Literature DB >> 22503819

The molecular architecture of the eukaryotic chaperonin TRiC/CCT.

Alexander Leitner1, Lukasz A Joachimiak, Andreas Bracher, Leonie Mönkemeyer, Thomas Walzthoeni, Bryan Chen, Sebastian Pechmann, Susan Holmes, Yao Cong, Boxue Ma, Steve Ludtke, Wah Chiu, F Ulrich Hartl, Ruedi Aebersold, Judith Frydman.   

Abstract

TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. Previously proposed TRiC models differ substantially in their subunit arrangements and ring register. Here, we integrate chemical crosslinking, mass spectrometry, and combinatorial modeling to reveal the definitive subunit arrangement of TRiC. In vivo disulfide mapping provided additional validation for the crosslinking-derived arrangement as the definitive TRiC topology. This subunit arrangement allowed the refinement of a structural model using existing X-ray diffraction data. The structure described here explains all available crosslink experiments, provides a rationale for previously unexplained structural features, and reveals a surprising asymmetry of charges within the chaperonin folding chamber.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22503819      PMCID: PMC3350567          DOI: 10.1016/j.str.2012.03.007

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  45 in total

1.  Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

Authors:  Tal Pupko; Rachel E Bell; Itay Mayrose; Fabian Glaser; Nir Ben-Tal
Journal:  Bioinformatics       Date:  2002       Impact factor: 6.937

2.  Tumorigenic mutations in VHL disrupt folding in vivo by interfering with chaperonin binding.

Authors:  Douglas E Feldman; Christoph Spiess; Daniel E Howard; Judith Frydman
Journal:  Mol Cell       Date:  2003-11       Impact factor: 17.970

Review 3.  Crosslinking combined with mass spectrometry for structural proteomics.

Authors:  Evgeniy V Petrotchenko; Christoph H Borchers
Journal:  Mass Spectrom Rev       Date:  2010 Nov-Dec       Impact factor: 10.946

4.  Identification of cross-linked peptides from large sequence databases.

Authors:  Oliver Rinner; Jan Seebacher; Thomas Walzthoeni; Lukas N Mueller; Martin Beck; Alexander Schmidt; Markus Mueller; Ruedi Aebersold
Journal:  Nat Methods       Date:  2008-03-09       Impact factor: 28.547

5.  Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins.

Authors:  Stefanie Reissmann; Charles Parnot; Christopher R Booth; Wah Chiu; Judith Frydman
Journal:  Nat Struct Mol Biol       Date:  2007-04-29       Impact factor: 15.369

Review 6.  Molecular chaperones in protein folding and proteostasis.

Authors:  F Ulrich Hartl; Andreas Bracher; Manajit Hayer-Hartl
Journal:  Nature       Date:  2011-07-20       Impact factor: 49.962

7.  The structure of CCT-Hsc70 NBD suggests a mechanism for Hsp70 delivery of substrates to the chaperonin.

Authors:  Jorge Cuéllar; Jaime Martín-Benito; Sjors H W Scheres; Rui Sousa; Fernando Moro; Eduardo López-Viñas; Paulino Gómez-Puertas; Arturo Muga; José L Carrascosa; José M Valpuesta
Journal:  Nat Struct Mol Biol       Date:  2008-07-27       Impact factor: 15.369

Review 8.  Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.

Authors:  Alexander Leitner; Thomas Walzthoeni; Abdullah Kahraman; Franz Herzog; Oliver Rinner; Martin Beck; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2010-03-31       Impact factor: 5.911

9.  Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.

Authors:  Yao Cong; Gunnar F Schröder; Anne S Meyer; Joanita Jakana; Boxue Ma; Matthew T Dougherty; Michael F Schmid; Stefanie Reissmann; Michael Levitt; Steven L Ludtke; Judith Frydman; Wah Chiu
Journal:  EMBO J       Date:  2011-11-01       Impact factor: 11.598

10.  Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies.

Authors:  Alice Y Yam; Yu Xia; Hen-Tzu Jill Lin; Alma Burlingame; Mark Gerstein; Judith Frydman
Journal:  Nat Struct Mol Biol       Date:  2008-11-16       Impact factor: 15.369

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  129 in total

1.  XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Authors:  Devin K Schweppe; Juan D Chavez; James E Bruce
Journal:  Bioinformatics       Date:  2015-09-26       Impact factor: 6.937

2.  Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry.

Authors:  Fan Liu; Dirk T S Rijkers; Harm Post; Albert J R Heck
Journal:  Nat Methods       Date:  2015-09-28       Impact factor: 28.547

3.  Structure and mechanism of the Rubisco-assembly chaperone Raf1.

Authors:  Thomas Hauser; Javaid Y Bhat; Goran Miličić; Petra Wendler; F Ulrich Hartl; Andreas Bracher; Manajit Hayer-Hartl
Journal:  Nat Struct Mol Biol       Date:  2015-08-03       Impact factor: 15.369

Review 4.  Chaperone machines for protein folding, unfolding and disaggregation.

Authors:  Helen Saibil
Journal:  Nat Rev Mol Cell Biol       Date:  2013-09-12       Impact factor: 94.444

5.  Matching cross-linked peptide spectra: only as good as the worse identification.

Authors:  Michael J Trnka; Peter R Baker; Philip J J Robinson; A L Burlingame; Robert J Chalkley
Journal:  Mol Cell Proteomics       Date:  2013-12-12       Impact factor: 5.911

Review 6.  The Mechanism and Function of Group II Chaperonins.

Authors:  Tom Lopez; Kevin Dalton; Judith Frydman
Journal:  J Mol Biol       Date:  2015-04-30       Impact factor: 5.469

7.  Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica.

Authors:  Nur Athirah Yusof; Shazilah Kamaruddin; Farah Diba Abu Bakar; Nor Muhammad Mahadi; Abdul Munir Abdul Murad
Journal:  Cell Stress Chaperones       Date:  2019-01-16       Impact factor: 3.667

Review 8.  Single-Particle Refinement and Variability Analysis in EMAN2.1.

Authors:  S J Ludtke
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

9.  Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states.

Authors:  Dan Tan; Qiang Li; Mei-Jun Zhang; Chao Liu; Chengying Ma; Pan Zhang; Yue-He Ding; Sheng-Bo Fan; Li Tao; Bing Yang; Xiangke Li; Shoucai Ma; Junjie Liu; Boya Feng; Xiaohui Liu; Hong-Wei Wang; Si-Min He; Ning Gao; Keqiong Ye; Meng-Qiu Dong; Xiaoguang Lei
Journal:  Elife       Date:  2016-03-08       Impact factor: 8.140

10.  Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes.

Authors:  Clinton Yu; Alexander Huszagh; Rosa Viner; Eric J Novitsky; Scott D Rychnovsky; Lan Huang
Journal:  Anal Chem       Date:  2016-09-27       Impact factor: 6.986

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