1
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Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Nat Struct Mol Biol 2024:10.1038/s41594-024-01352-0. [PMID: 38951622 DOI: 10.1038/s41594-024-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/07/2024] [Indexed: 07/03/2024]
Abstract
The mitochondrial chaperonin, mitochondrial heat shock protein 60 (mtHsp60), promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin progresses through its ATP-dependent client folding cycle are not clear. Here, we determined cryo-EM structures of a hyperstable disease-associated human mtHsp60 mutant, V72I. Client density is identified in three distinct states, revealing interactions with the mtHsp60 apical domains and C termini that coordinate client positioning in the folding chamber. We further identify an asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60-10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify distinct roles for the apical domains in coordinating client capture and progression through the chaperone cycle, supporting a conserved mechanism of group I chaperonin function.
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Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
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2
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Liebermann DG, Jungwirth J, Riven I, Barak Y, Levy D, Horovitz A, Haran G. From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study. J Phys Chem Lett 2023:6513-6521. [PMID: 37440608 PMCID: PMC10388350 DOI: 10.1021/acs.jpclett.3c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the Escherichia coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the cochaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-ligated conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis. These coinciding results from bulk measurements for an entire ring and single-molecule measurements for a single subunit provide new evidence for the concerted allosteric transition of all seven subunits.
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3
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Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540872. [PMID: 37293102 PMCID: PMC10245740 DOI: 10.1101/2023.05.15.540872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mitochondrial chaperonin, mtHsp60, promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin binds to clients and progresses through its ATP-dependent reaction cycle are not clear. Here, we determined cryo-electron microscopy (cryo-EM) structures of a hyperstable disease-associated mtHsp60 mutant, V72I, at three stages in this cycle. Unexpectedly, client density is identified in all states, revealing interactions with mtHsp60's apical domains and C-termini that coordinate client positioning in the folding chamber. We further identify a striking asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60/mtHsp10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify a new role for the apical domains in coordinating client capture and progression through the cycle, and suggest a conserved mechanism of group I chaperonin function.
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Affiliation(s)
- Julian R. Braxton
- Graduate Program in Chemistry and Chemical Biology; University of California, San Francisco; San Francisco, CA 94158, USA
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Daniel R. Southworth
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
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4
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Walker T, Sun HM, Gunnels T, Wysocki V, Laganowsky A, Rye H, Russell D. Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time. ACS CENTRAL SCIENCE 2023; 9:466-475. [PMID: 36968544 PMCID: PMC10037461 DOI: 10.1021/acscentsci.2c01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 06/18/2023]
Abstract
Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to determine the thermodynamics for stepwise binding of up to 14 ATP molecules to the 801 kDa GroEL tetradecamer chaperonin complex. Detailed analysis reveals strong enthalpy-entropy compensation (EEC) for the ATP binding events leading to formation of GroEL-ATP7 and GroEL-ATP14 complexes. The observed variations in EEC and stepwise free energy changes of specific ATP binding are consistent with the well-established nested cooperativity model describing GroEL-ATP interactions, viz., intraring positive cooperativity and inter-ring negative cooperativity (Dyachenko A.; Proc. Natl. Acad. Sci. U.S.A.2013, 110, 7235-7239). Entropy-driven ATP binding is to be expected for ligand-induced conformational changes of the GroEL tetradecamer, though the magnitude of the entropy change suggests that reorganization of GroEL-hydrating water molecules and/or expulsion of water from the GroEL cavity may also play key roles. The capability for determining complete thermodynamic signatures (ΔG, ΔH, and -TΔS) for individual ligand binding reactions for the large, nearly megadalton GroEL complex expands our fundamental view of chaperonin functional chemistry. Moreover, this work and related studies of protein-ligand interactions illustrate important new capabilities of vT-ESI-nMS for thermodynamic studies of protein interactions with ligands and other molecules such as proteins and drugs.
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Affiliation(s)
- Thomas Walker
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - He Mirabel Sun
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tiffany Gunnels
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Vicki Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - David Russell
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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5
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Naqvi MM, Avellaneda MJ, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. Protein chain collapse modulation and folding stimulation by GroEL-ES. SCIENCE ADVANCES 2022; 8:eabl6293. [PMID: 35245117 PMCID: PMC8896798 DOI: 10.1126/sciadv.abl6293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery.
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Affiliation(s)
| | | | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | | | | | | | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | - Sander J. Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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6
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Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
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7
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Takenaka T, Nakamura T, Yanaka S, Yagi-Utsumi M, Chandak MS, Takahashi K, Paul S, Makabe K, Arai M, Kato K, Kuwajima K. Formation of the chaperonin complex studied by 2D NMR spectroscopy. PLoS One 2017; 12:e0187022. [PMID: 29059240 PMCID: PMC5653362 DOI: 10.1371/journal.pone.0187022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 11/21/2022] Open
Abstract
We studied the interaction between GroES and a single-ring mutant (SR1) of GroEL by the NMR titration of 15N-labeled GroES with SR1 at three different temperatures (20, 25 and 30°C) in the presence of 3 mM ADP in 100 mM KCl and 10 mM MgCl2 at pH 7.5. We used SR1 instead of wild-type double-ring GroEL to precisely control the stoichiometry of the GroES binding to be 1:1 ([SR1]:[GroES]). Native heptameric GroES was very flexible, showing well resolved cross peaks of the residues in a mobile loop segment (residue 17–34) and at the top of a roof hairpin (Asn51) in the heteronuclear single quantum coherence spectra. The binding of SR1 to GroES caused the cross peaks to disappear simultaneously, and hence it occurred in a single-step cooperative manner with significant immobilization of the whole GroES structure. The binding was thus entropic with a positive entropy change (219 J/mol/K) and a positive enthalpy change (35 kJ/mol), and the binding constant was estimated at 1.9×105 M−1 at 25°C. The NMR titration in 3 mM ATP also indicated that the binding constant between GroES and SR1 increased more than tenfold as compared with the binding constant in 3 mM ADP. These results will be discussed in relation to the structure and mechanisms of the chaperonin GroEL/GroES complex.
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Affiliation(s)
- Toshio Takenaka
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Takashi Nakamura
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Saeko Yanaka
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Maho Yagi-Utsumi
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Mahesh S. Chandak
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Kazunobu Takahashi
- Department of Physics, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Subhankar Paul
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Koki Makabe
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
- Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
- Department of Physics, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Dongdaemun-gu, Seoul, Korea
- * E-mail: ,
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8
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Ho CW, Van Meervelt V, Tsai KC, De Temmerman PJ, Mast J, Maglia G. Engineering a nanopore with co-chaperonin function. SCIENCE ADVANCES 2015; 1:e1500905. [PMID: 26824063 PMCID: PMC4730846 DOI: 10.1126/sciadv.1500905] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
The emergence of an enzymatic function can reveal functional insights and allows the engineering of biological systems with enhanced properties. We engineered an alpha hemolysin nanopore to function as GroES, a protein that, in complex with GroEL, forms a two-stroke protein-folding nanomachine. The transmembrane co-chaperonin was prepared by recombination of GroES functional elements with the nanopore, suggesting that emergent functions in molecular machines can be added bottom-up by incorporating modular elements into preexisting protein scaffolds. The binding of a single-ring version of GroEL to individual GroES nanopores prompted large changes to the unitary nanopore current, most likely reflecting the allosteric transitions of the chaperonin apical domains. One of the GroEL-induced current levels showed fast fluctuations (<1 ms), a characteristic that might be instrumental for efficient substrate encapsulation or folding. In the presence of unfolded proteins, the pattern of current transitions changed, suggesting a possible mechanism in which the free energy of adenosine triphosphate binding and hydrolysis is expended only when substrate proteins are occupied.
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Affiliation(s)
- Ching-Wen Ho
- Department of Chemistry, University of Leuven, Leuven 3001, Belgium
| | | | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Pieter-Jan De Temmerman
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Giovanni Maglia
- Groningen Biotechnology Institute, University of Groningen, Groningen 9747AG, Netherlands
- Corresponding author. E-mail:
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9
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The Mechanism and Function of Group II Chaperonins. J Mol Biol 2015; 427:2919-30. [PMID: 25936650 DOI: 10.1016/j.jmb.2015.04.013] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022]
Abstract
Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis.
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10
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Mizuta T, Ando K, Uemura T, Kawata Y, Mizobata T. Probing the dynamic process of encapsulation in Escherichia coli GroEL. PLoS One 2013; 8:e78135. [PMID: 24205127 PMCID: PMC3813556 DOI: 10.1371/journal.pone.0078135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/16/2013] [Indexed: 11/24/2022] Open
Abstract
Kinetic analyses of GroE-assisted folding provide a dynamic sequence of molecular events that underlie chaperonin function. We used stopped-flow analysis of various fluorescent GroEL mutants to obtain details regarding the sequence of events that transpire immediately after ATP binding to GroEL and GroEL with prebound unfolded proteins. Characterization of GroEL CP86, a circularly permuted GroEL with the polypeptide ends relocated to the vicinity of the ATP binding site, showed that GroES binding and protection of unfolded protein from solution is achieved surprisingly early in the functional cycle, and in spite of greatly reduced apical domain movement. Analysis of fluorescent GroEL SR-1 and GroEL D398A variants suggested that among other factors, the presence of two GroEL rings and a specific conformational rearrangement of Helix M in GroEL contribute significantly to the rapid release of unfolded protein from the GroEL apical domain.
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Affiliation(s)
- Toshifumi Mizuta
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
| | - Kasumi Ando
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
| | - Tatsuya Uemura
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
| | - Yasushi Kawata
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
| | - Tomohiro Mizobata
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
- * E-mail:
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11
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Chen DH, Madan D, Weaver J, Lin Z, Schröder GF, Chiu W, Rye HS. Visualizing GroEL/ES in the act of encapsulating a folding protein. Cell 2013; 153:1354-65. [PMID: 23746846 DOI: 10.1016/j.cell.2013.04.052] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 01/06/2013] [Accepted: 04/19/2013] [Indexed: 11/16/2022]
Abstract
The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry-free, single-particle cryo-electron microscopy, we have characterized a chemically modified mutant of GroEL (EL43Py) that is trapped at a normally transient stage of substrate protein encapsulation. We show that the symmetric pattern of the GroEL subunits is broken as the GroEL cis-ring apical domains reorient to accommodate the simultaneous binding of GroES and an incompletely folded substrate protein (RuBisCO). The collapsed RuBisCO folding intermediate binds to the lower segment of two apical domains, as well as to the normally unstructured GroEL C-terminal tails. A comparative structural analysis suggests that the allosteric transitions leading to substrate protein release and folding involve concerted shifts of GroES and the GroEL apical domains and C-terminal tails.
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Affiliation(s)
- Dong-Hua Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Abstract
We have been studying chaperonins these past twenty years through an initial discovery of an action in protein folding, analysis of structure, and elucidation of mechanism. Some of the highlights of these studies were presented recently upon sharing the honor of the 2013 Herbert Tabor Award with my early collaborator, Ulrich Hartl, at the annual meeting of the American Society for Biochemistry and Molecular Biology in Boston. Here, some of the major findings are recounted, particularly recognizing my collaborators, describing how I met them and how our great times together propelled our thinking and experiments.
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Affiliation(s)
- Arthur L Horwich
- Howard Hughes Medical Institute, Yale School of Medicine, New Haven, Connecticut 06510, USA.
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13
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Abstract
Chaperonins are intricate allosteric machines formed of two back-to-back, stacked rings of subunits presenting end cavities lined with hydrophobic binding sites for nonnative polypeptides. Once bound, substrates are subjected to forceful, concerted movements that result in their ejection from the binding surface and simultaneous encapsulation inside a hydrophilic chamber that favors their folding. Here, we review the allosteric machine movements that are choreographed by ATP binding, which triggers concerted tilting and twisting of subunit domains. These movements distort the ring of hydrophobic binding sites and split it apart, potentially unfolding the multiply bound substrate. Then, GroES binding is accompanied by a 100° twist of the binding domains that removes the hydrophobic sites from the cavity lining and forms the folding chamber. ATP hydrolysis is not needed for a single round of binding and encapsulation but is necessary to allow the next round of ATP binding in the opposite ring. It is this remote ATP binding that triggers dismantling of the folding chamber and release of the encapsulated substrate, whether folded or not. The basis for these ordered actions is an elegant system of nested cooperativity of the ATPase machinery. ATP binds to a ring with positive cooperativity, and movements of the interlinked subunit domains are concerted. In contrast, there is negative cooperativity between the rings, so that they act in alternation. It is remarkable that a process as specific as protein folding can be guided by the chaperonin machine in a way largely independent of substrate protein structure or sequence.
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Affiliation(s)
- Helen R Saibil
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College London, Malet Street, London WC1E 7HX, UK
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14
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Clare DK, Vasishtan D, Stagg S, Quispe J, Farr GW, Topf M, Horwich AL, Saibil HR. ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin. Cell 2012; 149:113-23. [PMID: 22445172 PMCID: PMC3326522 DOI: 10.1016/j.cell.2012.02.047] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/24/2011] [Accepted: 02/06/2012] [Indexed: 11/24/2022]
Abstract
The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the association of the cochaperonin GroES, followed by further large movements that eject the substrate polypeptide from hydrophobic binding sites into a GroES-capped, hydrophilic folding chamber. We used cryo-electron microscopy, statistical analysis, and flexible fitting to resolve a set of distinct GroEL-ATP conformations that can be ordered into a trajectory of domain rotation and elevation. The initial conformations are likely to be the ones that capture polypeptide substrate. Then the binding domains extend radially to separate from each other but maintain their binding surfaces facing the cavity, potentially exerting mechanical force upon kinetically trapped, misfolded substrates. The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the “power stroke” that ejects substrate into the folding chamber.
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Affiliation(s)
- Daniel K Clare
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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15
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Piggot TJ, Sessions RB, Burston SG. Toward a detailed description of the pathways of allosteric communication in the GroEL chaperonin through atomistic simulation. Biochemistry 2012; 51:1707-18. [PMID: 22289022 DOI: 10.1021/bi201237a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GroEL, along with its coprotein GroES, is essential for ensuring the correct folding of unfolded or newly synthesized proteins in bacteria. GroEL is a complex, allosteric molecule, composed of two heptameric rings stacked back to back, that undergoes large structural changes during its reaction cycle. These structural changes are driven by the cooperative binding and subsequent hydrolysis of ATP, by GroEL. Despite numerous previous studies, the precise mechanisms of allosteric communication and the associated structural changes remain elusive. In this paper, we describe a series of all-atom, unbiased, molecular dynamics simulations over relatively long (50-100 ns) time scales of a single, isolated GroEL subunit and also a heptameric GroEL ring, in the presence and absence of ATP. Combined with results from a distance restraint-biased simulation of the single ring, the atomistic details of the earliest stages of ATP-driven structural changes within this complex molecule are illuminated. Our results are in broad agreement with previous modeling studies of isolated subunits and with a coarse-grained, forcing simulation of the single ring. These are the first reported all-atom simulations of the GroEL single-ring complex and provide a unique insight into the role of charged residues K80, K277, R284, R285, and E388 at the subunit interface in transmission of the allosteric signal. These simulations also demonstrate the feasibility of performing all-atom simulations of very large systems on sufficiently long time scales on typical high performance computing facilities to show the origins of the earliest events in biologically relevant processes.
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Affiliation(s)
- Thomas J Piggot
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
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16
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Illingworth M, Ramsey A, Zheng Z, Chen L. Stimulating the substrate folding activity of a single ring GroEL variant by modulating the cochaperonin GroES. J Biol Chem 2011; 286:30401-30408. [PMID: 21757689 DOI: 10.1074/jbc.m111.255935] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mediating protein folding, chaperonin GroEL and cochaperonin GroES form an enclosed chamber for substrate proteins in an ATP-dependent manner. The essential role of the double ring assembly of GroEL is demonstrated by the functional deficiency of the single ring GroEL(SR). The GroEL(SR)-GroES is highly stable with minimal ATPase activity. To restore the ATP cycle and the turnover of the folding chamber, we sought to weaken the GroEL(SR)-GroES interaction systematically by concatenating seven copies of groES to generate groES(7). GroES Ile-25, Val-26, and Leu-27, residues on the GroEL-GroES interface, were substituted with Asp on different groES modules of groES(7). GroES(7) variants activate ATP activity of GroEL(SR), but only some restore the substrate folding function of GroEL(SR), indicating a direct role of GroES in facilitating substrate folding through its dynamics with GroEL. Active GroEL(SR)-GroES(7) systems may resemble mammalian mitochondrial chaperonin systems.
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Affiliation(s)
- Melissa Illingworth
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Andrew Ramsey
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Zhida Zheng
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Lingling Chen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405.
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17
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Chen J, Makabe K, Nakamura T, Inobe T, Kuwajima K. Dissecting a bimolecular process of MgATP²- binding to the chaperonin GroEL. J Mol Biol 2011; 410:343-56. [PMID: 21620859 DOI: 10.1016/j.jmb.2011.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/17/2011] [Accepted: 05/11/2011] [Indexed: 11/29/2022]
Abstract
Although allosteric transitions of GroEL by MgATP(2)(-) have been widely studied, the initial bimolecular step of MgATP(2-) binding to GroEL remains unclear. Here, we studied the equilibrium and kinetics of MgATP(2)(-) binding to a variant of GroEL, in which Tyr485 was replaced by tryptophan, via isothermal titration calorimetry (ITC) and stopped-flow fluorescence spectroscopy. In the absence of K(+) at 4-5 °C, the allosteric transitions and the subsequent ATP hydrolysis by GroEL are halted, and hence, the stopped-flow fluorescence kinetics induced by rapid mixing of MgATP(2)(-) and the GroEL variant solely reflected MgATP(2)(-) binding, which was well represented by bimolecular noncooperative binding with a binding rate constant, k(on), of 9.14×10(4) M(-1) s(-1) and a dissociation rate constant, k(off), of 14.2 s(-1), yielding a binding constant, K(b) (=k(on)/k(off)), of 6.4×10(3) M(-1). We also successfully performed ITC to measure binding isotherms of MgATP(2)(-) to GroEL and obtained a K(b) of 9.5×10(3) M(-1) and a binding stoichiometric number of 6.6. K(b) was thus in good agreement with that obtained by stopped-flow fluorescence. In the presence of 10-50 mM KCl, the fluorescence kinetics consisted of three to four phases (the first fluorescence-increasing phase, followed by one or two exponential fluorescence-decreasing phases, and the final slow fluorescence-increasing phase), and comparison of the kinetics in the absence and presence of K(+) clearly demonstrated that the first fluorescence-increasing phase corresponds to bimolecular MgATP(2)(-) binding to GroEL. The temperature dependence of the kinetics indicated that MgATP(2)(-) binding to GroEL was activation-controlled with an activation enthalpy as large as 14-16 kcal mol(-1).
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Affiliation(s)
- Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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18
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Polypeptide in the chaperonin cage partly protrudes out and then folds inside or escapes outside. EMBO J 2010; 29:4008-19. [PMID: 20959808 DOI: 10.1038/emboj.2010.262] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 09/22/2010] [Indexed: 11/08/2022] Open
Abstract
The current mechanistic model of chaperonin-assisted protein folding assumes that the substrate protein in the cage, formed by GroEL central cavity capped with GroES, is isolated from outside and exists as a free polypeptide. However, using ATPase-deficient GroEL mutants that keep GroES bound, we found that, in the rate-limiting intermediate of a chaperonin reaction, the unfolded polypeptide in the cage partly protrudes through a narrow space near the GroEL/GroES interface. Then, the entire polypeptide is released either into the cage or to the outside medium. The former adopts a native structure very rapidly and the latter undergoes spontaneous folding. Partition of the in-cage folding and the escape varies among substrate proteins and is affected by hydrophobic interaction between the polypeptide and GroEL cavity wall. The ATPase-active GroEL with decreased in-cage folding produced less of a native model substrate protein in Escherichia coli cells. Thus, the polypeptide in the critical GroEL-GroES complex is neither free nor completely confined in the cage, but it is interacting with GroEL's apical region, partly protruding to outside.
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19
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ATP-triggered ADP release from the asymmetric chaperonin GroEL/GroES/ADP7 is not the rate-limiting step of the GroEL/GroES reaction cycle. FEBS Lett 2010; 584:951-3. [PMID: 20083109 PMCID: PMC2849271 DOI: 10.1016/j.febslet.2010.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 11/23/2022]
Abstract
The GroEL/GroES protein folding chamber is formed and dissociated by ATP binding and hydrolysis. ATP hydrolysis in the GroES-bound (cis) ring gates entry of ATP into the opposite unoccupied trans ring, which allosterically ejects cis ligands. While earlier studies suggested that hydrolysis of cis ATP is the rate-limiting step of the cycle (t1/2 approximately 10 s), a recent study suggested that ADP release from the cis ring may be rate-limiting (t1/2 approximately 15-20 s). Here we have measured ADP release using a coupled enzyme assay and observed a t1/2 for release of <or=4-5 s, indicating that this is not the rate-limiting step of the reaction cycle.
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20
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Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell Mol Life Sci 2010; 67:255-76. [PMID: 19851829 PMCID: PMC11115962 DOI: 10.1007/s00018-009-0164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/14/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.
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Affiliation(s)
- Andrew I. Jewett
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
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21
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Kovács E, Sun Z, Liu H, Scott DJ, Karsisiotis AI, Clarke AR, Burston SG, Lund PA. Characterisation of a GroEL single-ring mutant that supports growth of Escherichia coli and has GroES-dependent ATPase activity. J Mol Biol 2009; 396:1271-83. [PMID: 20006619 DOI: 10.1016/j.jmb.2009.11.074] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/26/2009] [Accepted: 11/30/2009] [Indexed: 11/30/2022]
Abstract
Binding and folding of substrate proteins by the molecular chaperone GroEL alternates between its two seven-membered rings in an ATP-regulated manner. The association of ATP and GroES to a polypeptide-bound ring of GroEL encapsulates the folding proteins in the central cavity of that ring (cis ring) and allows it to fold in a protected environment where the risk of aggregation is reduced. ATP hydrolysis in the cis ring changes the potentials within the system such that ATP binding to the opposite (trans) ring triggers the release of all ligands from the cis ring of GroEL through a complex network of allosteric communication between the rings. Inter-ring allosteric communication thus appears indispensable for the function of GroEL, and an engineered single-ring version (SR1) cannot substitute for GroEL in vivo. We describe here the isolation and characterisation of an active single-ring form of the GroEL protein (SR-A92T), which has an exceptionally low ATPase activity that is strongly stimulated by the addition of GroES. Dissection of the kinetic pathway of the ATP-induced structural changes in this active single ring can be explained by the fact that the mutation effectively blocks progression through the full allosteric pathway of the GroEL reaction cycle, thus trapping an early allosteric intermediate. Addition of GroES is able to overcome this block by binding this intermediate and pulling the allosteric pathway to completion via mass action, explaining how bacterial cells expressing this protein as their only chaperonin are viable.
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Affiliation(s)
- Eszter Kovács
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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22
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GroEL/GroES cycling: ATP binds to an open ring before substrate protein favoring protein binding and production of the native state. Proc Natl Acad Sci U S A 2009; 106:20264-9. [PMID: 19915138 DOI: 10.1073/pnas.0911556106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The GroEL/GroES reaction cycle involves steps of ATP and polypeptide binding to an open GroEL ring before the GroES encapsulation step that triggers productive folding in a sequestered chamber. The physiological order of addition of ATP and nonnative polypeptide, typically to the open trans ring of an asymmetrical GroEL/GroES/ADP complex, has been unknown, although there have been assumptions that polypeptide binds first, allowing subsequent ATP-mediated movement of the GroEL apical domains to exert an action of forceful unfolding on the nonnative polypeptide. Here, using fluorescence measurements, we show that the physiological order of addition is the opposite, involving rapid binding of ATP, accompanied by nearly as rapid apical domain movements, followed by slower binding of nonnative polypeptide. In order-of-addition experiments, approximately twice as much Rubisco activity was recovered when nonnative substrate protein was added after ATP compared with it being added before ATP, associated with twice as much Rubisco protein recovered with the chaperonin. Furthermore, the rate of Rubisco binding to an ATP-exposed ring was twice that observed in the absence of nucleotide. Finally, when both ATP and Rubisco were added simultaneously to a GroEL ring, simulating the physiological situation, the rate of Rubisco binding corresponded to that observed when ATP had been added first. We conclude that the physiological order, ATP binding before polypeptide, enables more efficient capture of nonnative substrate proteins, and thus allows greater recovery of the native state for any given round of the chaperonin cycle.
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23
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Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding. Q Rev Biophys 2009; 42:83-116. [PMID: 19638247 DOI: 10.1017/s0033583509004764] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The chaperonin ring assembly GroEL provides kinetic assistance to protein folding in the cell by binding non-native protein in the hydrophobic central cavity of an open ring and subsequently, upon binding ATP and the co-chaperonin GroES to the same ring, releasing polypeptide into a now hydrophilic encapsulated cavity where productive folding occurs in isolation. The fate of polypeptide during binding, encapsulation, and folding in the chamber has been the subject of recent experimental studies and is reviewed and considered here. We conclude that GroEL, in general, behaves passively with respect to its substrate proteins during these steps. While binding appears to be able to rescue non-native polypeptides from kinetic traps, such rescue is most likely exerted at the level of maximizing hydrophobic contact, effecting alteration of the topology of weakly structured states. Encapsulation does not appear to involve 'forced unfolding', and if anything, polypeptide topology is compacted during this step. Finally, chamber-mediated folding appears to resemble folding in solution, except that major kinetic complications of multimolecular association are prevented.
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24
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Koeck T, Corbett JA, Crabb JW, Stuehr DJ, Aulak KS. Glucose-modulated tyrosine nitration in beta cells: targets and consequences. Arch Biochem Biophys 2009; 484:221-31. [PMID: 19402213 PMCID: PMC2759311 DOI: 10.1016/j.abb.2009.01.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hyperglycemia, key factor of the pre-diabetic and diabetic pathology, is associated with cellular oxidative stress that promotes oxidative protein modifications. We report that protein nitration is responsive to changes in glucose concentrations in islets of Langerhans and insulinoma beta cells. Alterations in the extent of tyrosine nitration as well as the cellular nitroproteome profile correlated tightly with changing glucose concentrations. The target proteins we identified function in protein folding, energy metabolism, antioxidant capacity, and membrane permeability. Nitration of heat shock protein 60 in vitro was found to decrease its ATP hydrolysis and interaction with proinsulin, suggesting a mechanism by which protein nitration could diminish insulin secretion. This was supported by our finding of a decrease in stimulated insulin secretion following glycolytic stress in cultured cells. Our results reveal that protein tyrosine nitration may be a previously unrecognized factor in beta-cell dysfunction and the pathogenesis of diabetes.
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Affiliation(s)
- Thomas Koeck
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - John A. Corbett
- The Comprehensive Diabetes Center, Department of Medicine, University of Alabama in Birmingham. Shel 12 floor, 1530 3rd Ave. So., Birmingham, AL 35249-2182
| | - John W. Crabb
- Departments of Cell Biology and Ophthalmic Research, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Dennis J. Stuehr
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Kulwant S. Aulak
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
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25
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GroEL assisted folding of large polypeptide substrates in Escherichia coli: Present scenario and assignments for the future. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 99:42-50. [DOI: 10.1016/j.pbiomolbio.2008.10.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Requirement for binding multiple ATPs to convert a GroEL ring to the folding-active state. Proc Natl Acad Sci U S A 2008; 105:19205-10. [PMID: 19050077 DOI: 10.1073/pnas.0810657105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Production of the folding-active state of a GroEL ring involves initial cooperative binding of ATP, recruiting GroES, followed by large rigid body movements that are associated with ejection of bound substrate protein into the encapsulated hydrophilic chamber where folding commences. Here, we have addressed how many of the 7 subunits of a GroEL ring are required to bind ATP to drive these events, by using mixed rings with different numbers of wild-type and variant subunits, the latter bearing a substitution in the nucleotide pocket that allows specific block of ATP binding and turnover by a pyrazolol pyrimidine inhibitor. We observed that at least 2 wild-type subunits were required to bind GroES. By contrast, the triggering of polypeptide release and folding required a minimum of 4 wild-type subunits, with the greatest extent of refolding observed when all 7 subunits were wild type. This is consistent with the requirement for a "power stroke" of forceful apical movement to eject polypeptide into the chamber.
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27
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Madan D, Lin Z, Rye HS. Triggering protein folding within the GroEL-GroES complex. J Biol Chem 2008; 283:32003-13. [PMID: 18782766 DOI: 10.1074/jbc.m802898200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The folding of many proteins depends on the assistance of chaperonins like GroEL and GroES and involves the enclosure of substrate proteins inside an internal cavity that is formed when GroES binds to GroEL in the presence of ATP. Precisely how assembly of the GroEL-GroES complex leads to substrate protein encapsulation and folding remains poorly understood. Here we use a chemically modified mutant of GroEL (EL43Py) to uncouple substrate protein encapsulation from release and folding. Although EL43Py correctly initiates a substrate protein encapsulation reaction, this mutant stalls in an intermediate allosteric state of the GroEL ring, which is essential for both GroES binding and the forced unfolding of the substrate protein. This intermediate conformation of the GroEL ring possesses simultaneously high affinity for both GroES and non-native substrate protein, thus preventing escape of the substrate protein while GroES binding and substrate protein compaction takes place. Strikingly, assembly of the folding-active GroEL-GroES complex appears to involve a strategic delay in ATP hydrolysis that is coupled to disassembly of the old, ADP-bound GroEL-GroES complex on the opposite ring.
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Affiliation(s)
- Damian Madan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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28
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Suzuki M, Ueno T, Iizuka R, Miura T, Zako T, Akahori R, Miyake T, Shimamoto N, Aoki M, Tanii T, Ohdomari I, Funatsu T. Effect of the C-terminal truncation on the functional cycle of chaperonin GroEL: implication that the C-terminal region facilitates the transition from the folding-arrested to the folding-competent state. J Biol Chem 2008; 283:23931-9. [PMID: 18583344 PMCID: PMC3259756 DOI: 10.1074/jbc.m804090200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 06/25/2008] [Indexed: 11/06/2022] Open
Abstract
To elucidate the exact role of the C-terminal region of GroEL in its functional cycle, the C-terminal 20-amino acid truncated mutant of GroEL was constructed. The steady-state ATPase rate and duration of GroES binding showed that the functional cycle of the truncated GroEL is extended by approximately 2 s in comparison with that of the wild type, without interfering with the basic functions of GroEL. We have proposed a model for the functional cycle of GroEL, which consists of two rate-limiting steps of approximately 3- and approximately 5-s duration (Ueno, T., Taguchi, H., Tadakuma, H., Yoshida, M., and Funatsu, T. (2004) Mol. Cell 14, 423-434 g). According to the model, detailed kinetic studies were performed. We found that a 20-residue truncation of the C terminus extends the time until inorganic phosphate is generated and the time for arresting protein folding in the central cavity, i.e. the lifetime of the first rate-limiting step in the functional cycle, to an approximately 5-s duration. These results suggest that the integrity of the C-terminal region facilitates the transition from the first to the second rate-limiting state.
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Affiliation(s)
- Mihoko Suzuki
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taro Ueno
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryo Iizuka
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takahiro Miura
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tamotsu Zako
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rena Akahori
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Miyake
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naonobu Shimamoto
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mutsuko Aoki
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Tanii
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Iwao Ohdomari
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Funatsu
- Graduate School of
Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, the Faculty of
Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo
169-8555, the Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the
Nanotechnology Research Center, Waseda
University, 513 Tsurumaki-chou, Shinjuku-ku, Tokyo 162-0041, and the
Center for NanoBio Integration, The
University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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29
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Clare DK, Stagg S, Quispe J, Farr GW, Horwich AL, Saibil HR. Multiple states of a nucleotide-bound group 2 chaperonin. Structure 2008; 16:528-34. [PMID: 18400175 PMCID: PMC2719814 DOI: 10.1016/j.str.2008.01.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 01/09/2008] [Accepted: 01/09/2008] [Indexed: 11/18/2022]
Abstract
Chaperonin action is controlled by cycles of nucleotide binding and hydrolysis. Here, we examine the effects of nucleotide binding on an archaeal group 2 chaperonin. In contrast to the ordered apo state of the group 1 chaperonin GroEL, the unliganded form of the homo-16-mer Methanococcus maripaludis group 2 chaperonin is very open and flexible, with intersubunit contacts only in the central double belt of equatorial domains. The intermediate and apical domains are free of contacts and deviate significantly from the overall 8-fold symmetry. Nucleotide binding results in three distinct, ordered 8-fold symmetric conformations--open, partially closed, and fully closed. The partially closed ring encloses a 40% larger volume than does the GroEL-GroES folding chamber, enabling it to encapsulate proteins up to 80 kDa, in contrast to the fully closed form, whose cavities are 20% smaller than those of the GroEL-GroES chamber.
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Affiliation(s)
- Daniel K. Clare
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Scott Stagg
- The National Resource for Automated Molecular Microscopy, Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joel Quispe
- The National Resource for Automated Molecular Microscopy, Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - George W. Farr
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510
| | - Arthur L. Horwich
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Helen R. Saibil
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
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30
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Bigotti MG, Clarke AR. Chaperonins: The hunt for the Group II mechanism. Arch Biochem Biophys 2008; 474:331-9. [PMID: 18395510 DOI: 10.1016/j.abb.2008.03.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/17/2008] [Accepted: 03/18/2008] [Indexed: 11/27/2022]
Abstract
Chaperonins are multi-subunit complexes that enhance the efficiency of protein-folding reactions by capturing protein substrates in their central cavities. They occur in all prokaryotic and eukaryotic cell types and, alone amongst molecular chaperones, chaperonin knockouts are always lethal. Chaperonins come in two forms; the Group I are found in bacteria, mitochondria and plastids [W.A. Fenton, A.L. Horwich, Q. Rev. Biophys. 36 (2003) 229-256, [1]] and the Group II in the eukaryotic cytoplasm and in archaea [N.J. Cowan, S.A. Lewis, Adv. Protein Chem. 59 (2001) 73-104, [2]]. Both use energy derived from ATP binding and hydrolysis to drive a series of structural rearrangements that enable them to capture, engulf and then release polypeptide chains that have either not yet acquired the native, biologically active state or have been denatured in the cell.
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Affiliation(s)
- Maria Giulia Bigotti
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol B58 1TD, UK.
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31
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Abstract
How do chaperones operate in cells? For some major chaperones it is clear what they do, though mostly not how they do it. Hsp60, 70 and 100 families carry out folding, unfolding or disaggregation of proteins. Regarding mechanisms of action, we have the clearest picture of the ATP-driven mechanism of the bacterial Hsp60s, and structures of full-length Hsp70 and 90 family members are beginning to give insights into their allosteric mechanisms. Recent advances are giving an improved understanding of the nature of chaperone interactions with their non-native substrate proteins. There have also been significant advances in understanding the engagement of chaperones in preventing the formation of toxic aggregates in degenerative disease and the relationship of protein quality control to complex biological processes such as ageing.
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32
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Abstract
Chaperonins are large ring assemblies that assist protein folding to the native state by binding nonnative proteins in their central cavities and then, upon binding ATP, release the substrate protein into a now-encapsulated cavity to fold productively. Two families of such components have been identified: type I in mitochondria, chloroplasts, and the bacterial cytosol, which rely on a detachable "lid" structure for encapsulation, and type II in archaea and the eukaryotic cytosol, which contain a built-in protrusion structure. We discuss here a number of issues under current study. What is the range of substrates acted on by the two classes of chaperonin, in particular by GroEL in the bacterial cytoplasm and CCT in the eukaryotic cytosol, and are all these substrates subject to encapsulation? What are the determinants for substrate binding by the type II chaperonins? And is the encapsulated chaperonin cavity a passive container that prevents aggregation, or could it be playing an active role in polypeptide folding?
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Affiliation(s)
- Arthur L Horwich
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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33
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Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR. Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell 2007; 26:415-26. [PMID: 17499047 PMCID: PMC1885994 DOI: 10.1016/j.molcel.2007.04.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 03/19/2007] [Accepted: 04/04/2007] [Indexed: 12/22/2022]
Abstract
The chaperonin GroEL assists polypeptide folding through sequential steps of binding nonnative protein in the central cavity of an open ring, via hydrophobic surfaces of its apical domains, followed by encapsulation in a hydrophilic cavity. To examine the binding state, we have classified a large data set of GroEL binary complexes with nonnative malate dehydrogenase (MDH), imaged by cryo-electron microscopy, to sort them into homogeneous subsets. The resulting electron density maps show MDH associated in several characteristic binding topologies either deep inside the cavity or at its inlet, contacting three to four consecutive GroEL apical domains. Consistent with visualization of bound polypeptide distributed over many parts of the central cavity, disulfide crosslinking could be carried out between a cysteine in a bound substrate protein and cysteines substituted anywhere inside GroEL. Finally, substrate binding induced adjustments in GroEL itself, observed mainly as clustering together of apical domains around sites of substrate binding.
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Affiliation(s)
- Nadav Elad
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - George W. Farr
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Daniel K. Clare
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Elena V. Orlova
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Arthur L. Horwich
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Helen R. Saibil
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
- Corresponding author
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34
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Reissmann S, Parnot C, Booth CR, Chiu W, Frydman J. Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nat Struct Mol Biol 2007; 14:432-40. [PMID: 17460696 PMCID: PMC3339572 DOI: 10.1038/nsmb1236] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 03/20/2007] [Indexed: 11/09/2022]
Abstract
Chaperonins are allosteric double-ring ATPases that mediate cellular protein folding. ATP binding and hydrolysis control opening and closing of the central chaperonin chamber, which transiently provides a protected environment for protein folding. During evolution, two strategies to close the chaperonin chamber have emerged. Archaeal and eukaryotic group II chaperonins contain a built-in lid, whereas bacterial chaperonins use a ring-shaped cofactor as a detachable lid. Here we show that the built-in lid is an allosteric regulator of group II chaperonins, which helps synchronize the subunits within one ring and, to our surprise, also influences inter-ring communication. The lid is dispensable for substrate binding and ATP hydrolysis, but is required for productive substrate folding. These regulatory functions of the lid may serve to allow the symmetrical chaperonins to function as 'two-stroke' motors and may also provide a timer for substrate encapsulation within the closed chamber.
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Affiliation(s)
- Stefanie Reissmann
- Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305, USA
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35
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Bigotti MG, Bellamy SRW, Clarke AR. The asymmetric ATPase cycle of the thermosome: elucidation of the binding, hydrolysis and product-release steps. J Mol Biol 2006; 362:835-43. [PMID: 16942780 DOI: 10.1016/j.jmb.2006.07.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 07/26/2006] [Accepted: 07/26/2006] [Indexed: 11/15/2022]
Abstract
Using a combination of intrinsic fluorescence to report ATP-induced rearrangements, quenched-flow to measure ATP hydrolysis "on-enzyme" and optical methods to probe the kinetics of product release, we have begun to dissect the process of energy transduction in the thermosome, a type II chaperonin from Thermoplasma acidophilum. Stoichiometric measurements of ATP binding reveal the tight association of eight nucleotide molecules per hexa-decamer, implying the filling of only one ring owing to strong negative cooperativity. After binding, we show that these eight ATP molecules are hydrolysed over the next 50 s, after which hydrolysis slows down markedly during the establishment of the steady state in the ATPase reaction, demonstrating that the kinetic system is off-rate limited. Looking in more detail, this rapid first-turnover can be dissected into two phases; the first occurring with a half-time of 0.8 s, the second with a half-time of 14 s, possibly reflecting the differential behaviour of the four alpha and four beta subunits in a single thermosome ring. To investigate the post-hydrolytic events, we used two heat-stable enzyme-linked optical assays to measure the rate of evolution of ADP and of phosphate from the thermosome active site. Neither product showed a rapid dissociation phase prior to the establishment of the steady state, showing that both are released slowly at a rate that limits the cycle. These data highlight the importance of the highly populated thermosome/ADP/Pi complex in the molecular mechanism.
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Affiliation(s)
- Maria Giulia Bigotti
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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