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  • 1
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    Folding of large multidomain proteins by TRiC [Biochemistry] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-12-27
    Description: The eukaryotic chaperonin, TRiC/CCT (TRiC, TCP-1 ring complex; CCT, chaperonin containing TCP-1), uses a built-in lid to mediate protein folding in an enclosed central cavity. Recent structural data suggest an effective size limit for the TRiC folding chamber of ∼70 kDa, but numerous chaperonin substrates are substantially larger. Using artificial...
    Keywords: Inaugural Articles
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Modeling Photoprotection at Global Scale: the Relative Role of Non‐Photosynthetic Pigments, Physiological State and Species Composition (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Microalgae are capable of acclimating to dynamic light environments as they have developed mechanisms to optimize light harvesting and photosynthetic electron transport. When absorption of light exceeds photosynthetic capacity, various physiological protective mechanisms prevent damage of the photosynthetic apparatus. Xanthophyll pigments provide one of the most important photoprotective mechanisms to dissipate the excess light energy and prevent photoinhibition. In this study, we coupled a mechanistic model for phytoplankton photoinhibition with the global biogeochemical model Regulated Ecosystem Model version 2 (REcoM2). The assumption that photoinhibition is small in phytoplankton communities acclimated to ambient light allowed us to predict the photoprotective needs of phytoplankton. When comparing the predicted photoprotective needs to observations of pigment content determined by high‐performance liquid chromatography, our results showed that photoprotective response seems to be mediated in most parts of the ocean by a variable ratio of xanthophyll pigments to chlorophyll. The variability in the ratio appeared to be mainly driven by changes in phytoplankton community composition. Exceptions appeared at high latitudes where other energy dissipating mechanisms seem to play a role in photoprotection and both taxonomic changes and physiological acclimation determine community pigment signature. Understanding the variability of community pigment signature is crucial for modeling the coupling of light absorption to carbon fixation in the ocean. Insights about how much of this variability is attributable to changes in community composition may allow us to improve the match between remotely‐sensed optical data and the underlying phytoplankton community.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Assimilation of Global Total Chlorophyll OC‐CCI Data and Its Impact on Individual Phytoplankton Fields (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract The coupled ocean circulation‐ecosystem model MITgcm‐REcoM2 is used to simulate biogeochemical variables in a global configuration. The ecosystem model REcoM2 simulates two phytoplankton groups, diatoms and small phytoplankton, using a quota formulation with variable carbon, nitrogen, and chlorophyll contents of the cells. To improve the simulation of the phytoplankton variables, chlorophyll‐a data from the European Space Agency Ocean‐Color Climate Change Initiative (OC‐CCI) for 2008 and 2009 are assimilated with an ensemble Kalman filter. Utilizing the multivariate cross covariances estimated by the model ensemble, the assimilation constrains all model variables describing the two phytoplankton groups. Evaluating the assimilation results against the satellite data product SynSenPFT shows an improvement of total chlorophyll and more importantly of individual phytoplankton groups. The assimilation improves both phytoplankton groups in the tropical and midlatitude regions, whereas the assimilation has a mixed response in the high‐latitude regions. Diatoms are most improved in the major ocean basins, whereas small phytoplankton show small deteriorations in the Southern Ocean. The improvement of diatoms is larger when the multivariate assimilation is computed using the ensemble‐estimated cross covariances between total chlorophyll and the phytoplankton groups than when the groups are updated so that their ratio to total chlorophyll is preserved. The comparison with in situ observations shows that the correlation of the simulated chlorophyll of both phytoplankton groups with these data is increased whereas the bias and error are decreased. Overall, the multivariate assimilation of total chlorophyll modifies the two phytoplankton groups separately, even though the sum of their individual chlorophyll concentrations represents the total chlorophyll.
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Coupled chaperone action in folding and assembly of hexadecameric Rubisco (2010)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 5
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    Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: The identification of proximate amino acids by chemical cross-linking and mass spectrometry (XL-MS) facilitates the structural analysis of homogeneous protein complexes. We gained distance restraints on a modular interaction network of protein complexes affinity-purified from human cells by applying an adapted XL-MS protocol. Systematic analysis of human protein phosphatase 2A (PP2A) complexes identified 176 interprotein and 570 intraprotein cross-links that link specific trimeric PP2A complexes to a multitude of adaptor proteins that control their cellular functions. Spatial restraints guided molecular modeling of the binding interface between immunoglobulin binding protein 1 (IGBP1) and PP2A and revealed the topology of TCP1 ring complex (TRiC) chaperonin interacting with the PP2A regulatory subunit 2ABG. This study establishes XL-MS as an integral part of hybrid structural biology approaches for the analysis of endogenous protein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzog, Franz -- Kahraman, Abdullah -- Boehringer, Daniel -- Mak, Raymond -- Bracher, Andreas -- Walzthoeni, Thomas -- Leitner, Alexander -- Beck, Martin -- Hartl, Franz-Ulrich -- Ban, Nenad -- Malmstrom, Lars -- Aebersold, Ruedi -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1348-52. doi: 10.1126/science.1221483.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22984071" target="_blank"〉PubMed〈/a〉
    Keywords: Chaperonins/chemistry ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; Humans ; Mass Spectrometry/*methods ; *Metabolic Networks and Pathways ; Protein Conformation ; Protein Interaction Mapping/*methods ; Protein Phosphatase 2/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Rubisco condensate formation by CcmM in β-carboxysome biogenesis (2019)
    Springer Nature
    In: Nature
    Details
    Publication Date: 2019
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 7
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    Molecular chaperones in protein folding and proteostasis (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-22
    Description: Most proteins must fold into defined three-dimensional structures to gain functional activity. But in the cellular environment, newly synthesized proteins are at great risk of aberrant folding and aggregation, potentially forming toxic species. To avoid these dangers, cells invest in a complex network of molecular chaperones, which use ingenious mechanisms to prevent aggregation and promote efficient folding. Because protein molecules are highly dynamic, constant chaperone surveillance is required to ensure protein homeostasis (proteostasis). Recent advances suggest that an age-related decline in proteostasis capacity allows the manifestation of various protein-aggregation diseases, including Alzheimer's disease and Parkinson's disease. Interventions in these and numerous other pathological states may spring from a detailed understanding of the pathways underlying proteome maintenance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartl, F Ulrich -- Bracher, Andreas -- Hayer-Hartl, Manajit -- England -- Nature. 2011 Jul 20;475(7356):324-32. doi: 10.1038/nature10317.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. uhartl@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21776078" target="_blank"〉PubMed〈/a〉
    Keywords: Aging ; Animals ; Disease ; Humans ; Molecular Chaperones/classification/*metabolism ; *Protein Folding ; Proteins/*metabolism ; Proteome/metabolism ; Ribosomes/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-11-04
    Description: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (RuBP). In plants, Rubisco is reactivated by the AAA(+) (ATPases associated with various cellular activities) protein Rubisco activase (Rca), but no such protein is known for the Rubisco of red algae. Here we identify the protein CbbX as an activase of red-type Rubisco. The 3.0-A crystal structure of unassembled CbbX from Rhodobacter sphaeroides revealed an AAA(+) protein architecture. Electron microscopy and biochemical analysis showed that ATP and RuBP must bind to convert CbbX into functionally active, hexameric rings. The CbbX ATPase is strongly stimulated by RuBP and Rubisco. Mutational analysis suggests that CbbX functions by transiently pulling the carboxy-terminal peptide of the Rubisco large subunit into the hexamer pore, resulting in the release of the inhibitory RuBP. Understanding Rubisco activation may facilitate efforts to improve CO(2) uptake and biomass production by photosynthetic organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mueller-Cajar, Oliver -- Stotz, Mathias -- Wendler, Petra -- Hartl, F Ulrich -- Bracher, Andreas -- Hayer-Hartl, Manajit -- England -- Nature. 2011 Nov 2;479(7372):194-9. doi: 10.1038/nature10568.〈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/22048315" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation/drug effects ; Bacterial Proteins/*chemistry/genetics/*metabolism/ultrastructure ; Carbon Dioxide/metabolism ; Crystallography, X-Ray ; Enzyme Activation/drug effects ; Models, Molecular ; Protein Multimerization/drug effects ; Protein Structure, Quaternary/drug effects ; Rhodobacter sphaeroides/*enzymology ; Ribulose-Bisphosphate Carboxylase/*metabolism ; Ribulosephosphates/metabolism/pharmacology ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11 (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-02-10
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-12-20
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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