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  • *Models, Molecular  (6)
  • GEOPHYSICS
  • Geophysics
  • METEOROLOGY AND CLIMATOLOGY
  • 2010-2014  (11)
  • 1
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2010 Jun 10;465(7299):823-6. doi: 10.1038/465823a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Computational Biology ; Computer Simulation ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Drug Design ; Humans ; Lipid Bilayers/chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Membranes, Artificial ; *Models, Molecular ; Movement ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry/isolation & purification/metabolism ; Solubility ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2011-05-14
    Description: We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164876/" 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/PMC3164876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fleishman, Sarel J -- Whitehead, Timothy A -- Ekiert, Damian C -- Dreyfus, Cyrille -- Corn, Jacob E -- Strauch, Eva-Maria -- Wilson, Ian A -- Baker, David -- AI057141/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-07/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):816-21. doi: 10.1126/science.1202617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566186" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Binding Sites ; Computational Biology ; *Computer Simulation ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptide Library ; Protein Binding ; Protein Conformation ; *Protein Engineering ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/*metabolism ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-08-23
    Description: Proteins are inherently plastic molecules, whose function often critically depends on excursions between different molecular conformations (conformers). However, a rigorous understanding of the relation between a protein's structure, dynamics and function remains elusive. This is because many of the conformers on its energy landscape are only transiently formed and marginally populated (less than a few per cent of the total number of molecules), so that they cannot be individually characterized by most biophysical tools. Here we study a lysozyme mutant from phage T4 that binds hydrophobic molecules and populates an excited state transiently (about 1 ms) to about 3% at 25 degrees C (ref. 5). We show that such binding occurs only via the ground state, and present the atomic-level model of the 'invisible', excited state obtained using a combined strategy of relaxation-dispersion NMR (ref. 6) and CS-Rosetta model building that rationalizes this observation. The model was tested using structure-based design calculations identifying point mutants predicted to stabilize the excited state relative to the ground state. In this way a pair of mutations were introduced, inverting the relative populations of the ground and excited states and altering function. Our results suggest a mechanism for the evolution of a protein's function by changing the delicate balance between the states on its energy landscape. More generally, they show that our approach can generate and validate models of excited protein states.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706084/" 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/PMC3706084/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouvignies, Guillaume -- Vallurupalli, Pramodh -- Hansen, D Flemming -- Correia, Bruno E -- Lange, Oliver -- Bah, Alaji -- Vernon, Robert M -- Dahlquist, Frederick W -- Baker, David -- Kay, Lewis E -- R01 GM092802/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Aug 21;477(7362):111-4. doi: 10.1038/nature10349.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, 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/21857680" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/*enzymology/*genetics ; Evolution, Molecular ; Hydrophobic and Hydrophilic Interactions ; Ligands ; *Models, Molecular ; Muramidase/*chemistry/*genetics ; *Mutation ; Protein Binding ; Temperature
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2011-05-03
    Description: Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 A resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with 〉20% sequence identity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" 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/PMC3365536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiMaio, Frank -- Terwilliger, Thomas C -- Read, Randy J -- Wlodawer, Alexander -- Oberdorfer, Gustav -- Wagner, Ulrike -- Valkov, Eugene -- Alon, Assaf -- Fass, Deborah -- Axelrod, Herbert L -- Das, Debanu -- Vorobiev, Sergey M -- Iwai, Hideo -- Pokkuluri, P Raj -- Baker, David -- 082961/Wellcome Trust/United Kingdom -- 5R01GM092802/GM/NIGMS NIH HHS/ -- GM074898/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41RR002250/RR/NCRR NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM074958/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21532589" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*methods ; Crystallography, X-Ray ; Databases, Protein ; Electrons ; *Models, Molecular ; Proteins/*chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; *Structural Homology, Protein
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-11-09
    Description: Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked alpha-helices, bulged beta-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of alpha-helices, beta-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705962/" 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/PMC3705962/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koga, Nobuyasu -- Tatsumi-Koga, Rie -- Liu, Gaohua -- Xiao, Rong -- Acton, Thomas B -- Montelione, Gaetano T -- Baker, David -- U54 GM094597/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Nov 8;491(7423):222-7. doi: 10.1038/nature11600.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23135467" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer Simulation ; *Models, Molecular ; *Protein Folding ; *Protein Stability ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-06-16
    Description: Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies, resulting in low-resolution and medium-resolution models. However, such approaches cannot deliver atomic details, especially of the crucial subunit-subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be alpha-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598588/" 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/PMC3598588/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loquet, Antoine -- Sgourakis, Nikolaos G -- Gupta, Rashmi -- Giller, Karin -- Riedel, Dietmar -- Goosmann, Christian -- Griesinger, Christian -- Kolbe, Michael -- Baker, David -- Becker, Stefan -- Lange, Adam -- 1R01GM092802-01/GM/NIGMS NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 May 20;486(7402):276-9. doi: 10.1038/nature11079.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22699623" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Secretion Systems ; HeLa Cells ; Humans ; Microscopy, Electron ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Salmonella typhimurium/*chemistry
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2019-07-13
    Description: Six flux transfer events (FTEs) were encountered during MESSENGER's first two flybys of Mercury (MI and M2). For MI the interplanetary magnetic field (IMF) was predominantly northward and four FTEs with durations of 1 to 6 s were observed in the magnetosheath following southward 1M F turnings. The IMF was steadily southward during M2, and an FTE 4 s in duration was observed just inside the dawn magnetopause followed approx.32 s later by a 7-s FTE in the magnetosheath. Flux rope models were fit to the magnetic field data to detem11ne PTE dimensions and flux content The largest FTE observed by MESSENGER had a diameter of approx. 1 R(sub M) (where R(sub M) is Mercury's radius), and its open magnetic field increased the fraction of the surface exposed to the solar wind by 10 - 20 percent and contributed up to approx.30 kV to the cross-magnetospheric electric potential.
    Keywords: Geophysics
    Type: GSFC.JA.4591.2011 , Geophysical Research Letters; 37
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  • 8
    Publication Date: 2019-07-12
    Description: Convection plays an important role in the transport of heat, moisture and trace gases. In this study, we simulated CO2 concentrations with an atmospheric general circulation model (GCM). Three different convective transport algorithms were used. One is a modified Arakawa-Shubert scheme that was native to the GCM; two others used in two off-line chemical transport models (CTMs) were added to the GCM here for comparison purposes. Advanced CO2 surfaced fluxes were used for the simulations. The results were compared to a large quantity of CO2 observation data. We find that the simulation results are sensitive to the convective transport algorithms. Overall, the three simulations are quite realistic and similar to each other in the remote marine regions, but are significantly different in some land regions with strong fluxes such as Amazon and Siberia during the convection seasons. Large biases against CO2 measurements are found in these regions in the control run, which uses the original GCM. The simulation with the simple diffusive algorithm is better. The difference of the two simulations is related to the very different convective transport speed.
    Keywords: Geophysics
    Type: GSFC-E-DAA-TN13279
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  • 9
    Publication Date: 2019-07-13
    Description: The El Nino Southern Oscillation is the dominant year-to-year mode of global climate variability. El Nino effects on terrestrial carbon cycling are mediated by associated climate anomalies, primarily drought, influencing fire emissions and biotic net ecosystem exchange (NEE). Here we evaluate whether El Nino produces a consistent response from the global carbon cycle. We apply a novel bottom-up approach to estimating global NEE anomalies based on FLUXNET data using land cover maps and weather reanalysis. We analyze 13 years (1997-2009) of globally gridded observational NEE anomalies derived from eddy covariance flux data, remotely-sensed fire emissions at the monthly time step, and NEE estimated from an atmospheric transport inversion. We evaluate the overall consistency of biospheric response to El Nino and, more generally, the link between global CO2 flux anomalies and El Nino-induced drought. Our findings, which are robust relative to uncertainty in both methods and time-lags in response, indicate that each event has a different spatial signature with only limited spatial coherence in Amazonia, Australia and southern Africa. For most regions, the sign of response changed across El Nino events. Biotic NEE anomalies, across 5 El Nino events, ranged from -1.34 to +0.98 Pg Cyr(exp -1, whereas fire emissions anomalies were generally smaller in magnitude (ranging from -0.49 to +0.53 Pg C yr(exp -1). Overall drought does not appear to impose consistent terrestrial CO2 flux anomalies during El Ninos, finding large variation in globally integrated responses from 11.15 to +0.49 Pg Cyr(exp -1). Despite the significant correlation between the CO2 flux and El Nino indices, we find that El Nino events have, when globally integrated, both enhanced and weakened terrestrial sink strength, with no consistent response across events
    Keywords: Geophysics
    Type: GSFC.JA.6430.2012 , Biogeosciences; 8; 2493-2506
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  • 10
    Publication Date: 2019-07-13
    Description: Martian rocks and sediments contain weathering products including evaporite salts and clay minerals that only form as a result of interaction between rocks and water [1-6]. These weathering products are key to studying the history of water on Mars because their type, abundance and location provide clues to past conditions on the surface of the planet, as well as to the possible location of present-day reservoirs of water. Weathering of terrestrial volcanic rocks similar to those on Mars produces nano-sized, variably hydrated aluminosilicate and iron oxide minerals [7-10] including allophane, imogolite, halloysite, hisingerite, and ferrihydrite. The nanoaluminosilicates can contain isomorphically substituted Fe, which affects their spectral and physical properties. Detection and quantification of such minerals in natural environments on earth is difficult due to their variable chemical composition and lack of long-range crystalline order [9, 11, 12]. Despite the difficulty in characterizing these materials, they are common on Earth, and data from orbital remote sensing and rover-based instruments suggest that they are also present on Mars [9, 10, 13-17]. Their accurate detection and quantification require a better understanding of how composition affects their spectral properties. We present here the results of XAFS spectroscopy; these results will be corroborated with planned Mossbauer and reflectance spectroscopy.
    Keywords: Geophysics
    Type: JSC-CN-22629 , 42nd Lunar and Planetary Science Conference; Mar 07, 2011 - Mar 11, 2011; The Woodlands, TX; United States
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