1
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Potapov S, Krasnopeev A, Tikhonova I, Podlesnaya G, Gorshkova A, Belykh O. The Viral Fraction Metatranscriptomes of Lake Baikal. Microorganisms 2022; 10:1937. [PMID: 36296212 PMCID: PMC9611531 DOI: 10.3390/microorganisms10101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to Pithovirus sibericum, a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya, 664033 Irkutsk, Russia
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2
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Walker TE, Shirzadeh M, Sun HM, McCabe JW, Roth A, Moghadamchargari Z, Clemmer DE, Laganowsky A, Rye H, Russell DH. Temperature Regulates Stability, Ligand Binding (Mg 2+ and ATP), and Stoichiometry of GroEL-GroES Complexes. J Am Chem Soc 2022; 144:2667-2678. [PMID: 35107280 PMCID: PMC8939001 DOI: 10.1021/jacs.1c11341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, a chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL-GroES complexes. The results show clear evidence for destabilization of both GroEL14 and GroES7 at temperatures of 50 and 45 °C, respectively, substantially below the previously reported melting temperature (Tm ∼ 70 °C). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL14-GroESy-ATPn, where y = 1, 2, 8 and n = 0, 1, 2, 8, that are also dependent on Mg2+ and ATP concentrations. Variable-temperature native mass spectrometry reveals new insights about the stability of GroEL in response to temperature effects: (i) temperature-dependent ATP binding to GroEL; (ii) effects of temperature as well as Mg2+ and ATP concentrations on the stoichiometry of the GroEL-GroES complex, with Mg2+ showing greater effects compared to ATP; and (iii) a change in the temperature-dependent stoichiometries of the GroEL-GroES complex (GroEL14-GroES7 vs GroEL14-GroES8) between 24 and 40 °C. The similarities between results obtained by using native MS and cryo-EM [Clare et al. An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-911; Ranson et al. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.Nat. Struct. Mol. Biol. 2006, 13, 147-152] underscore the utility of native MS for investigations of molecular machines as well as identification of key intermediates involved in the chaperonin-assisted protein folding cycle.
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Affiliation(s)
- Thomas E. Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- 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
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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3
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Yang D, Klebl DP, Zeng S, Sobott F, Prévost M, Soumillion P, Vandenbussche G, Fontaine V. Interplays between copper and Mycobacterium tuberculosis GroEL1. Metallomics 2020; 12:1267-1277. [DOI: 10.1039/d0mt00101e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The chaperone GroEL1 enhances copper tolerance during Mycobacterium bovis BCG biofilm formation. The binding of copper ions to the GroEL1 histidine-rich region protects the chaperone from destabilization and increases its ATPase activity.
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Affiliation(s)
- Dong Yang
- Microbiology, Bioorganic and Macromolecular Chemistry Unit
- Faculty of Pharmacy
- Université Libre de Bruxelles (ULB)
- Brussels
- Belgium
| | - David P. Klebl
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
- School of Biomedical Sciences
| | - Sheng Zeng
- Microbiology, Bioorganic and Macromolecular Chemistry Unit
- Faculty of Pharmacy
- Université Libre de Bruxelles (ULB)
- Brussels
- Belgium
| | - Frank Sobott
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
- School of Molecular and Cellular Biology
| | - Martine Prévost
- Laboratory for the Structure and Function of Biological Membranes
- Faculty of Sciences
- Université Libre de Bruxelles (ULB)
- Brussels
- Belgium
| | - Patrice Soumillion
- Biochemistry and Genetics of Microorganisms
- Louvain Institute of Biomolecular Science and Technology
- Université Catholique de Louvain (UCL)
- Louvain-la-Neuve
- Belgium
| | - Guy Vandenbussche
- Laboratory for the Structure and Function of Biological Membranes
- Faculty of Sciences
- Université Libre de Bruxelles (ULB)
- Brussels
- Belgium
| | - Véronique Fontaine
- Microbiology, Bioorganic and Macromolecular Chemistry Unit
- Faculty of Pharmacy
- Université Libre de Bruxelles (ULB)
- Brussels
- Belgium
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4
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Zhao Q, Zhang X, Sommer F, Ta N, Wang N, Schroda M, Cong Y, Liu C. Hetero-oligomeric CPN60 resembles highly symmetric group-I chaperonin structure revealed by Cryo-EM. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:798-812. [PMID: 30735603 DOI: 10.1111/tpj.14273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/07/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as a model system, we found that in vivo the chloroplast chaperonin consists of CPN60α, CPN60β1 and CPN60β2 and the co-chaperonin of the three subunits CPN20, CPN11 and CPN23. In Escherichia coli, CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only that consisting of CPN11/20/23-CPN60αβ1β2 can fully replace GroES/GroEL under stringent stress conditions. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60α:CPN60β1:CPN60β2. The cryo-EM structures of endogenous CPN60αβ1β2/ADP and CPN60αβ1β2/co-chaperonin/ADP were solved at resolutions of 4.06 and 3.82 Å, respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. Through hetero-oligomerization, the chloroplast co-chaperonin CPN11/20/23 forms seven GroES-like domains, which symmetrically interact with CPN60αβ1β2. Our structure also reveals an uneven distribution of roof-forming domains in the dome-shaped CPN11/20/23 co-chaperonin and potentially diversified surface properties in the folding cavity of the CPN60αβ1β2 chaperonin that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.
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Affiliation(s)
- Qian Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Frederik Sommer
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Na Ta
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Erwin-Schroedinger Str. 70, 67663, Kaiserslautern, Germany
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
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5
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Dyachenko A, Tamara S, Heck AJR. Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:7-15. [PMID: 29736602 PMCID: PMC6318259 DOI: 10.1007/s13361-018-1910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.
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Affiliation(s)
- Andrey Dyachenko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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6
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Tekpinar M. Flexible fitting to cryo-electron microscopy maps with coarse-grained elastic network models. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1431835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Tamara S, Dyachenko A, Fort KL, Makarov AA, Scheltema RA, Heck AJR. Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies. J Am Chem Soc 2016; 138:10860-8. [PMID: 27480281 PMCID: PMC6392339 DOI: 10.1021/jacs.6b05147] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 01/08/2023]
Abstract
Tandem mass spectrometry can provide structural information on intact protein assemblies, generating mass fingerprints indicative of the stoichiometry and quaternary arrangement of the subunits. However, in such experiments, collision-induced dissociation yields restricted information due to simultaneous subunit unfolding, charge rearrangement, and subsequent ejection of a highly charged unfolded single subunit. Alternative fragmentation strategies can potentially overcome this and supply a deeper level of structural detail. Here, we implemented ultraviolet photodissociation (UVPD) on an Orbitrap mass spectrometer optimized for native MS and benchmark its performance to HCD fragmentation using various protein oligomers. We investigated dimeric β-lactoglobulin, dimeric superoxide dismutase, dimeric and tetrameric concanavalin A, and heptameric GroES and Gp31; ranging in molecular weight from 32 to 102 kDa. We find that, for the investigated systems, UVPD produces more symmetric charge partitioning than HCD. While HCD spectra show sporadic fragmentation over the full protein backbone sequence of the subunits with a bias toward fragmenting labile bonds, UVPD spectra provided higher sequence coverage. Taken together, we conclude that UVPD is a strong addition to the toolbox of fragmentation methods for top-down proteomics experiments, especially for native protein assemblies.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Andrey Dyachenko
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Kyle L. Fort
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexander A. Makarov
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
- Thermo
Fisher Scientific (Bremen), 28199 Bremen, Germany
| | - Richard A. Scheltema
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
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8
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Clare DK, Saibil HR. ATP-driven molecular chaperone machines. Biopolymers 2016; 99:846-59. [PMID: 23877967 PMCID: PMC3814418 DOI: 10.1002/bip.22361] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.
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Affiliation(s)
- Daniel K Clare
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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9
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Molugu SK, Hildenbrand ZL, Morgan DG, Sherman MB, He L, Georgopoulos C, Sernova NV, Kurochkina LP, Mesyanzhinov VV, Miroshnikov KA, Bernal RA. Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin. Structure 2016; 24:537-546. [PMID: 26996960 DOI: 10.1016/j.str.2016.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 01/05/2023]
Abstract
Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly large viral proteins via profoundly different nucleotide-binding conformations. Our structural investigations indicate that ATP likely binds to both rings simultaneously and that a misfolded substrate acts as the trigger for ATP hydrolysis. More importantly, the φEL complex dissociates into two single rings resulting from an evolutionarily altered residue in the highly conserved ATP-binding pocket. Conformational changes also more than double the volume of the single-ring internal chamber such that larger viral proteins are accommodated. This is illustrated by the fact that φEL is capable of folding β-galactosidase, a 116-kDa protein. Collectively, the architecture and protein-folding mechanism of the φEL chaperonin are significantly different from those observed in group I and II chaperonins.
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Affiliation(s)
- Sudheer K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | | | - David Gene Morgan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Lilin He
- Neutron Scattering Science Division, Oak Ridge National Laboratory, C23, Building 7964K, Oak Ridge, TN 37831-6430, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah, 4100 EEJMRB, Salt Lake City, UT 84112-5650, USA
| | - Natalia V Sernova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Pereulok, 19, Moscow 127994, Russia
| | - Lidia P Kurochkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vadim V Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ricardo A Bernal
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA.
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10
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Saibil H. Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 2013; 14:630-42. [PMID: 24026055 DOI: 10.1038/nrm3658] [Citation(s) in RCA: 703] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular chaperones are diverse families of multidomain proteins that have evolved to assist nascent proteins to reach their native fold, protect subunits from heat shock during the assembly of complexes, prevent protein aggregation or mediate targeted unfolding and disassembly. Their increased expression in response to stress is a key factor in the health of the cell and longevity of an organism. Unlike enzymes with their precise and finely tuned active sites, chaperones are heavy-duty molecular machines that operate on a wide range of substrates. The structural basis of their mechanism of action is being unravelled (in particular for the heat shock proteins HSP60, HSP70, HSP90 and HSP100) and typically involves massive displacements of 20-30 kDa domains over distances of 20-50 Å and rotations of up to 100°.
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Affiliation(s)
- Helen Saibil
- Department of Crystallography, Institute for Structural and Molecular Biology, Birkbeck College London, UK
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11
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Tsai YCC, Mueller-Cajar O, Saschenbrecker S, Hartl FU, Hayer-Hartl M. Chaperonin cofactors, Cpn10 and Cpn20, of green algae and plants function as hetero-oligomeric ring complexes. J Biol Chem 2012; 287:20471-81. [PMID: 22518837 DOI: 10.1074/jbc.m112.365411] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The chloroplast chaperonin system of plants and green algae is a curiosity as both the chaperonin cage and its lid are encoded by multiple genes, in contrast to the single genes encoding the two components of the bacterial and mitochondrial systems. In the green alga Chlamydomonas reinhardtii (Cr), three genes encode chaperonin cofactors, with cpn10 encoding a single ∼10-kDa domain and cpn20 and cpn23 encoding tandem cpn10 domains. Here, we characterized the functional interaction of these proteins with the Escherichia coli chaperonin, GroEL, which normally cooperates with GroES, a heptamer of ∼10-kDa subunits. The C. reinhardtii cofactor proteins alone were all unable to assist GroEL-mediated refolding of bacterial ribulose-bisphosphate carboxylase/oxygenase but gained this ability when CrCpn20 and/or CrCpn23 was combined with CrCpn10. Native mass spectrometry indicated the formation of hetero-oligomeric species, consisting of seven ∼10-kDa domains. The cofactor "heptamers" interacted with GroEL and encapsulated substrate protein in a nucleotide-dependent manner. Different hetero-oligomer arrangements, generated by constructing cofactor concatamers, indicated a preferential heptamer configuration for the functional CrCpn10-CrCpn23 complex. Formation of heptamer Cpn10/Cpn20 hetero-oligomers was also observed with the Arabidopsis thaliana (At) cofactors, which functioned with the chloroplast chaperonin, AtCpn60α(7)β(7). It appears that hetero-oligomer formation occurs more generally for chloroplast chaperonin cofactors, perhaps adapting the chaperonin system for the folding of specific client proteins.
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Affiliation(s)
- Yi-Chin C Tsai
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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12
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Abstract
The bacteriophage T4 head is an elongated icosahedron packed with 172 kb of linear double-stranded DNA and numerous proteins. The capsid is built from three essential proteins: gp23*, which forms the hexagonal capsid lattice; gp24*, which forms pentamers at 11 of the 12 vertices; and gp20, which forms the unique dodecameric portal vertex through which DNA enters during packaging and exits during infection. Intensive work over more than half a century has led to a deep understanding of the phage T4 head. The atomic structure of gp24 has been determined. A structural model built for gp23 using its similarity to gp24 showed that the phage T4 major capsid protein has the same fold as numerous other icosahedral bacteriophages. However, phage T4 displays an unusual membrane and portal initiated assembly of a shape determining self-sufficient scaffolding core. Folding of gp23 requires the assistance of two chaperones, the Escherichia coli chaperone GroEL acting with the phage-coded gp23-specific cochaperone, gp31. The capsid also contains two nonessential outer capsid proteins, Hoc and Soc, which decorate the capsid surface. Through binding to adjacent gp23 subunits, Soc reinforces the capsid structure. Hoc and Soc have been used extensively in bipartite peptide display libraries and to display pathogen antigens, including those from human immunodeficiency virus (HIV), Neisseria meningitides, Bacillus anthracis, and foot and mouth disease virus. The structure of Ip1*, one of a number of multiple (>100) copy proteins packed and injected with DNA from the full head, shows it to be an inhibitor of one specific restriction endonuclease specifically targeting glycosylated hydroxymethyl cytosine DNA. Extensive mutagenesis, combined with atomic structures of the DNA packaging/terminase proteins gp16 and gp17, elucidated the ATPase and nuclease functional motifs involved in DNA translocation and headful DNA cutting. The cryoelectron microscopy structure of the T4 packaging machine showed a pentameric motor assembled with gp17 subunits on the portal vertex. Single molecule optical tweezers and fluorescence studies showed that the T4 motor packages DNA at the highest rate known and can package multiple segments. Förster resonance energy transfer-fluorescence correlation spectroscopy studies indicate that DNA gets compressed in the stalled motor and that the terminase-to-portal distance changes during translocation. Current evidence suggests a linear two-component (large terminase plus portal) translocation motor in which electrostatic forces generated by ATP hydrolysis drive DNA translocation by alternating the motor between tensed and relaxed states.
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Affiliation(s)
- Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, Maryland, USA
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13
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Shahar A, Melamed-Frank M, Kashi Y, Shimon L, Adir N. The dimeric structure of the Cpn60.2 chaperonin of Mycobacterium tuberculosis at 2.8 Å reveals possible modes of function. J Mol Biol 2011; 412:192-203. [PMID: 21802426 DOI: 10.1016/j.jmb.2011.07.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/13/2011] [Accepted: 07/14/2011] [Indexed: 11/25/2022]
Abstract
Mycobacterium tuberculosis expresses two proteins (Cpn60.1 and Cpn60.2) that belong to the chaperonin (Cpn) family of heat shock proteins. Studies have shown that the two proteins have different functional roles in the bacterial life cycle and that Cpn60.2 is essential for cell viability and may be involved in M. tuberculosis pathogenicity. Cpn60.2 does not form a tetradecameric double ring, which is typical of other Cpns. We have determined the crystal structure of recombinant Cpn60.2 to 2.8 Å resolution by molecular replacement; the asymmetric unit (AU) contains a dimer, which is consistent with size-exclusion high-performance liquid chromatography and dynamic light-scattering measurements of the soluble recombinant protein. However, we suggest that the actual Cpn60.2 dimer may be different from that identified within the AU on the basis of surface contact stability, solvation free-energy gain, and functional aspects. Unlike the dimer found in the AU, which is formed through apical domain interactions, the dimeric form we propose here provides a free apical domain that is required for normal chaperone activity and may be involved in M. tuberculosis association with macrophages and arthrosclerosis plaque formation. Here we describe in detail the structural aspects that lead to Cpn60.2 dimer formation and prevent the formation of heptameric rings and tetradecameric double rings.
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Affiliation(s)
- Anat Shahar
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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14
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Rao VB, Black LW. Structure and assembly of bacteriophage T4 head. Virol J 2010; 7:356. [PMID: 21129201 PMCID: PMC3012670 DOI: 10.1186/1743-422x-7-356] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 12/03/2010] [Indexed: 12/20/2022] Open
Abstract
The bacteriophage T4 capsid is an elongated icosahedron, 120 nm long and 86 nm wide, and is built with three essential proteins; gp23*, which forms the hexagonal capsid lattice, gp24*, which forms pentamers at eleven of the twelve vertices, and gp20, which forms the unique dodecameric portal vertex through which DNA enters during packaging and exits during infection. The past twenty years of research has greatly elevated the understanding of phage T4 head assembly and DNA packaging. The atomic structure of gp24 has been determined. A structural model built for gp23 using its similarity to gp24 showed that the phage T4 major capsid protein has the same fold as that found in phage HK97 and several other icosahedral bacteriophages. Folding of gp23 requires the assistance of two chaperones, the E. coli chaperone GroEL and the phage coded gp23-specific chaperone, gp31. The capsid also contains two non-essential outer capsid proteins, Hoc and Soc, which decorate the capsid surface. The structure of Soc shows two capsid binding sites which, through binding to adjacent gp23 subunits, reinforce the capsid structure. Hoc and Soc have been extensively used in bipartite peptide display libraries and to display pathogen antigens including those from HIV, Neisseria meningitides, Bacillus anthracis, and FMDV. The structure of Ip1*, one of the components of the core, has been determined, which provided insights on how IPs protect T4 genome against the E. coli nucleases that degrade hydroxymethylated and glycosylated T4 DNA. Extensive mutagenesis combined with the atomic structures of the DNA packaging/terminase proteins gp16 and gp17 elucidated the ATPase and nuclease functional motifs involved in DNA translocation and headful DNA cutting. Cryo-EM structure of the T4 packaging machine showed a pentameric motor assembled with gp17 subunits on the portal vertex. Single molecule optical tweezers and fluorescence studies showed that the T4 motor packages DNA at a rate of up to 2000 bp/sec, the fastest reported to date of any packaging motor. FRET-FCS studies indicate that the DNA gets compressed during the translocation process. The current evidence suggests a mechanism in which electrostatic forces generated by ATP hydrolysis drive the DNA translocation by alternating the motor between tensed and relaxed states.
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Affiliation(s)
- Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA.
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15
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Dauter Z, Jaskolski M. How to read (and understand) Volume A ofInternational Tables for Crystallography: an introduction for nonspecialists. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810026956] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Calmat S, Hendriks J, van Heerikhuizen H, Schmidt CF, van der Vies SM, Peterman EJG. Dissociation kinetics of the GroEL-gp31 chaperonin complex studied with Förster resonance energy transfer. Biochemistry 2010; 48:11692-8. [PMID: 19899806 DOI: 10.1021/bi9013962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Propagation of bacteriophage T4 in its host Escherichia coli involves the folding of the major capsid protein gp23, which is facilitated by a hybrid chaperone complex consisting of the bacterial chaperonin GroEL and the phage-encoded co-chaperonin, gp31. It has been well established that the GroEL-gp31 complex is capable of folding gp23 whereas the homologous GroEL-GroES complex cannot perform this function. To assess whether this is a consequence of differences in the interactions of the proteins within the chaperonin complex, we have investigated the dissociation kinetics of GroEL-gp31 and GroEL-GroES complexes using Forster resonance energy transfer. Here we report that the dissociation of gp31 from GroEL is slightly faster than that of GroES from GroEL and is further accelerated by the binding of gp23. In contrast to what had been observed previously, we found that gp23 is able to interact with the GroEL-GroES complex, which might explain how bacteriophage T4 redirects the folding machinery of Escherichia coli during morphogenesis.
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Affiliation(s)
- Stéphane Calmat
- Department of Physics and Astronomy and Laser Centre, VU University, Amsterdam, The Netherlands
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17
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Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol 2009; 5:e1000360. [PMID: 19381265 PMCID: PMC2664929 DOI: 10.1371/journal.pcbi.1000360] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 03/13/2009] [Indexed: 11/19/2022] Open
Abstract
Identification of pathways involved in the structural transitions of biomolecular
systems is often complicated by the transient nature of the conformations
visited across energy barriers and the multiplicity of paths accessible in the
multidimensional energy landscape. This task becomes even more challenging in
exploring molecular systems on the order of megadaltons. Coarse-grained models
that lend themselves to analytical solutions appear to be the only possible
means of approaching such cases. Motivated by the utility of elastic network
models for describing the collective dynamics of biomolecular systems and by the
growing theoretical and experimental evidence in support of the intrinsic
accessibility of functional substates, we introduce a new method,
adaptive anisotropic network model (aANM),
for exploring functional transitions. Application to bacterial chaperonin GroEL
and comparisons with experimental data, results from action minimization
algorithm, and previous simulations support the utility of aANM
as a computationally efficient, yet physically plausible, tool for unraveling
potential transition pathways sampled by large complexes/assemblies. An
important outcome is the assessment of the critical inter-residue interactions
formed/broken near the transition state(s), most of which involve conserved
residues. Most proteins are biomolecular machines. They perform their function by
undergoing changes between different structures. Understanding the mechanism of
transition between these structures is of major importance to design methods for
controlling such transitions, and thereby modulating protein function. Although
there are many computational methods for exploring the transitions of small
proteins, the task of exploring the transition pathways becomes prohibitively
expensive in the case of supramolecular systems. The bacterial chaperonin GroEL
is such a supramolecular machine. It plays an important role in assisting
protein folding. During its function, GroEL undergoes structural transitions
between multiple forms. Here, we are introducing a new methodology, based on
elastic network models, for elucidating the transition mechanisms in such
supramolecular systems. Application to GroEL provides us with biologically
significant information on critical interactions and sequence of events
occurring during the chaperonin machinery and key contacts that make and break
at the transition. The method can be readily applied to other supramolecular
machines.
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18
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Clare DK, Bakkes PJ, van Heerikhuizen H, van der Vies SM, Saibil HR. Chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature 2009; 457:107-10. [PMID: 19122642 PMCID: PMC2728927 DOI: 10.1038/nature07479] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/12/2008] [Indexed: 11/08/2022]
Abstract
A subset of essential cellular proteins requires the assistance of chaperonins (in Escherichia coli, GroEL and GroES), double-ring complexes in which the two rings act alternately to bind, encapsulate and fold a wide range of nascent or stress-denatured proteins. This process starts by the trapping of a substrate protein on hydrophobic surfaces in the central cavity of a GroEL ring. Then, binding of ATP and co-chaperonin GroES to that ring ejects the non-native protein from its binding sites, through forced unfolding or other major conformational changes, and encloses it in a hydrophilic chamber for folding. ATP hydrolysis and subsequent ATP binding to the opposite ring trigger dissociation of the chamber and release of the substrate protein. The bacteriophage T4 requires its own version of GroES, gp31, which forms a taller folding chamber, to fold the major viral capsid protein gp23 (refs 16-20). Polypeptides are known to fold inside the chaperonin complex, but the conformation of an encapsulated protein has not previously been visualized. Here we present structures of gp23-chaperonin complexes, showing both the initial captured state and the final, close-to-native state with gp23 encapsulated in the folding chamber. Although the chamber is expanded, it is still barely large enough to contain the elongated gp23 monomer, explaining why the GroEL-GroES complex is not able to fold gp23 and showing how the chaperonin structure distorts to enclose a large, physiological substrate protein.
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Affiliation(s)
- D K Clare
- Department of Crystallography and Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK
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19
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Geels RBJ, Calmat S, Heck AJR, van der Vies SM, Heeren RMA. Thermal activation of the co-chaperonins GroES and gp31 probed by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3633-3641. [PMID: 18972453 DOI: 10.1002/rcm.3782] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many biological active proteins are assembled in protein complexes. Understanding the (dis)assembly of such complexes is therefore of major interest. Here we use mass spectrometry to monitor the disassembly induced by thermal activation of the heptameric co-chaperonins GroES and gp31. We use native electrospray ionization mass spectrometry (ESI-MS) on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer to monitor the stoichiometry of the chaperonins. A thermally controlled electrospray setup was employed to analyze conformational and stoichiometric changes of the chaperonins at varying temperature. The native ESI-MS data agreed well with data obtained from fluorescence spectroscopy as the measured thermal dissociation temperatures of the complexes were in good agreement. Furthermore, we observed that thermal denaturing of GroES and gp31 proceeds via intermediate steps of all oligomeric forms, with no evidence of a transiently stable unfolded heptamer. We also evaluated the thermal dissociation of the chaperonins in the gas phase using infrared multiphoton dissociation (IRMPD) for thermal activation. Using gas-phase activation the smaller (2-4) oligomers were not detected, only down to the pentamer, whereafter the complex seemed to dissociate completely. These results demonstrate clearly that conformational changes of GroES and gp31 due to heating in solution and in the gas phase are significantly different.
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Affiliation(s)
- Rimco B J Geels
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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20
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Sorzano C, Velázquez-Muriel J, Marabini R, Herman G, Carazo J. Volumetric restrictions in single particle 3DEM reconstruction. PATTERN RECOGNITION 2008; 41:616. [PMID: 20119498 PMCID: PMC2812911 DOI: 10.1016/j.patcog.2007.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
3D electron microsscopy aims at the reconstruction of density volumes corresponding to the electrostatic potential distribution of macro-molecules. There are many factors limiting the resolution achievable when this technique is applied to biological macromolecules: microscope imperfections, molecule flexibility, lack of projections from certain directions, unknown angular distribution, noise, etc. In this communication we explore the quality gain in the reconstruction by including a priori knowledge such as particle symmetry, occupied volume, known surface relief, density nonnegativity and similarity to a known volume in order to improve the quality of the reconstruction. If the reconstruction is represented as a series expansion, such constraints can be expressed by set of equations that the expansion coefficients must satisfy. In this work, these equation sets are specified and combined in a novel way with the ART + blobs reconstruction algorithm. The effect of each one on the reconstruction of a realistic phantom is explored. Finally, the application of these restrictions to 3D reconstructions from experimental data are studied.
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Affiliation(s)
- C.O.S. Sorzano
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain
- Dept. Ingeniería de Sistemas Electrónicos y de Telecomunicación, Escuela Politécnica Superior, Univ. San Pablo—CEU, Campus Urb. Montepríncipe s/n, 28668 Boadilla del Monte, Madrid, Spain
| | - J.A. Velázquez-Muriel
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain
| | - R. Marabini
- Dept. Informática, Escuela Politécnica Superior, c/Francisco Tomás y Valiente, 11, Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - G.T. Herman
- Department of Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - J.M. Carazo
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain
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21
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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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