Dimyristoylphosphatidylcholine/chemistry/metabolism ; Hydrogen-Ion Concentration ; Influenza A virus/*chemistry/drug effects ; Lipid Bilayers/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Structure-Activity Relationship ; Temperature ; Viral Matrix Proteins/antagonists & inhibitors/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 73
    Publication Date: 2010-05-28
    Description: Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the alpha-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 A resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-A long amphipathic alpha-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 A resolution. The L-shaped assembly consists of the alpha-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic alpha-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Efremov, Rouslan G -- Baradaran, Rozbeh -- Sazanov, Leonid A -- MC_U105674180/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2010 May 27;465(7297):441-5. doi: 10.1038/nature09066.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505720" target="_blank"〉PubMed〈/a〉
    Keywords: Benzoquinones/metabolism ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry/*metabolism ; Escherichia coli/*enzymology ; Models, Molecular ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/*metabolism ; Structure-Activity Relationship ; Thermus thermophilus/*enzymology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 74
    Publication Date: 2010-04-09
    Description: Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hehemann, Jan-Hendrik -- Correc, Gaelle -- Barbeyron, Tristan -- Helbert, William -- Czjzek, Mirjam -- Michel, Gurvan -- England -- Nature. 2010 Apr 8;464(7290):908-12. doi: 10.1038/nature08937.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite Pierre et Marie Curie, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20376150" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/physiology ; Bacteroides/*enzymology/genetics ; Biological Evolution ; Crystallography, X-Ray ; Cultural Diversity ; Diet ; Eukaryota/chemistry/metabolism ; Feces/enzymology/microbiology ; *Food Microbiology ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Glycoside Hydrolases/chemistry/isolation & purification/*metabolism ; Humans ; Intestines/*microbiology ; Japan ; *Marine Biology ; *Metagenome ; Models, Molecular ; North America ; Phylogeny ; Porphyra/chemistry/metabolism/microbiology ; Protein Conformation ; Sepharose/*analogs & derivatives/chemistry/metabolism ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 75
    Publication Date: 2010-10-15
    Description: Eukaryotes and archaea use a protease called the proteasome that has an integral role in maintaining cellular function through the selective degradation of proteins. Proteolysis occurs in a barrel-shaped 20S core particle, which in Thermoplasma acidophilum is built from four stacked homoheptameric rings of subunits, alpha and beta, arranged alpha(7)beta(7)beta(7)alpha(7) (ref. 5). These rings form three interconnected cavities, including a pair of antechambers (formed by alpha(7)beta(7)) through which substrates are passed before degradation and a catalytic chamber (beta(7)beta(7)) where the peptide-bond hydrolysis reaction occurs. Although it is clear that substrates must be unfolded to enter through narrow, gated passageways (13 A in diameter) located on the alpha-rings, the structural and dynamical properties of substrates inside the proteasome antechamber remain unclear. Confinement in the antechamber might be expected to promote folding and thus impede proteolysis. Here we investigate the folding, stability and dynamics of three small protein substrates in the antechamber by methyl transverse-relaxation-optimized NMR spectroscopy. We show that these substrates interact actively with the antechamber walls and have drastically altered kinetic and equilibrium properties that maintain them in unstructured states so as to be accessible for hydrolysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruschak, Amy M -- Religa, Tomasz L -- Breuer, Sarah -- Witt, Susanne -- Kay, Lewis E -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Oct 14;467(7317):868-71. doi: 10.1038/nature09444.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944750" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Hydrolysis ; Kinetics ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Proteasome Endopeptidase Complex/*chemistry/*metabolism ; Protein Folding ; *Protein Processing, Post-Translational ; Protein Stability ; Protein Subunits/chemistry/metabolism ; *Protein Unfolding ; Thermodynamics ; Thermoplasma/enzymology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 76
    Publication Date: 2010-07-24
    Description: Graphene nanoribbons-narrow and straight-edged stripes of graphene, or single-layer graphite-are predicted to exhibit electronic properties that make them attractive for the fabrication of nanoscale electronic devices. In particular, although the two-dimensional parent material graphene exhibits semimetallic behaviour, quantum confinement and edge effects should render all graphene nanoribbons with widths smaller than 10 nm semiconducting. But exploring the potential of graphene nanoribbons is hampered by their limited availability: although they have been made using chemical, sonochemical and lithographic methods as well as through the unzipping of carbon nanotubes, the reliable production of graphene nanoribbons smaller than 10 nm with chemical precision remains a significant challenge. Here we report a simple method for the production of atomically precise graphene nanoribbons of different topologies and widths, which uses surface-assisted coupling of molecular precursors into linear polyphenylenes and their subsequent cyclodehydrogenation. The topology, width and edge periphery of the graphene nanoribbon products are defined by the structure of the precursor monomers, which can be designed to give access to a wide range of different graphene nanoribbons. We expect that our bottom-up approach to the atomically precise fabrication of graphene nanoribbons will finally enable detailed experimental investigations of the properties of this exciting class of materials. It should even provide a route to graphene nanoribbon structures with engineered chemical and electronic properties, including the theoretically predicted intraribbon quantum dots, superlattice structures and magnetic devices based on specific graphene nanoribbon edge states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cai, Jinming -- Ruffieux, Pascal -- Jaafar, Rached -- Bieri, Marco -- Braun, Thomas -- Blankenburg, Stephan -- Muoth, Matthias -- Seitsonen, Ari P -- Saleh, Moussa -- Feng, Xinliang -- Mullen, Klaus -- Fasel, Roman -- England -- Nature. 2010 Jul 22;466(7305):470-3. doi: 10.1038/nature09211.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Empa, Swiss Federal Laboratories for Materials Science and Technology, Thun and 8600 Dubendorf, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20651687" target="_blank"〉PubMed〈/a〉
    Keywords: Electronics/*instrumentation ; Graphite/*chemistry ; Hydrogenation ; Models, Molecular ; Molecular Conformation ; Nanotubes, Carbon/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 77
    Publication Date: 2010-06-01
    Description: In termination of protein synthesis, the bacterial release factors RF1 and RF2 bind to the ribosome through specific recognition of messenger RNA stop codons and trigger hydrolysis of the bond between the nascent polypeptide and the transfer RNA at the peptidyl-tRNA site, thereby releasing the newly synthesized protein. The release factors are highly specific for a U in the first stop-codon position and recognize different combinations of purines in the second and third positions, with RF1 reading UAA and UAG and RF2 reading UAA and UGA. With recently determined crystal structures of termination complexes, it has become possible to decipher the energetics of stop-codon reading by computational analysis and to clarify the origin of the high release-factor binding accuracy. Here we report molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes. The simulations quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. The overall reading mechanism involves hitherto unidentified interactions and recognition switches that cannot be described in terms of a tripeptide anticodon model. Further simulations of complexes with tRNA(Trp), the tRNA recognizing the triplet codon for Trp, explain the observation of a 'leaky' stop codon and highlight the fundamentally different third position reading by RF2, which leads to a high stop-codon specificity with strong discrimination against the Trp codon. The simulations clearly illustrate the versatility of codon reading by protein, which goes far beyond tRNA mimicry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sund, Johan -- Ander, Martin -- Aqvist, Johan -- England -- Nature. 2010 Jun 17;465(7300):947-50. doi: 10.1038/nature09082. Epub 2010 May 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20512119" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/chemistry/genetics/*metabolism ; Codon, Terminator/*chemistry/genetics/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Peptide Termination Factors/chemistry/genetics/*metabolism ; Protein Binding/genetics ; Protein Structure, Tertiary ; RNA, Transfer/metabolism ; Ribosomes/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 78
    Publication Date: 2010-11-12
    Description: Mononuclear iron-containing oxygenases conduct a diverse variety of oxidation functions in biology, including the oxidative demethylation of methylated nucleic acids and histones. Escherichia coli AlkB is the first such enzyme that was discovered to repair methylated nucleic acids, which are otherwise cytotoxic and/or mutagenic. AlkB human homologues are known to play pivotal roles in various processes. Here we present structural characterization of oxidation intermediates for these demethylases. Using a chemical cross-linking strategy, complexes of AlkB-double stranded DNA (dsDNA) containing 1,N(6)-etheno adenine (epsilonA), N(3)-methyl thymine (3-meT) and N(3)-methyl cytosine (3-meC) are stabilized and crystallized, respectively. Exposing these crystals, grown under anaerobic conditions containing iron(II) and alpha-ketoglutarate (alphaKG), to dioxygen initiates oxidation in crystallo. Glycol (from epsilonA) and hemiaminal (from 3-meT) intermediates are captured; a zwitterionic intermediate (from 3-meC) is also proposed, based on crystallographic observations and computational analysis. The observation of these unprecedented intermediates provides direct support for the oxidative demethylation mechanism for these demethylases. This study also depicts a general mechanistic view of how a methyl group is oxidatively removed from different biological substrates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058853/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058853/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yi, Chengqi -- Jia, Guifang -- Hou, Guanhua -- Dai, Qing -- Zhang, Wen -- Zheng, Guanqun -- Jian, Xing -- Yang, Cai-Guang -- Cui, Qiang -- He, Chuan -- GM071440/GM/NIGMS NIH HHS/ -- GM084028/GM/NIGMS NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440-06/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Nov 11;468(7321):330-3. doi: 10.1038/nature09497.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068844" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Cross-Linking Reagents/chemistry ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; *DNA Repair ; DNA Repair Enzymes/metabolism ; Dioxygenases/chemistry/*metabolism ; Escherichia coli/*enzymology ; Escherichia coli Proteins/chemistry/*metabolism ; Humans ; Iron/*metabolism ; Ketoglutaric Acids/metabolism ; Methylation ; Mixed Function Oxygenases/chemistry/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Static Electricity ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 79
    Publication Date: 2010-04-13
    Description: Rhodopsin is a prototypical heptahelical family A G-protein-coupled receptor (GPCR) responsible for dim-light vision. Light isomerizes rhodopsin's retinal chromophore and triggers concerted movements of transmembrane helices, including an outward tilting of helix 6 (H6) and a smaller movement of H5, to create a site for G-protein binding and activation. However, the precise temporal sequence and mechanism underlying these helix rearrangements is unclear. We used site-directed non-natural amino acid mutagenesis to engineer rhodopsin with p-azido-l-phenylalanine residues incorporated at selected sites, and monitored the azido vibrational signatures using infrared spectroscopy as rhodopsin proceeded along its activation pathway. Here we report significant changes in electrostatic environments of the azido probes even in the inactive photoproduct Meta I, well before the active receptor state was formed. These early changes suggest a significant rotation of H6 and movement of the cytoplasmic part of H5 away from H3. Subsequently, a large outward tilt of H6 leads to opening of the cytoplasmic surface to form the active receptor photoproduct Meta II. Thus, our results reveal early conformational changes that precede larger rigid-body helix movements, and provide a basis to interpret recent GPCR crystal structures and to understand conformational sub-states observed during the activation of other GPCRs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ye, Shixin -- Zaitseva, Ekaterina -- Caltabiano, Gianluigi -- Schertler, Gebhard F X -- Sakmar, Thomas P -- Deupi, Xavier -- Vogel, Reiner -- England -- Nature. 2010 Apr 29;464(7293):1386-9. doi: 10.1038/nature08948. Epub 2010 Apr 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20383122" target="_blank"〉PubMed〈/a〉
    Keywords: Azides/analysis/*metabolism/radiation effects ; Cell Line ; Humans ; *Infrared Rays ; Models, Molecular ; Movement ; Phenylalanine/*analogs & derivatives/analysis/genetics/metabolism/radiation ; effects ; Protein Conformation ; Rhodopsin/chemistry/*genetics/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Static Electricity ; Vibration
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 80
    Publication Date: 2010-10-15
    Description: The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron microscopy reconstruction of the human Ndc80 complex bound to microtubules, sufficient for precise docking of crystal structures of the component proteins. We find that the Ndc80 complex binds the microtubule with a tubulin monomer repeat, recognizing alpha- and beta-tubulin at both intra- and inter-tubulin dimer interfaces in a manner that is sensitive to tubulin conformation. Furthermore, Ndc80 complexes self-associate along protofilaments through interactions mediated by the amino-terminal tail of the NDC80 protein, which is the site of phospho-regulation by Aurora B kinase. The complex's mode of interaction with the microtubule and its oligomerization suggest a mechanism by which Aurora B could regulate the stability of load-bearing kinetochore-microtubule attachments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957311/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957311/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alushin, Gregory M -- Ramey, Vincent H -- Pasqualato, Sebastiano -- Ball, David A -- Grigorieff, Nikolaus -- Musacchio, Andrea -- Nogales, Eva -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Oct 14;467(7317):805-10. doi: 10.1038/nature09423.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944740" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Humans ; Kinetochores/*chemistry/ultrastructure ; Microtubules/chemistry/*metabolism/ultrastructure ; Mitosis ; Models, Biological ; Models, Molecular ; Nuclear Proteins/*chemistry/*metabolism/ultrastructure ; Protein Conformation ; Tubulin/chemistry/metabolism/ultrastructure
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 81
    Publication Date: 2010-06-26
    Description: Tumour-necrosis factor (TNF) receptor-associated factor 2 (TRAF2) is a key component in NF-kappaB signalling triggered by TNF-alpha. Genetic evidence indicates that TRAF2 is necessary for the polyubiquitination of receptor interacting protein 1 (RIP1) that then serves as a platform for recruitment and stimulation of IkappaB kinase, leading to activation of the transcription factor NF-kappaB. Although TRAF2 is a RING domain ubiquitin ligase, direct evidence that TRAF2 catalyses the ubiquitination of RIP1 is lacking. TRAF2 binds to sphingosine kinase 1 (SphK1), one of the isoenzymes that generates the pro-survival lipid mediator sphingosine-1-phosphate (S1P) inside cells. Here we show that SphK1 and the production of S1P is necessary for lysine-63-linked polyubiquitination of RIP1, phosphorylation of IkappaB kinase and IkappaBalpha, and IkappaBalpha degradation, leading to NF-kappaB activation. These responses were mediated by intracellular S1P independently of its cell surface G-protein-coupled receptors. S1P specifically binds to TRAF2 at the amino-terminal RING domain and stimulates its E3 ligase activity. S1P, but not dihydro-S1P, markedly increased recombinant TRAF2-catalysed lysine-63-linked, but not lysine-48-linked, polyubiquitination of RIP1 in vitro in the presence of the ubiquitin conjugating enzymes (E2) UbcH13 or UbcH5a. Our data show that TRAF2 is a novel intracellular target of S1P, and that S1P is the missing cofactor for TRAF2 E3 ubiquitin ligase activity, indicating a new paradigm for the regulation of lysine-63-linked polyubiquitination. These results also highlight the key role of SphK1 and its product S1P in TNF-alpha signalling and the canonical NF-kappaB activation pathway important in inflammatory, antiapoptotic and immune processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946785/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946785/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alvarez, Sergio E -- Harikumar, Kuzhuvelil B -- Hait, Nitai C -- Allegood, Jeremy -- Strub, Graham M -- Kim, Eugene Y -- Maceyka, Michael -- Jiang, Hualiang -- Luo, Cheng -- Kordula, Tomasz -- Milstien, Sheldon -- Spiegel, Sarah -- R01 AI050094/AI/NIAID NIH HHS/ -- R01 AI050094-09/AI/NIAID NIH HHS/ -- R01 CA061774/CA/NCI NIH HHS/ -- R01 CA061774-15/CA/NCI NIH HHS/ -- R01 CA061774-16/CA/NCI NIH HHS/ -- R01AI50094/AI/NIAID NIH HHS/ -- R01CA61774/CA/NCI NIH HHS/ -- R37 GM043880/GM/NIGMS NIH HHS/ -- R37 GM043880-18/GM/NIGMS NIH HHS/ -- R37 GM043880-19/GM/NIGMS NIH HHS/ -- R37 GM043880-20/GM/NIGMS NIH HHS/ -- R37 GM043880-21/GM/NIGMS NIH HHS/ -- R37GM043880/GM/NIGMS NIH HHS/ -- U19 AI077435/AI/NIAID NIH HHS/ -- U19 AI077435-020004/AI/NIAID NIH HHS/ -- U19 AI077435-02S10004/AI/NIAID NIH HHS/ -- U19 AI077435-030004/AI/NIAID NIH HHS/ -- U19AI077435/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Jun 24;465(7301):1084-8. doi: 10.1038/nature09128.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, 1101 E. Marshall Street, Richmond, Virginia 23298, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577214" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Cell Line ; Enzyme Activation ; Humans ; I-kappa B Kinase/metabolism ; I-kappa B Proteins/metabolism ; Lysine/metabolism ; Lysophospholipids/biosynthesis/chemistry/*metabolism ; Mice ; Models, Molecular ; NF-kappa B/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptor-Interacting Protein Serine-Threonine Kinases/metabolism ; Sphingosine/*analogs & derivatives/biosynthesis/chemistry/metabolism ; Substrate Specificity ; TNF Receptor-Associated Factor 2/chemistry/*metabolism ; Tumor Necrosis Factor-alpha/pharmacology ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Ubiquitination/drug effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 82
    Publication Date: 2010-12-03
    Description: The multi-subunit DNA-dependent RNA polymerase (RNAP) is the principal enzyme of transcription for gene expression. Transcription is regulated by various transcription factors. Gre factor homologue 1 (Gfh1), found in the Thermus genus, is a close homologue of the well-conserved bacterial transcription factor GreA, and inhibits transcription initiation and elongation by binding directly to RNAP. The structural basis of transcription inhibition by Gfh1 has remained elusive, although the crystal structures of RNAP and Gfh1 have been determined separately. Here we report the crystal structure of Thermus thermophilus RNAP complexed with Gfh1. The amino-terminal coiled-coil domain of Gfh1 fully occludes the channel formed between the two central modules of RNAP; this channel would normally be used for nucleotide triphosphate (NTP) entry into the catalytic site. Furthermore, the tip of the coiled-coil domain occupies the NTP beta-gamma phosphate-binding site. The NTP-entry channel is expanded, because the central modules are 'ratcheted' relative to each other by approximately 7 degrees , as compared with the previously reported elongation complexes. This 'ratcheted state' is an alternative structural state, defined by a newly acquired contact between the central modules. Therefore, the shape of Gfh1 is appropriate to maintain RNAP in the ratcheted state. Simultaneously, the ratcheting expands the nucleic-acid-binding channel, and kinks the bridge helix, which connects the central modules. Taken together, the present results reveal that Gfh1 inhibits transcription by preventing NTP binding and freezing RNAP in the alternative structural state. The ratcheted state might also be associated with other aspects of transcription, such as RNAP translocation and transcription termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tagami, Shunsuke -- Sekine, Shun-Ichi -- Kumarevel, Thirumananseri -- Hino, Nobumasa -- Murayama, Yuko -- Kamegamori, Syunsuke -- Yamamoto, Masaki -- Sakamoto, Kensaku -- Yokoyama, Shigeyuki -- England -- Nature. 2010 Dec 16;468(7326):978-82. doi: 10.1038/nature09573. Epub 2010 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21124318" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Thermus thermophilus/chemistry/*enzymology ; *Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 83
    Publication Date: 2010-03-20
    Description: Cobalamin (Cbl, vitamin B(12)) is a bacterial organic compound and an essential coenzyme in mammals, which take it up from the diet. This occurs by the combined action of the gastric intrinsic factor (IF) and the ileal endocytic cubam receptor formed by the 460-kilodalton (kDa) protein cubilin and the 45-kDa transmembrane protein amnionless. Loss of function of any of these proteins ultimately leads to Cbl deficiency in man. Here we present the crystal structure of the complex between IF-Cbl and the cubilin IF-Cbl-binding-region (CUB(5-8)) determined at 3.3 A resolution. The structure provides insight into how several CUB (for 'complement C1r/C1s, Uegf, Bmp1') domains collectively function as modular ligand-binding regions, and how two distant CUB domains embrace the Cbl molecule by binding the two IF domains in a Ca(2+)-dependent manner. This dual-point model provides a probable explanation of how Cbl indirectly induces ligand-receptor coupling. Finally, the comparison of Ca(2+)-binding CUB domains and the low-density lipoprotein (LDL) receptor-type A modules suggests that the electrostatic pairing of a basic ligand arginine/lysine residue with Ca(2+)-coordinating acidic aspartates/glutamates is a common theme of Ca(2+)-dependent ligand-receptor interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Christian Brix Folsted -- Madsen, Mette -- Storm, Tina -- Moestrup, Soren K -- Andersen, Gregers R -- England -- Nature. 2010 Mar 18;464(7287):445-8. doi: 10.1038/nature08874.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry, Aarhus University, 8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237569" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/metabolism ; Binding Sites ; Calcium/metabolism ; Crystallography, X-Ray ; Glutamic Acid/metabolism ; Humans ; Intrinsic Factor/*chemistry/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/*metabolism ; Static Electricity ; Vitamin B 12/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 84
    Publication Date: 2010-06-11
    Description: Regulation of the expression of the human immunodeficiency virus (HIV) genome is accomplished in large part by controlling transcription elongation. The viral protein Tat hijacks the host cell's RNA polymerase II elongation control machinery through interaction with the positive transcription elongation factor, P-TEFb, and directs the factor to promote productive elongation of HIV mRNA. Here we describe the crystal structure of the Tat.P-TEFb complex containing HIV-1 Tat, human Cdk9 (also known as CDK9), and human cyclin T1 (also known as CCNT1). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the Cdk9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb. This finding lays a foundation for the design of compounds that would specifically inhibit the Tat.P-TEFb complex and block HIV replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885016/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885016/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tahirov, Tahir H -- Babayeva, Nigar D -- Varzavand, Katayoun -- Cooper, Jeffrey J -- Sedore, Stanley C -- Price, David H -- AI074392/AI/NIAID NIH HHS/ -- GM082923/GM/NIGMS NIH HHS/ -- GM35500/GM/NIGMS NIH HHS/ -- P30CA036727/CA/NCI NIH HHS/ -- P41 RR015301/RR/NCRR NIH HHS/ -- P41 RR015301-075443/RR/NCRR NIH HHS/ -- R01 GM035500/GM/NIGMS NIH HHS/ -- R01 GM035500-20/GM/NIGMS NIH HHS/ -- R01 GM035500-21/GM/NIGMS NIH HHS/ -- R01 GM035500-22/GM/NIGMS NIH HHS/ -- R01 GM035500-23/GM/NIGMS NIH HHS/ -- R01 GM035500-24/GM/NIGMS NIH HHS/ -- R01 GM082923/GM/NIGMS NIH HHS/ -- R01 GM082923-01A2/GM/NIGMS NIH HHS/ -- R01 GM082923-02/GM/NIGMS NIH HHS/ -- R01 GM082923-02S1/GM/NIGMS NIH HHS/ -- R21 AI074392/AI/NIAID NIH HHS/ -- R21 AI074392-01A1/AI/NIAID NIH HHS/ -- R21 AI074392-02/AI/NIAID NIH HHS/ -- R33 AI074392/AI/NIAID NIH HHS/ -- R33 AI074392-03/AI/NIAID NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Jun 10;465(7299):747-51. doi: 10.1038/nature09131.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA. ttahirov@unmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535204" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Cyclin T/chemistry/metabolism ; Cyclin-Dependent Kinase 9/chemistry/metabolism ; Enzyme Activation ; HIV-1/*chemistry ; Humans ; Models, Molecular ; Molecular Sequence Data ; Positive Transcriptional Elongation Factor B/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; tat Gene Products, Human Immunodeficiency Virus/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 85
    Publication Date: 2010-02-16
    Description: The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision. The Methanococcus jannaschii tyrosyl-transfer-RNA synthetase-tRNA(CUA) (MjTyrRS-tRNA(CUA)) and the Methanosarcina barkeri pyrrolysyl-tRNA synthetase-tRNA(CUA) (MbPylRS-tRNA(CUA)) orthogonal pairs have been evolved to incorporate a range of unnatural amino acids in response to the amber codon in Escherichia coli. However, the potential of synthetic genetic code expansion is generally limited to the low efficiency incorporation of a single type of unnatural amino acid at a time, because every triplet codon in the universal genetic code is used in encoding the synthesis of the proteome. To encode efficiently many distinct unnatural amino acids into proteins we require blank codons and mutually orthogonal aminoacyl-tRNA synthetase-tRNA pairs that recognize unnatural amino acids and decode the new codons. Here we synthetically evolve an orthogonal ribosome (ribo-Q1) that efficiently decodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthogonal messenger RNA, which it specifically translates. By creating mutually orthogonal aminoacyl-tRNA synthetase-tRNA pairs and combining them with ribo-Q1 we direct the incorporation of distinct unnatural amino acids in response to two of the new blank codons on the orthogonal mRNA. Using this code, we genetically direct the formation of a specific, redox-insensitive, nanoscale protein cross-link by the bio-orthogonal cycloaddition of encoded azide- and alkyne-containing amino acids. Because the synthetase-tRNA pairs used have been evolved to incorporate numerous unnatural amino acids, it will be possible to encode more than 200 unnatural amino acid combinations using this approach. As ribo-Q1 independently decodes a series of quadruplet codons, this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumann, Heinz -- Wang, Kaihang -- Davis, Lloyd -- Garcia-Alai, Maria -- Chin, Jason W -- MC_U105181009/Medical Research Council/United Kingdom -- MC_UP_A024_1008/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2010 Mar 18;464(7287):441-4. doi: 10.1038/nature08817. Epub 2010 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20154731" target="_blank"〉PubMed〈/a〉
    Keywords: Alkynes/metabolism ; Amino Acids/genetics/*metabolism ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Azides/metabolism ; Biocatalysis/drug effects ; Calmodulin/chemistry/genetics/metabolism ; Codon/*genetics ; Copper/metabolism/pharmacology ; Cyclization/drug effects ; *Directed Molecular Evolution ; *Genetic Code/genetics ; Genetic Engineering/*methods ; Methanococcus ; Models, Molecular ; *Protein Biosynthesis/genetics/physiology ; Protein Conformation ; Protein Engineering/methods ; RNA, Messenger/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Ribosomes/chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 86
    Publication Date: 2010-05-14
    Description: Nature's high-performance polymer, spider silk, consists of specific proteins, spidroins, with repetitive segments flanked by conserved non-repetitive domains. Spidroins are stored as a highly concentrated fluid dope. On silk formation, intermolecular interactions between repeat regions are established that provide strength and elasticity. How spiders manage to avoid premature spidroin aggregation before self-assembly is not yet established. A pH drop to 6.3 along the spider's spinning apparatus, altered salt composition and shear forces are believed to trigger the conversion to solid silk, but no molecular details are known. Miniature spidroins consisting of a few repetitive spidroin segments capped by the carboxy-terminal domain form metre-long silk-like fibres irrespective of pH. We discovered that incorporation of the amino-terminal domain of major ampullate spidroin 1 from the dragline of the nursery web spider Euprosthenops australis (NT) into mini-spidroins enables immediate, charge-dependent self-assembly at pH values around 6.3, but delays aggregation above pH 7. The X-ray structure of NT, determined to 1.7 A resolution, shows a homodimer of dipolar, antiparallel five-helix bundle subunits that lack homologues. The overall dimeric structure and observed charge distribution of NT is expected to be conserved through spider evolution and in all types of spidroins. Our results indicate a relay-like mechanism through which the N-terminal domain regulates spidroin assembly by inhibiting precocious aggregation during storage, and accelerating and directing self-assembly as the pH is lowered along the spider's silk extrusion duct.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Askarieh, Glareh -- Hedhammar, My -- Nordling, Kerstin -- Saenz, Alejandra -- Casals, Cristina -- Rising, Anna -- Johansson, Jan -- Knight, Stefan D -- England -- Nature. 2010 May 13;465(7295):236-8. doi: 10.1038/nature08962.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Oslo University, 1033 Blindern, 0315 Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463740" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Circular Dichroism ; Conserved Sequence ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Alignment ; Silk/*chemistry/*metabolism/ultrastructure ; Spiders/*chemistry ; Static Electricity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 87
    Publication Date: 2010-11-12
    Description: Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defence, is frequently deleterious to the host due to the exaggerated production of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signalling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a critical step in the regulation of gene expression. Here we present a novel pharmacological approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compound (I-BET) that by 'mimicking' acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compounds specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nicodeme, Edwige -- Jeffrey, Kate L -- Schaefer, Uwe -- Beinke, Soren -- Dewell, Scott -- Chung, Chun-Wa -- Chandwani, Rohit -- Marazzi, Ivan -- Wilson, Paul -- Coste, Herve -- White, Julia -- Kirilovsky, Jorge -- Rice, Charles M -- Lora, Jose M -- Prinjha, Rab K -- Lee, Kevin -- Tarakhovsky, Alexander -- England -- Nature. 2010 Dec 23;468(7327):1119-23. doi: 10.1038/nature09589. Epub 2010 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Recherche GSK, 27 Avenue du Quebec, 91140 Villebon Sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068722" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation/drug effects ; Animals ; Anti-Inflammatory Agents/chemistry/*pharmacology/therapeutic use ; Benzodiazepines ; Cells, Cultured ; Epigenomics ; Gene Expression Regulation/*drug effects ; Genome-Wide Association Study ; Heterocyclic Compounds with 4 or More Rings/chemistry/*pharmacology/therapeutic ; use ; Histone Deacetylase Inhibitors/pharmacology ; Hydroxamic Acids/pharmacology ; *Inflammation/drug therapy/prevention & control ; Kaplan-Meier Estimate ; Lipopolysaccharides/pharmacology ; Macrophages/*drug effects ; Mice ; Mice, Inbred C57BL ; Models, Molecular ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/metabolism ; Salmonella Infections/drug therapy/immunology/physiopathology/prevention & ; control ; Salmonella typhimurium ; Sepsis/drug therapy/prevention & control ; Shock, Septic/drug therapy/prevention & control
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 88
    Publication Date: 2010-07-09
    Description: Histone lysine acetylation and methylation have an important role during gene transcription in a chromatin context. Knowledge concerning the types of protein modules that can interact with acetyl-lysine has so far been limited to bromodomains. Recently, a tandem plant homeodomain (PHD) finger (PHD1-PHD2, or PHD12) of human DPF3b, which functions in association with the BAF chromatin remodelling complex to initiate gene transcription during heart and muscle development, was reported to bind histones H3 and H4 in an acetylation-sensitive manner, making it the first alternative to bromodomains for acetyl-lysine binding. Here we report the structural mechanism of acetylated histone binding by the double PHD fingers of DPF3b. Our three-dimensional solution structures and biochemical analysis of DPF3b highlight the molecular basis of the integrated tandem PHD finger, which acts as one functional unit in the sequence-specific recognition of lysine-14-acetylated histone H3 (H3K14ac). Whereas the interaction with H3 is promoted by acetylation at lysine 14, it is inhibited by methylation at lysine 4, and these opposing influences are important during transcriptional activation of the mouse DPF3b target genes Pitx2 and Jmjd1c. Binding of this tandem protein module to chromatin can thus be regulated by different histone modifications during the initiation of gene transcription.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901902/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeng, Lei -- Zhang, Qiang -- Li, Side -- Plotnikov, Alexander N -- Walsh, Martin J -- Zhou, Ming-Ming -- R01 CA087658/CA/NCI NIH HHS/ -- R01 CA087658-10/CA/NCI NIH HHS/ -- R01 HG004508/HG/NHGRI NIH HHS/ -- R01 HG004508-02/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Jul 8;466(7303):258-62. doi: 10.1038/nature09139.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20613843" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Line ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histones/*chemistry/*metabolism ; Humans ; Lysine/chemistry/metabolism ; Mice ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Folding ; Structure-Activity Relationship ; Substrate Specificity ; Thermodynamics ; Transcription Factors/*chemistry/genetics/*metabolism ; Transcription, Genetic ; Transcriptional Activation ; Up-Regulation ; *Zinc Fingers
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 89
    Publication Date: 2010-08-13
    Description: The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA-DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921665/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921665/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Adrianna P P -- Pigli, Ying Z -- Rice, Phoebe A -- GM058827/GM/NIGMS NIH HHS/ -- R01 GM058827/GM/NIGMS NIH HHS/ -- R01 GM058827-09/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 12;466(7308):883-6. doi: 10.1038/nature09200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703307" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/*metabolism ; Base Sequence ; Crystallography, X-Ray ; DNA Damage ; DNA Repair/genetics ; DNA, Bacterial/chemistry/*genetics/*metabolism ; Electrophoretic Mobility Shift Assay ; *Escherichia coli/chemistry/genetics ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Models, Molecular ; Protein Binding ; *Protein Multimerization ; Protein Structure, Tertiary ; Rec A Recombinases/metabolism ; Repressor Proteins/chemistry/metabolism ; SOS Response (Genetics)/*genetics ; Serine Endopeptidases/*chemistry/*metabolism ; Winged-Helix Transcription Factors/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 90
    Publication Date: 2010-10-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thomine, Sebastien -- Barbier-Brygoo, Helene -- England -- Nature. 2010 Oct 28;467(7319):1058-9. doi: 10.1038/4671058a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20981091" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/cytology/genetics/metabolism ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Haemophilus influenzae/*chemistry/genetics ; Ion Channel Gating ; Membrane Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Phenylalanine/genetics/metabolism ; Plant Stomata/*metabolism ; Protein Folding ; *Structural Homology, Protein
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 91
    Publication Date: 2010-01-15
    Description: In an effort to find new pharmacological modalities to overcome resistance to ATP-binding-site inhibitors of Bcr-Abl, we recently reported the discovery of GNF-2, a selective allosteric Bcr-Abl inhibitor. Here, using solution NMR, X-ray crystallography, mutagenesis and hydrogen exchange mass spectrometry, we show that GNF-2 binds to the myristate-binding site of Abl, leading to changes in the structural dynamics of the ATP-binding site. GNF-5, an analogue of GNF-2 with improved pharmacokinetic properties, when used in combination with the ATP-competitive inhibitors imatinib or nilotinib, suppressed the emergence of resistance mutations in vitro, displayed additive inhibitory activity in biochemical and cellular assays against T315I mutant human Bcr-Abl and displayed in vivo efficacy against this recalcitrant mutant in a murine bone-marrow transplantation model. These results show that therapeutically relevant inhibition of Bcr-Abl activity can be achieved with inhibitors that bind to the myristate-binding site and that combining allosteric and ATP-competitive inhibitors can overcome resistance to either agent alone.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901986/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901986/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Jianming -- Adrian, Francisco J -- Jahnke, Wolfgang -- Cowan-Jacob, Sandra W -- Li, Allen G -- Iacob, Roxana E -- Sim, Taebo -- Powers, John -- Dierks, Christine -- Sun, Fangxian -- Guo, Gui-Rong -- Ding, Qiang -- Okram, Barun -- Choi, Yongmun -- Wojciechowski, Amy -- Deng, Xianming -- Liu, Guoxun -- Fendrich, Gabriele -- Strauss, Andre -- Vajpai, Navratna -- Grzesiek, Stephan -- Tuntland, Tove -- Liu, Yi -- Bursulaya, Badry -- Azam, Mohammad -- Manley, Paul W -- Engen, John R -- Daley, George Q -- Warmuth, Markus -- Gray, Nathanael S -- R01 CA130876/CA/NCI NIH HHS/ -- R01 CA130876-03/CA/NCI NIH HHS/ -- England -- Nature. 2010 Jan 28;463(7280):501-6. doi: 10.1038/nature08675. Epub 2010 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Harvard Medical School, Department of Cancer Biology, Seeley G. Mudd Building 628, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20072125" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/*chemistry/metabolism/*pharmacology ; Antineoplastic Combined Chemotherapy Protocols ; Benzamides ; Binding Sites ; Bone Marrow Transplantation ; Cell Line, Tumor ; Crystallization ; Disease Models, Animal ; Drug Resistance, Neoplasm/*drug effects ; Female ; Fusion Proteins, bcr-abl/*chemistry/genetics/metabolism ; Humans ; Imatinib Mesylate ; Inhibitory Concentration 50 ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug ; therapy/enzymology/*metabolism ; Male ; Mass Spectrometry ; Mice ; Models, Molecular ; Mutation/genetics ; Piperazines/chemistry/pharmacology ; Protein Structure, Tertiary ; Pyrimidines/chemistry/metabolism/pharmacology ; Transplantation, Heterologous
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 92
    Publication Date: 2010-01-22
    Description: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Junjie -- Baker, Matthew L -- Schroder, Gunnar F -- Douglas, Nicholai R -- Reissmann, Stefanie -- Jakana, Joanita -- Dougherty, Matthew -- Fu, Caroline J -- Levitt, Michael -- Ludtke, Steven J -- Frydman, Judith -- Chiu, Wah -- P41 RR002250/RR/NCRR NIH HHS/ -- P41 RR002250-23/RR/NCRR NIH HHS/ -- P41 RR002250-237254/RR/NCRR NIH HHS/ -- P41 RR002250-24/RR/NCRR NIH HHS/ -- P41 RR002250-247897/RR/NCRR NIH HHS/ -- PN2 EY016525/EY/NEI NIH HHS/ -- PN2 EY016525-02S1/EY/NEI NIH HHS/ -- PN2 EY016525-03/EY/NEI NIH HHS/ -- PN2 EY016525-04/EY/NEI NIH HHS/ -- PN2 EY016525-05/EY/NEI NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- R01 GM079429/GM/NIGMS NIH HHS/ -- R01 GM079429-03/GM/NIGMS NIH HHS/ -- R01 GM080139/GM/NIGMS NIH HHS/ -- R01 GM080139-03/GM/NIGMS NIH HHS/ -- R01 GM080139-04/GM/NIGMS NIH HHS/ -- R90 DK071504/DK/NIDDK NIH HHS/ -- R90 DK071504-03/DK/NIDDK NIH HHS/ -- T32 GM007276-30/GM/NIGMS NIH HHS/ -- T32 GM007276-31/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):379-83. doi: 10.1038/nature08701.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090755" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism/pharmacology ; Allosteric Regulation ; Binding Sites ; Cryoelectron Microscopy ; Group II Chaperonins/*chemistry/*metabolism/ultrastructure ; Hydrolysis/drug effects ; Methanococcus/*chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation/drug effects ; *Protein Folding ; Protein Subunits/chemistry/metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 93
    Publication Date: 2010-08-03
    Description: The flagellar motor drives the rotation of flagellar filaments at hundreds of revolutions per second, efficiently propelling bacteria through viscous media. The motor uses the potential energy from an electrochemical gradient of cations across the cytoplasmic membrane to generate torque. A rapid switch from anticlockwise to clockwise rotation determines whether a bacterium runs smoothly forward or tumbles to change its trajectory. A protein called FliG forms a ring in the rotor of the flagellar motor that is involved in the generation of torque through an interaction with the cation-channel-forming stator subunit MotA. FliG has been suggested to adopt distinct conformations that induce switching but these structural changes and the molecular mechanism of switching are unknown. Here we report the molecular structure of the full-length FliG protein, identify conformational changes that are involved in rotational switching and uncover the structural basis for the formation of the FliG torque ring. This allows us to propose a model of the complete ring and switching mechanism in which conformational changes in FliG reverse the electrostatic charges involved in torque generation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159035/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159035/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Lawrence K -- Ginsburg, Michael A -- Crovace, Claudia -- Donohoe, Mhairi -- Stock, Daniela -- MC_U105170645/Medical Research Council/United Kingdom -- P41 RR007707/RR/NCRR NIH HHS/ -- P41 RR007707-17/RR/NCRR NIH HHS/ -- RR007707/RR/NCRR NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2010 Aug 19;466(7309):996-1000. doi: 10.1038/nature09300. Epub 2010 Aug 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, New South Wales 2010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20676082" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Flagella/*chemistry/genetics/*physiology ; Models, Molecular ; Molecular Motor Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; *Rotation ; Static Electricity ; Structure-Activity Relationship ; Thermotoga maritima/chemistry ; *Torque
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 94
    Publication Date: 2010-10-26
    Description: The energy-coupling factor (ECF) transporters, responsible for vitamin uptake in prokaryotes, are a unique family of membrane transporters. Each ECF transporter contains a membrane-embedded, substrate-binding protein (known as the S component), an energy-coupling module that comprises two ATP-binding proteins (known as the A and A' components) and a transmembrane protein (known as the T component). The structure and transport mechanism of the ECF family remain unknown. Here we report the crystal structure of RibU, the S component of the ECF-type riboflavin transporter from Staphylococcus aureus at 3.6-A resolution. RibU contains six transmembrane segments, adopts a previously unreported transporter fold and contains a riboflavin molecule bound to the L1 loop and the periplasmic portion of transmembrane segments 4-6. Structural analysis reveals the essential ligand-binding residues, identifies the putative transport path and, with sequence alignment, uncovers conserved structural features and suggests potential mechanisms of action among the ECF transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Peng -- Wang, Jiawei -- Shi, Yigong -- R01 GM084964/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Dec 2;468(7324):717-20. doi: 10.1038/nature09488. Epub 2010 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20972419" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Ligands ; Membrane Transport Proteins/*chemistry/classification/*metabolism ; Models, Molecular ; Movement ; Periplasm/metabolism ; Protein Folding ; Protein Structure, Tertiary ; Riboflavin/chemistry/*metabolism ; Sequence Alignment ; Staphylococcus aureus/*chemistry ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 95
    Publication Date: 2010-10-01
    Description: Semaphorins and their receptor plexins constitute a pleiotropic cell-signalling system that is used in a wide variety of biological processes, and both protein families have been implicated in numerous human diseases. The binding of soluble or membrane-anchored semaphorins to the membrane-distal region of the plexin ectodomain activates plexin's intrinsic GTPase-activating protein (GAP) at the cytoplasmic region, ultimately modulating cellular adhesion behaviour. However, the structural mechanism underlying the receptor activation remains largely unknown. Here we report the crystal structures of the semaphorin 6A (Sema6A) receptor-binding fragment and the plexin A2 (PlxnA2) ligand-binding fragment in both their pre-signalling (that is, before binding) and signalling (after complex formation) states. Before binding, the Sema6A ectodomain was in the expected 'face-to-face' homodimer arrangement, similar to that adopted by Sema3A and Sema4D, whereas PlxnA2 was in an unexpected 'head-on' homodimer arrangement. In contrast, the structure of the Sema6A-PlxnA2 signalling complex revealed a 2:2 heterotetramer in which the two PlxnA2 monomers dissociated from one another and docked onto the top face of the Sema6A homodimer using the same interface as the head-on homodimer, indicating that plexins undergo 'partner exchange'. Cell-based activity measurements using mutant ligands/receptors confirmed that the Sema6A face-to-face dimer arrangement is physiologically relevant and is maintained throughout signalling events. Thus, homodimer-to-heterodimer transitions of cell-surface plexin that result in a specific orientation of its molecular axis relative to the membrane may constitute the structural mechanism by which the ligand-binding 'signal' is transmitted to the cytoplasmic region, inducing GAP domain rearrangements and activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nogi, Terukazu -- Yasui, Norihisa -- Mihara, Emiko -- Matsunaga, Yukiko -- Noda, Masanori -- Yamashita, Naoya -- Toyofuku, Toshihiko -- Uchiyama, Susumu -- Goshima, Yoshio -- Kumanogoh, Atsushi -- Takagi, Junichi -- England -- Nature. 2010 Oct 28;467(7319):1123-7. doi: 10.1038/nature09473. Epub 2010 Sep 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20881961" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/genetics/*metabolism ; Semaphorins/*chemistry/genetics/*metabolism ; *Signal Transduction ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 96
    Publication Date: 2010-08-21
    Description: Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants. The holoenzyme of PCC is an alpha(6)beta(6) dodecamer, with a molecular mass of 750 kDa. The alpha-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the beta-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-A resolution of a bacterial PCC alpha(6)beta(6) holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-A resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the alpha-subunits are arranged as monomers in the holoenzyme, decorating a central beta(6) hexamer. A hitherto unrecognized domain in the alpha-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the beta-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 A, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the beta-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC) and eukaryotic acetyl-CoA carboxylase (ACC).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925307/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925307/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Christine S -- Sadre-Bazzaz, Kianoush -- Shen, Yang -- Deng, Binbin -- Zhou, Z Hong -- Tong, Liang -- AI069015/AI/NIAID NIH HHS/ -- DK067238/DK/NIDDK NIH HHS/ -- GM071940/GM/NIGMS NIH HHS/ -- GM08281/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 AI069015/AI/NIAID NIH HHS/ -- R01 AI069015-04/AI/NIAID NIH HHS/ -- R01 DK067238/DK/NIDDK NIH HHS/ -- R01 DK067238-07/DK/NIDDK NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- R01 GM071940-05/GM/NIGMS NIH HHS/ -- T32 GM008281/GM/NIGMS NIH HHS/ -- T32 GM008281-23/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 19;466(7309):1001-5. doi: 10.1038/nature09302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725044" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/chemistry/metabolism/ultrastructure ; Biocatalysis ; Biotin/metabolism ; Carbon-Nitrogen Ligases/chemistry/metabolism/ultrastructure ; Carrier Proteins/chemistry/metabolism/ultrastructure ; Catalytic Domain ; *Cryoelectron Microscopy ; Crystallography, X-Ray ; Fatty Acid Synthase, Type II ; Holoenzymes/*chemistry/genetics/metabolism/*ultrastructure ; Humans ; Methylmalonyl-CoA Decarboxylase/*chemistry/genetics/metabolism/*ultrastructure ; Models, Molecular ; Mutation/genetics ; Propionic Acidemia/enzymology/genetics ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Rhodobacteraceae/enzymology ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 97
    Publication Date: 2010-05-14
    Description: Neurotransmitter:Na(+) symporters (NSS) remove neurotransmitters from the synapse in a reuptake process that is driven by the Na(+) gradient. Drugs that interfere with this reuptake mechanism, such as cocaine and antidepressants, profoundly influence behaviour and mood. To probe the nature of the conformational changes that are associated with substrate binding and transport, we have developed a single-molecule fluorescence imaging assay and combined it with functional and computational studies of the prokaryotic NSS homologue LeuT. Here we show molecular details of the modulation of intracellular gating of LeuT by substrates and inhibitors, as well as by mutations that alter binding, transport or both. Our direct observations of single-molecule transitions, reflecting structural dynamics of the intracellular region of the transporter that might be masked by ensemble averaging or suppressed under crystallographic conditions, are interpreted in the context of an allosteric mechanism that couples ion and substrate binding to transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940119/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940119/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Yongfang -- Terry, Daniel -- Shi, Lei -- Weinstein, Harel -- Blanchard, Scott C -- Javitch, Jonathan A -- DA022413/DA/NIDA NIH HHS/ -- DA023694/DA/NIDA NIH HHS/ -- DA12408/DA/NIDA NIH HHS/ -- DA17293/DA/NIDA NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- K99 DA023694/DA/NIDA NIH HHS/ -- K99 DA023694-02/DA/NIDA NIH HHS/ -- R01 DA017293/DA/NIDA NIH HHS/ -- England -- Nature. 2010 May 13;465(7295):188-93. doi: 10.1038/nature09057.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, 630 W. 168th, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463731" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/metabolism ; Allosteric Regulation ; Aquifoliaceae/*chemistry ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Cysteine/chemistry/metabolism ; Escherichia coli ; Fluorescence Resonance Energy Transfer ; Leucine/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Plasma Membrane Neurotransmitter Transport ; Proteins/*chemistry/genetics/*metabolism ; Protein Conformation ; Sodium/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 98
    Publication Date: 2010-04-30
    Description: Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 A resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF(4)(-).The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879890/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879890/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chappie, Joshua S -- Acharya, Sharmistha -- Leonard, Marilyn -- Schmid, Sandra L -- Dyda, Fred -- F31 MH081419/MH/NIMH NIH HHS/ -- F31 MH081419-02/MH/NIMH NIH HHS/ -- GM42455/GM/NIGMS NIH HHS/ -- MH081419/MH/NIMH NIH HHS/ -- MH61345/MH/NIMH NIH HHS/ -- R01 GM042455/GM/NIGMS NIH HHS/ -- R01 GM042455-20/GM/NIGMS NIH HHS/ -- R37 MH061345/MH/NIMH NIH HHS/ -- R37 MH061345-10/MH/NIMH NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2010 May 27;465(7297):435-40. doi: 10.1038/nature09032. Epub 2010 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428113" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/metabolism ; Amino Acid Sequence ; Biocatalysis ; Catalytic Domain/genetics ; Conserved Sequence ; Crystallography, X-Ray ; Dynamin I/*chemistry/genetics/*metabolism ; Enzyme Activation ; Fluorides/metabolism ; GTP Phosphohydrolases/*chemistry/genetics/*metabolism ; Guanosine Diphosphate/analogs & derivatives/metabolism ; Humans ; Hydrolysis ; Models, Molecular ; *Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Sodium/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 99
    Publication Date: 2010-07-27
    Description: One of the detrimental effects of ultraviolet radiation on DNA is the formation of the (6-4) photoproduct, 6-4PP, between two adjacent pyrimidine rings. This lesion interferes with replication and transcription, and may result in mutation and cell death. In many organisms, a flavoenzyme called photolyase uses blue light energy to repair the 6-4PP (ref. 3). The molecular mechanism of the repair reaction is poorly understood. Here, we use ultrafast spectroscopy to show that the key step in the repair photocycle is acyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, we followed the function evolution and observed direct electron transfer from the excited flavin cofactor to the 6-4PP in 225 picoseconds, but surprisingly fast back electron transfer in 50 picoseconds without repair. We found that the catalytic proton transfer between a histidine residue in the active site and the 6-4PP, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6-4PP, occurs in 425 picoseconds and leads to 6-4PP repair in tens of nanoseconds. These key dynamics define the repair photocycle and explain the underlying molecular mechanism of the enzyme's modest efficiency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018752/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018752/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Jiang -- Liu, Zheyun -- Tan, Chuang -- Guo, Xunmin -- Wang, Lijuan -- Sancar, Aziz -- Zhong, Dongping -- GM074813/GM/NIGMS NIH HHS/ -- P30 ES010126/ES/NIEHS NIH HHS/ -- R01 GM031082/GM/NIGMS NIH HHS/ -- R01 GM074813/GM/NIGMS NIH HHS/ -- R01 GM074813-04/GM/NIGMS NIH HHS/ -- R01 HG002779-05/HG/NHGRI NIH HHS/ -- R01 HG002779-06/HG/NHGRI NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- England -- Nature. 2010 Aug 12;466(7308):887-890. doi: 10.1038/nature09192.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Program of Biophysics, The Ohio State University, Columbus, Ohio 43210, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20657578" target="_blank"〉PubMed〈/a〉
    Keywords: Absorption ; Animals ; Arabidopsis/*enzymology/genetics ; Biocatalysis ; DNA Damage ; *DNA Repair/radiation effects ; Deoxyribodipyrimidine Photo-Lyase/chemistry/genetics/*metabolism ; Drosophila melanogaster/enzymology ; Electrons ; Flavins/chemistry/metabolism ; Histidine/genetics/metabolism ; Kinetics ; Models, Molecular ; Protons ; Pyrimidine Dimers/chemistry/*metabolism/*radiation effects ; Time Factors ; *Ultraviolet Rays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
  • 100
    Publication Date: 2010-12-03
    Description: Alphaviruses are enveloped RNA viruses that have a diameter of about 700 A and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope glycoproteins, E1 and E2. The E2-E1 heterodimers form 80 trimeric spikes on the icosahedral virus surface, 60 with quasi-three-fold symmetry and 20 coincident with the icosahedral three-fold axes arranged with T = 4 quasi-symmetry. The E1 glycoprotein has a hydrophobic fusion loop at one end and is responsible for membrane fusion. The E2 protein is responsible for receptor binding and protects the fusion loop at neutral pH. The lower pH in the endosome induces the virions to undergo an irreversible conformational change in which E2 and E1 dissociate and E1 forms homotrimers, triggering fusion of the viral membrane with the endosomal membrane and then releasing the viral genome into the cytoplasm. Here we report the structure of an alphavirus spike, crystallized at low pH, representing an intermediate in the fusion process and clarifying the maturation process. The trimer of E2-E1 in the crystal structure is similar to the spikes in the neutral pH virus except that the E2 middle region is disordered, exposing the fusion loop. The amino- and carboxy-terminal domains of E2 each form immunoglobulin-like folds, consistent with the receptor attachment properties of E2.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057476/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057476/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Long -- Jose, Joyce -- Xiang, Ye -- Kuhn, Richard J -- Rossmann, Michael G -- P01 AI055672/AI/NIAID NIH HHS/ -- P01 AI055672-07/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Dec 2;468(7324):705-8. doi: 10.1038/nature09546.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21124457" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Drosophila melanogaster ; Endosomes/metabolism ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Membrane Fusion ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Sindbis Virus/*chemistry/*metabolism ; Viral Envelope Proteins/*chemistry/*metabolism ; Viral Fusion Proteins/chemistry/metabolism ; Virion/chemistry/metabolism ; *Virus Internalization
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...