Visualizing chaperone-assisted protein folding

Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S.; Martin, Raoul; Quan, Shu; Afonine, Pavel V.; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C.; Brooks, Charles L.; Bardwell, James C. A.

doi:10.1038/nsmb.3237

Visualizing chaperone-assisted protein folding

Journal Article · Mon May 30 04:00:00 EDT 2016 · Nature Structural & Molecular Biology

DOI:https://doi.org/10.1038/nsmb.3237· OSTI ID:1419059

Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S.; Martin, Raoul; Quan, Shu; Afonine, Pavel V.; ; Wang, Lili; Xu, Qingping; Trievel, Raymond C.; Brooks, Charles L.; Bardwell, James C. A.

Abstract not provided

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: NIHFOREIGN

OSTI ID:: 1419059

Journal Information:: Nature Structural & Molecular Biology, Journal Name: Nature Structural & Molecular Biology Journal Issue: 7 Vol. 23; ISSN 1545-9993

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: ENGLISH

References (49)

A structural model for GroEL-polypeptide recognition Buckle, A. M.; Zahn, R.; Fersht, A. R. Proceedings of the National Academy of Sciences, Vol. 94, Issue 8 https://doi.org/10.1073/pnas.94.8.3571	journal	April 1997
Conformational Properties of the Unfolded State of Im7 in Nondenaturing Conditions Pashley, Clare L.; Morgan, Gareth J.; Kalverda, Arnout P. Journal of Molecular Biology, Vol. 416, Issue 2 https://doi.org/10.1016/j.jmb.2011.12.041	journal	February 2012
The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins Dekker, Carien; Roe, S. Mark; McCormack, Elizabeth A. The EMBO Journal, Vol. 30, Issue 15 https://doi.org/10.1038/emboj.2011.208	journal	June 2011
Conformational backbone dynamics of the cyclic decapeptide antamanide. Application of a new multiconformational search algorithm based on NMR data Blackledge, M. J.; Brueschweiler, R.; Griesinger, C. Biochemistry, Vol. 32, Issue 41 https://doi.org/10.1021/bi00092a005	journal	October 1993
Structural Basis for Protein Antiaggregation Activity of the Trigger Factor Chaperone Saio, T.; Guan, X.; Rossi, P. Science, Vol. 344, Issue 6184 https://doi.org/10.1126/science.1250494	journal	May 2014
New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy Kay, Lewis E. Journal of Molecular Biology, Vol. 428, Issue 2 https://doi.org/10.1016/j.jmb.2015.11.028	journal	January 2016
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers van den Bedem, Henry; Dhanik, Ankur; Latombe, Jean-Claude Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10 https://doi.org/10.1107/s0907444909030613	journal	September 2009
Reshaping of the conformational search of a protein by the chaperone trigger factor Mashaghi, Alireza; Kramer, Günter; Bechtluft, Philipp Nature, Vol. 500, Issue 7460 https://doi.org/10.1038/nature12293	journal	July 2013
Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact? Keskin, Ozlem; Gursoy, Attila; Ma, Buyong Chemical Reviews, Vol. 108, Issue 4 https://doi.org/10.1021/cr040409x	journal	April 2008
Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone Martinez-Hackert, Erik; Hendrickson, Wayne A. Cell, Vol. 138, Issue 5 https://doi.org/10.1016/j.cell.2009.07.044	journal	September 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Topologies of a Substrate Protein Bound to the Chaperonin GroEL Elad, Nadav; Farr, George W.; Clare, Daniel K. Molecular Cell, Vol. 26, Issue 3 https://doi.org/10.1016/j.molcel.2007.04.004	journal	May 2007
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers van den Bedem, Henry; Dhanik, Ankur; Latombe, Jean-Claude Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10 https://doi.org/10.1107/S0907444909030613	journal	September 2009
Folding on the Chaperone: Yield Enhancement Through Loose Binding Jewett, A. I.; Shea, J. -E. Journal of Molecular Biology, Vol. 363, Issue 5 https://doi.org/10.1016/j.jmb.2006.08.040	journal	November 2006
The origins of asymmetry in the folding transition states of protein L and protein G Karanicolas, John; Brooks, Charles L. Protein Science, Vol. 11, Issue 10 https://doi.org/10.1110/ps.0205402	journal	October 2002
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review Salmon, Loïc; Blackledge, Martin Reports on Progress in Physics, Vol. 78, Issue 12 https://doi.org/10.1088/0034-4885/78/12/126601	journal	October 2015
Isolation of Bacteria Envelope Proteins Quan, Shu; Hiniker, Annie; Collet, Jean-François Bacterial Cell Surfaces. Methods in Molecular Biology https://doi.org/10.1007/978-1-62703-245-2_22	book	November 2012
One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites Fischer, Marcus; Shoichet, Brian K.; Fraser, James S. ChemBioChem, Vol. 16, Issue 11 https://doi.org/10.1002/cbic.201500196	journal	June 2015
Hsp90-Tau Complex Reveals Molecular Basis for Specificity in Chaperone Action Karagöz, G. Elif; Duarte, Afonso M. S.; Akoury, Elias Cell, Vol. 156, Issue 5 https://doi.org/10.1016/j.cell.2014.01.037	journal	February 2014
The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface. Chak, K. F.; Safo, M. K.; Ku, W. Y. Proceedings of the National Academy of Sciences, Vol. 93, Issue 13 https://doi.org/10.1073/pnas.93.13.6437	journal	June 1996
Substrate protein folds while it is bound to the ATP-independent chaperone Spy Stull, Frederick; Koldewey, Philipp; Humes, Julia R. Nature Structural & Molecular Biology, Vol. 23, Issue 1 https://doi.org/10.1038/nsmb.3133	journal	November 2015
The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints Friel, Claire T.; Alastair Smith, D.; Vendruscolo, Michele Nature Structural & Molecular Biology, Vol. 16, Issue 3 https://doi.org/10.1038/nsmb.1562	journal	March 2009
Accessing protein conformational ensembles using room-temperature X-ray crystallography Fraser, J. S.; van den Bedem, H.; Samelson, A. J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 39 https://doi.org/10.1073/pnas.1111325108	journal	September 2011
The Structural Basis of Substrate Recognition by the Eukaryotic Chaperonin TRiC/CCT Joachimiak, Lukasz A.; Walzthoeni, Thomas; Liu, Corey W. Cell, Vol. 159, Issue 5 https://doi.org/10.1016/j.cell.2014.10.042	journal	November 2014
Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling Schuck, Peter Biophysical Journal, Vol. 78, Issue 3 https://doi.org/10.1016/S0006-3495(00)76713-0	journal	March 2000
Super Spy variants implicate flexibility in chaperone action Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V. eLife, Vol. 3 https://doi.org/10.7554/elife.01584	journal	February 2014
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444910045749	journal	March 2011
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Structure of GroEL in Complex with an Early Folding Intermediate of Alanine Glyoxylate Aminotransferase Albert, Armando; Yunta, Cristina; Arranz, Rocío Journal of Biological Chemistry, Vol. 285, Issue 9 https://doi.org/10.1074/jbc.m109.062471	journal	January 2010
Secondary structure of bovine αS1- and β-casein in solution Creamer, L. K.; Richardson, T.; Parry, D. A. D. Archives of Biochemistry and Biophysics, Vol. 211, Issue 2 https://doi.org/10.1016/0003-9861(81)90505-1	journal	October 1981
Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases Burling, F. T.; Weis, W. I.; Flaherty, K. M. Science, Vol. 271, Issue 5245 https://doi.org/10.1126/science.271.5245.72	journal	January 1996
A suite of programs for calculating x‐ray absorption, reflection, and diffraction performance for a variety of materials at arbitrary wavelengths Brennan, S.; Cowan, P. L. Review of Scientific Instruments, Vol. 63, Issue 1 https://doi.org/10.1063/1.1142625	journal	January 1992
Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings Guerry, Paul; Salmon, Loïc; Mollica, Luca Angewandte Chemie International Edition, Vol. 52, Issue 11 https://doi.org/10.1002/anie.201209669	journal	February 2013
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444910048675	journal	March 2011
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910048675	journal	March 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin Muñoz, Inés G.; Yébenes, Hugo; Zhou, Min Nature Structural & Molecular Biology, Vol. 18, Issue 1 https://doi.org/10.1038/nsmb.1971	journal	December 2010
Genetic selection designed to stabilize proteins uncovers a chaperone called Spy Quan, Shu; Koldewey, Philipp; Tapley, Tim Nature Structural & Molecular Biology, Vol. 18, Issue 3 https://doi.org/10.1038/nsmb.2016	journal	February 2011
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Reconciling theories of chaperonin accelerated folding with experimental evidence Jewett, Andrew I.; Shea, Joan-Emma Cellular and Molecular Life Sciences, Vol. 67, Issue 2 https://doi.org/10.1007/s00018-009-0164-6	journal	October 2009
Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7: Dynamics of an Engineered Im Protein Figueiredo, Angelo Miguel; Whittaker, Sara B. -M.; Knowling, Stuart E. Protein Science, Vol. 22, Issue 12 https://doi.org/10.1002/pro.2372	journal	October 2013
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
Structure of GroEL in Complex with an Early Folding Intermediate of Alanine Glyoxylate Aminotransferase Albert, Armando; Yunta, Cristina; Arranz, Rocío Journal of Biological Chemistry, Vol. 285, Issue 9 https://doi.org/10.1074/jbc.M109.062471	journal	January 2010
Super Spy variants implicate flexibility in chaperone action Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V. eLife, Vol. 3 https://doi.org/10.7554/eLife.01584	journal	February 2014
Conditional disorder in chaperone action Bardwell, James C. A.; Jakob, Ursula Trends in Biochemical Sciences, Vol. 37, Issue 12 https://doi.org/10.1016/j.tibs.2012.08.006	journal	December 2012
The crystal structure Escherichia coli Spy : The Crystal Structure of EcSpy Kwon, Eunju; Kim, Dong Young; Gross, Carol A. Protein Science, Vol. 19, Issue 11 https://doi.org/10.1002/pro.489	journal	September 2010
Visualizing GroEL/ES in the Act of Encapsulating a Folding Protein Chen, Dong-Hua; Madan, Damian; Weaver, Jeremy Cell, Vol. 153, Issue 6 https://doi.org/10.1016/j.cell.2013.04.052	journal	June 2013

Cited By (10)

A molecular mechanism of chaperone–client recognition He, Lichun; Sharpe, Timothy; Mazur, Adam American Association for the Advancement of Science https://doi.org/10.5451/unibas-ep53663	text	January 2016
Reply to ‘Misreading chaperone–substrate complexes from random noise’ Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp Nature Structural & Molecular Biology, Vol. 25, Issue 11 https://doi.org/10.1038/s41594-018-0145-2	journal	October 2018
Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ) Salmon, Loïc; Ahlstrom, Logan S.; Bardwell, James C. A. Protein Complex Assembly https://doi.org/10.1007/978-1-4939-7759-8_31	book	January 2018
Dual Role of Ribosome-Binding Domain of NAC as a Potent Suppressor of Protein Aggregation and Aging-Related Proteinopathies Shen, Koning; Gamerdinger, Martin; Chan, Rebecca Molecular Cell, Vol. 74, Issue 4 https://doi.org/10.1016/j.molcel.2019.03.012	journal	May 2019
Identifying dynamic, partially occupied residues using anomalous scattering Rocchio, Serena; Duman, Ramona; El Omari, Kamel Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 12 https://doi.org/10.1107/s2059798319014475	journal	November 2019
Chaperone-client interactions: Non-specificity engenders multifunctionality Koldewey, Philipp; Horowitz, Scott; Bardwell, James C. A. Journal of Biological Chemistry, Vol. 292, Issue 29 https://doi.org/10.1074/jbc.r117.796862	journal	June 2017
Competing protein-protein interactions regulate binding of Hsp27 to its client protein tau Freilich, Rebecca; Betegon, Miguel; Tse, Eric Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07012-4	journal	November 2018
Misreading chaperone–substrate complexes from random noise Wang, Jimin Nature Structural & Molecular Biology, Vol. 25, Issue 11 https://doi.org/10.1038/s41594-018-0144-3	journal	October 2018
A molecular mechanism of chaperone-client recognition He, Lichun; Sharpe, Timothy; Mazur, Adam Science Advances, Vol. 2, Issue 11 https://doi.org/10.1126/sciadv.1601625	journal	November 2016
Protein folding while chaperone bound is dependent on weak interactions Wu, Kevin; Stull, Frederick; Lee, Changhan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12774-6	journal	October 2019

Similar Records

Visualizing chaperone-assisted protein folding

Journal Article · Sun May 29 20:00:00 EDT 2016 · Nature Structural & Molecular Biology · OSTI ID:1379420

Folding of a large protein at high structural resolution

Journal Article · Wed Dec 11 23:00:00 EST 2013 · Proc. Natl. Acad. Sci. USA · OSTI ID:1111162

Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein

Journal Article · Thu Mar 12 00:00:00 EDT 2020 · Nat. Struct. Mol. Biol. · OSTI ID:1605436

Visualizing chaperone-assisted protein folding

Citation Formats

References (49)

Cited By (10)

Similar Records

Related Subjects