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Rivera-Ramírez A, Salgado-Morales R, Onofre-Lemus J, García-Gómez BI, Lanz-Mendoza H, Dantán-González E. Evaluation and Characterization of the Insecticidal Activity and Synergistic Effects of Different GroEL Proteins from Bacteria Associated with Entomopathogenic Nematodes on Galleria mellonella. Toxins (Basel) 2023; 15:623. [PMID: 37999486 PMCID: PMC10674725 DOI: 10.3390/toxins15110623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023] Open
Abstract
GroEL is a chaperonin that helps other proteins fold correctly. However, alternative activities, such as acting as an insect toxin, have also been discovered. This work evaluates the chaperonin and insecticidal activity of different GroEL proteins from entomopathogenic nematodes on G. mellonella. The ability to synergize with the ExoA toxin of Pseudomonas aeruginosa was also investigated. The GroELXn protein showed the highest insecticidal activity among the different GroELs. In addition, it was able to significantly activate the phenoloxidase system of the target insects. This could tell us about the mechanism by which it exerts its toxicity on insects. GroEL proteins can enhance the toxic activity of the ExoA toxin, which could be related to its chaperonin activity. However, there is a significant difference in the synergistic effect that is more related to its alternative activity as an insecticidal toxin.
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Affiliation(s)
- Abraham Rivera-Ramírez
- Center for Population Health Research, National Institute of Public Health, Cuernavaca 62100, Mexico;
| | - Rosalba Salgado-Morales
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
| | - Janette Onofre-Lemus
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
| | - Blanca I. García-Gómez
- Biotechnology Institute, National Autonomous University of Mexico, A.P. 510-3, Cuernavaca 62250, Mexico;
| | - Humberto Lanz-Mendoza
- Center for Research on Infectious Diseases, National Institute of Public Health, Cuernavaca 62100, Mexico;
| | - Edgar Dantán-González
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
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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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Sokolova OS, Pichkur EB, Maslova ES, Kurochkina LP, Semenyuk PI, Konarev PV, Samygina VR, Stanishneva-Konovalova TB. Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 Bacillus subtilis. Biomedicines 2022; 10:biomedicines10102347. [PMID: 36289609 PMCID: PMC9598537 DOI: 10.3390/biomedicines10102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them. Here, using cryo-EM, we resolved a structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis. This structure has similarities and differences with members of both groups, as well as with other known phage chaperonins, which further proves their diversity.
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Affiliation(s)
- Olga S. Sokolova
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
| | - Evgeny B. Pichkur
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | | | - Lidia P. Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Petr V. Konarev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
| | - Valeriya R. Samygina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
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4
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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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5
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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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6
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Chang WH, Huang SH, Lin HH, Chung SC, Tu IP. Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules. FRONTIERS IN BIOINFORMATICS 2021; 1:788308. [PMID: 36303748 PMCID: PMC9580929 DOI: 10.3389/fbinf.2021.788308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
The functions of biological macromolecules are often associated with conformational malleability of the structures. This phenomenon of chemically identical molecules with different structures is coined structural polymorphism. Conventionally, structural polymorphism is observed directly by structural determination at the density map level from X-ray crystal diffraction. Although crystallography approach can report the conformation of a macromolecule with the position of each atom accurately defined in it, the exploration of structural polymorphism and interpreting biological function in terms of crystal structures is largely constrained by the crystal packing. An alternative approach to studying the macromolecule of interest in solution is thus desirable. With the advancement of instrumentation and computational methods for image analysis and reconstruction, cryo-electron microscope (cryo-EM) has been transformed to be able to produce “in solution” structures of macromolecules routinely with resolutions comparable to crystallography but without the need of crystals. Since the sample preparation of single-particle cryo-EM allows for all forms co-existing in solution to be simultaneously frozen, the image data contain rich information as to structural polymorphism. The ensemble of structure information can be subsequently disentangled through three-dimensional (3D) classification analyses. In this review, we highlight important examples of protein structural polymorphism in relation to allostery, subunit cooperativity and function plasticity recently revealed by cryo-EM analyses, and review recent developments in 3D classification algorithms including neural network/deep learning approaches that would enable cryo-EM analyese in this regard. Finally, we brief the frontier of cryo-EM structure determination of RNA molecules where resolving the structural polymorphism is at dawn.
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Affiliation(s)
- Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- *Correspondence: Wei-Hau Chang,
| | | | - Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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7
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Shinobu A, Kobayashi C, Matsunaga Y, Sugita Y. Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. J Chem Inf Model 2021; 61:2427-2443. [PMID: 33956432 DOI: 10.1021/acs.jcim.1c00286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large-scale conformational transitions in multi-domain proteins are often essential for their functions. To investigate the transitions, it is necessary to explore multiple potential pathways, which involve different intermediate structures. Here, we present a multi-basin (MB) coarse-grained (CG) structure-based Go̅ model for describing transitions in proteins with more than two moving domains. This model is an extension of our dual-basin Go̅ model in which system-dependent parameters are determined systematically using the multistate Bennett acceptance ratio method. In the MB Go̅ model for multi-domain proteins, we assume that intermediate structures may have partial inter-domain native contacts. This approach allows us to search multiple transition pathways that involve distinct intermediate structures using the CG molecular dynamics (MD) simulations. We apply this scheme to an enzyme, adenylate kinase (AdK), which has three major domains and can move along two different pathways. Using the optimized mixing parameters for each pathway, AdK shows frequent transitions between the Open, Closed, and the intermediate basins and samples a wide variety of conformations within each basin. The explored multiple transition pathways could be compared with experimental data and examined in more detail by atomistic MD simulations.
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Affiliation(s)
- Ai Shinobu
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Matsunaga
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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8
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Wälti MA, Kotler SA, Clore GM. Probing the Interaction of Huntingtin Exon-1 Polypeptides with the Chaperonin Nanomachine GroEL. Chembiochem 2021; 22:1985-1991. [PMID: 33644966 DOI: 10.1002/cbic.202100055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/28/2021] [Indexed: 12/14/2022]
Abstract
Huntington's disease arises from polyQ expansion within the exon-1 region of huntingtin (httex1 ), resulting in an aggregation-prone protein that accumulates in neuronal inclusion bodies. We investigate the interaction of various httex1 constructs with the bacterial analog (GroEL) of the human chaperonin Hsp60. Using fluorescence spectroscopy and electron and atomic force microscopy, we show that GroEL inhibits fibril formation. The binding kinetics of httex1 constructs with intact GroEL and a mini-chaperone comprising the apical domain is characterized by relaxation-based NMR measurements. The lifetimes of the complexes range from 100 to 400 μs with equilibrium dissociation constants (KD ) of ∼1-2 mM. The binding interface is formed by the N-terminal amphiphilic region of httex1 (which adopts a partially helical conformation) and the H and I helices of the GroEL apical domain. Sequestration of monomeric httex1 by GroEL likely increases the critical concentration required for fibrillization.
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Affiliation(s)
- Marielle A Wälti
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
| | - Samuel A Kotler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
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9
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Klebl DP, Feasey MC, Hesketh EL, Ranson NA, Wurdak H, Sobott F, Bon RS, Muench SP. Cryo-EM structure of human mitochondrial HSPD1. iScience 2021; 24:102022. [PMID: 33506187 PMCID: PMC7814154 DOI: 10.1016/j.isci.2020.102022] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/17/2020] [Accepted: 12/29/2020] [Indexed: 12/30/2022] Open
Abstract
Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these proteins. In comparison, its human homolog, known as mitochondrial heat shock protein family member D1 (HSPD1) is poorly understood. Here, we present the structure of HSPD1 in the apo state determined by cryo-electron microscopy (cryo-EM). Unlike GroEL, HSPD1 forms mostly single ring assemblies in the absence of co-chaperonin (HSPE1). Comparison with GroEL shows a rotation and increased flexibility of the apical domain. Together with published structures of the HSPD1/HSPE1 co-chaperonin complex, this work gives insight into the structural changes that occur during the catalytic cycle. This new understanding of HSPD1 structure and its rearrangements upon complex formation may provide new insights for the development of HSPD1-targeting treatments against a diverse range of diseases including glioblastoma. First cryo-EM structure of the apo HSPD1 chaperone complex Mass spectrometry has shown the presence of 7, 8, 15, and 16-mers of HSPD-1 In addition to a single ring, HSPD-1 can form an unusual inverted ring architecture Describe grid preparation conditions that alleviate preferred orientation
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Affiliation(s)
- David P Klebl
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Matthew C Feasey
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Emma L Hesketh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Neil A Ranson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Heiko Wurdak
- School of Medicine, Faculty of Medicine and Health, Stem Cell and Brain Tumour Group, University of Leeds, Leeds LS9 7TF, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.,Department of Chemistry, Biomolecular & Analytical Mass Spectrometry Group, University of Antwerp, Antwerp, Belgium
| | - Robin S Bon
- School of Medicine, Faculty of Medicine and Health & Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT Leeds, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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10
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Exome sequencing revealed a novel homozygous METTL23 gene mutation leading to familial mild intellectual disability with dysmorphic features. Eur J Med Genet 2020; 63:103951. [PMID: 32439618 DOI: 10.1016/j.ejmg.2020.103951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/06/2020] [Accepted: 05/09/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Genetic factors represent a considerable part of the etiologies of intellectual disability; however, the identification of causal genetic anomaly has long been complicated by the great clinical and genetic heterogeneity of this type of disease. With advances in next-generation sequencing technologies and functional studies, the identification of genes involved in intellectual development has led to more accurate diagnostics and better understanding of the underlying biological pathways. CASE REPORT We report on the case of two Moroccan siblings presenting mild intellectual disability with minimal dysmorphic features in which whole exome sequencing analysis revealed homozygous mutation in the METTL23 gene. Mutations in this gene have been reported to cause autosomal recessive mild intellectual disability but the association with dysmorphic features remains controversial. CONCLUSION Hereby, we highlight the similarity of the dysmorphic traits and the characteristic facial features in patients with METTL23-related intellectual disability, suggesting the consideration of a distinct clinical entity associating mild intellectual deficiency with specific facial dysmorphy for an efficient diagnosis orientation and a better phenotype-genotype correlation in intellectual disability disorders.
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11
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Bracher A, Paul SS, Wang H, Wischnewski N, Hartl FU, Hayer-Hartl M. Structure and conformational cycle of a bacteriophage-encoded chaperonin. PLoS One 2020; 15:e0230090. [PMID: 32339190 PMCID: PMC7185714 DOI: 10.1371/journal.pone.0230090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
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Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
| | - Simanta S. Paul
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Huping Wang
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Nadine Wischnewski
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - F. Ulrich Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
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12
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Stanishneva-Konovalova TB, Semenyuk PI, Kurochkina LP, Pichkur EB, Vasilyev AL, Kovalchuk MV, Kirpichnikov MP, Sokolova OS. Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin. J Struct Biol 2019; 209:107439. [PMID: 31870903 DOI: 10.1016/j.jsb.2019.107439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/15/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022]
Abstract
Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.
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Affiliation(s)
- Tatiana B Stanishneva-Konovalova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119991, Russia
| | - Pavel I Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Lidia P Kurochkina
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Evgeny B Pichkur
- National Research Center "Kurchatov Institute", Moscow 123098, Russia
| | | | | | - Mikhail P Kirpichnikov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Olga S Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119991, Russia.
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13
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Abstract
Supersecondary structure code (SSSC), which is represented as the combination of α-helix-type (SSSC: H), β-sheet-type (SSSC: S), the other (SSSC: T), and disorder residue or C-terminal (SSSC: D) patterns, has been produced by the developed concept of Ramachandran plot, in addition, with the ω angle and with the specification of positions of torsion angles in a protein by the registration of codes for torsion angles of each amino acid peptide unit, derived from the fuzzy search of structural code homology using the template patterns 3a5c4a (SSSC: H) and 6c4a4a (SSSC: S) with conformational codes. The DSSP (Dictionary of Secondary Structure in Proteins) method assigns the secondary structure including hydrogen bond well. In contrast, supersecondary structure code is very sensitive to the supersecondary structures of proteins. In this chapter, the protocol of homology search methods, the sequence alignment using supersecondary structure code, the assignment of supersecondary structure code T, the fuzzy search using supersecondary structure code, and the exact search using supersecondary structure code are described. Supersecondary structure code is variable with the conformational change. If possible, many Protein Data Bank (PDB) data of similar main chains of proteins should be used for the homology searches. The thorough check of SSSC sequences is also useful to reveal the role of target pattern.
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Affiliation(s)
- Hiroshi Izumi
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba West, Ibaraki, Japan.
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14
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Lorimer GH, Fei X, Ye X. The GroEL chaperonin: a protein machine with pistons driven by ATP binding and hydrolysis. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0179. [PMID: 29735733 PMCID: PMC5941174 DOI: 10.1098/rstb.2017.0179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 11/30/2022] Open
Abstract
In response to the binding of ATP, the two heptameric rings of the GroEL chaperonin protein interact with one another in a negatively cooperative manner. Owing to the helix dipole, the positively charged nitrogen of glycine 88 at the N-terminus of helix D binds to oxygen atoms on the β and γ phosphorus atoms of ATP. In apo-GroEL, the nucleotide-binding sites of different rings are connected to one another by the interaction of the ɛ-amino group of lysine 105 of one helix D across the twofold axis with the negatively charged carbonyl oxygen atom of alanine 109 at the C-terminus of the other helix D. Upon binding ATP, the K105–A109 salt bridge breaks and both helices move apart by approximately 3.5 Å en bloc toward the ATP. Upon hydrolysis of ATP, the helices return to their original position. The helices thus behave as pistons, their movement being driven by the binding and hydrolysis of ATP. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
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Affiliation(s)
- George H Lorimer
- Center for Biological Structure and Organization, University of Maryland, College Park, MD 20742, USA .,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Xue Fei
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.,Center for Biological Structure and Organization, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Xiang Ye
- Center for Biological Structure and Organization, University of Maryland, College Park, MD 20742, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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15
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Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy. Biophys J 2019; 114:1604-1613. [PMID: 29642030 PMCID: PMC5954442 DOI: 10.1016/j.bpj.2018.02.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/05/2018] [Accepted: 02/20/2018] [Indexed: 11/21/2022] Open
Abstract
Cryo-electron microscopy is rapidly emerging as a powerful technique to determine the structures of complex macromolecular systems elusive to other techniques. Because many of these systems are highly dynamical, characterizing their movements is also a crucial step to unravel their biological functions. To achieve this goal, we report an integrative modeling approach to simultaneously determine structure and dynamics of macromolecular systems from cryo-electron microscopy density maps. By quantifying the level of noise in the data and dealing with their ensemble-averaged nature, this approach enables the integration of multiple sources of information to model ensembles of structures and infer their populations. We illustrate the method by characterizing structure and dynamics of the integral membrane receptor STRA6, thus providing insights into the mechanisms by which it interacts with retinol binding protein and translocates retinol across the membrane.
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16
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Wälti MA, Clore GM. Disassembly/reassembly strategy for the production of highly pure GroEL, a tetradecameric supramolecular machine, suitable for quantitative NMR, EPR and mutational studies. Protein Expr Purif 2017; 142:8-15. [PMID: 28951283 DOI: 10.1016/j.pep.2017.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 11/20/2022]
Abstract
GroEL, a prototypical member of the chaperonin class of chaperones, is a large supramocular machine that assists protein folding and plays an important role in proteostasis. GroEL comprises two heptameric rings, each of which encloses a large cavity that provides a folding chamber for protein substrates. Many questions remain regarding the mechanistic details of GroEL facilitated protein folding. Thus, data at atomic resolution of the type provided by NMR and EPR are invaluable. Such studies often require complete deuteration of GroEL, uniform or residue specific 13C and 15N isotope labeling, and the introduction of selective cysteine mutations for site-specific spin labeling. In addition, high purity GroEL is essential for detailed studies of substrate-GroEL interactions as quantitative interpretation is impossible if the cavities are already occupied and blocked by other protein substrates present in the bacterial expression system. Here we present a new purification protocol designed to provide highly pure GroEL devoid of non-specific protein substrate contamination.
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Affiliation(s)
- Marielle A Wälti
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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17
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Chaperonin GroEL accelerates protofibril formation and decorates fibrils of the Het-s prion protein. Proc Natl Acad Sci U S A 2017; 114:9104-9109. [PMID: 28784759 DOI: 10.1073/pnas.1711645114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have studied the interaction of the prototypical chaperonin GroEL with the prion domain of the Het-s protein using solution and solid-state NMR, electron and atomic force microscopies, and EPR. While GroEL accelerates Het-s protofibril formation by several orders of magnitude, the rate of appearance of fibrils is reduced. GroEL remains bound to Het-s throughout the aggregation process and densely decorates the fibrils at a regular spacing of ∼200 Å. GroEL binds to the Het-s fibrils via its apical domain located at the top of the large open ring. Thus, apo GroEL and bullet-shaped GroEL/GroES complexes in which only a single ring is capped by GroES interact with the Het-s fibrils; no evidence is seen for any interaction with football-shaped GroEL/GroES complexes in which both rings are capped by GroES. EPR spectroscopy shows that rotational motion of a nitroxide spin label, placed at the N-terminal end of the first β-strand of Het-s fibrils, is significantly reduced in both Het-s/GroEL aggregates and Het-s fibrils, but virtually completely eliminated in Het-s/GroEL fibrils, suggesting that in the latter, GroEL may come into close proximity to the nitroxide label. Solid-state NMR measurements indicate that GroEL binds to the mobile regions of the Het-s fibril comprising the N-terminal tail and a loop connecting β-strands 4 and 5, consistent with interactions involving GroEL binding consensus sequences located therein.
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18
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Roh SH, Hryc CF, Jeong HH, Fei X, Jakana J, Lorimer GH, Chiu W. Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc Natl Acad Sci U S A 2017; 114:8259-8264. [PMID: 28710336 PMCID: PMC5547627 DOI: 10.1073/pnas.1704725114] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer.
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Affiliation(s)
- Soung-Hun Roh
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
| | - Hyun-Hwan Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Xue Fei
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030;
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
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19
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Weiss C, Jebara F, Nisemblat S, Azem A. Dynamic Complexes in the Chaperonin-Mediated Protein Folding Cycle. Front Mol Biosci 2016; 3:80. [PMID: 28008398 PMCID: PMC5143341 DOI: 10.3389/fmolb.2016.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 11/13/2022] Open
Abstract
The GroEL–GroES chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. Since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. During this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. Despite of almost three decades of research on this oligomeric protein, certain aspects of its function remain controversial. In this review, we highlight one central aspect of its function, namely, the active intermediates of its reaction cycle, and present how research to this day continues to change our understanding of chaperonin-mediated protein folding.
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Affiliation(s)
- Celeste Weiss
- George S. Weiss Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Fady Jebara
- George S. Weiss Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Shahar Nisemblat
- George S. Weiss Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Abdussalam Azem
- George S. Weiss Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University Tel Aviv, Israel
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20
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Schmidt T, Wälti MA, Baber JL, Hustedt EJ, Clore GM. Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609617] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - Marielle A. Wälti
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - James L. Baber
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - Eric J. Hustedt
- Department of Molecular Physiology and Biophysics; Vanderbilt University; Nashville TN 37232 USA
| | - G. Marius Clore
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
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21
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Schmidt T, Wälti MA, Baber JL, Hustedt EJ, Clore GM. Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:15905-15909. [PMID: 27860003 DOI: 10.1002/anie.201609617] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/06/2022]
Abstract
Current distance measurements between spin-labels on multimeric protonated proteins using double electron-electron resonance (DEER) EPR spectroscopy are generally limited to the 15-60 Å range. Here we show how DEER experiments can be extended to dipolar evolution times of ca. 80 μs, permitting distances up to 170 Å to be accessed in multimeric proteins. The method relies on sparse spin-labeling, supplemented by deuteration of protein and solvent, to minimize the deleterious impact of multispin effects and substantially increase the apparent spin-label phase memory relaxation time, complemented by high sensitivity afforded by measurements at Q-band. We demonstrate the approach using the tetradecameric molecular machine GroEL as an example. Two engineered surface-exposed mutants, R268C and E315C, are used to measure pairwise distance distributions with mean values ranging from 20 to 100 Å and from 30 to 160 Å, respectively, both within and between the two heptameric rings of GroEL. The measured distance distributions are consistent with the known crystal structure of apo GroEL. The methodology presented here should significantly expand the use of DEER for the structural characterization of conformational changes in higher order oligomers.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Marielle A Wälti
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - James L Baber
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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22
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New GroEL-like chaperonin of bacteriophage OBP Pseudomonas fluorescens suppresses thermal protein aggregation in an ATP-dependent manner. Biochem J 2016; 473:2383-93. [DOI: 10.1042/bcj20160367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/31/2016] [Indexed: 11/17/2022]
Abstract
Recently, we discovered and studied the first virus-encoded chaperonin of bacteriophage EL Pseudomonas aeruginosa, gene product (gp) 146. In the present study, we performed bioinformatics analysis of currently predicted GroEL-like proteins encoded by phage genomes in comparison with cellular and mitochondrial chaperonins. Putative phage chaperonins share a low similarity and do not form a monophyletic group; nevertheless, they are closer to bacterial chaperonins in the phylogenetic tree. Experimental investigation of putative GroEL-like chaperonin proteins has been continued by physicochemical and functional characterization of gp246 encoded by the genome of Pseudomonas fluorescens bacteriophage OBP. Unlike the more usual double-ring architecture of chaperonins, including the EL gp146, the recombinant gp246 produced by Escherichia coli cells has been purified as a single heptameric ring. It possesses ATPase activity and does not require a co-chaperonin for its function. In vitro experiments demonstrated that gp246 is able to suppress the thermal protein inactivation and aggregation in an ATP-dependent manner, thus indicating chaperonin function. Single-particle electron microscopy analysis revealed the different conformational states of OBP chaperonin, depending on the bound nucleotide.
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23
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Iizuka R, Funatsu T. Chaperonin GroEL uses asymmetric and symmetric reaction cycles in response to the concentration of non-native substrate proteins. Biophys Physicobiol 2016; 13:63-69. [PMID: 27924258 PMCID: PMC5042173 DOI: 10.2142/biophysico.13.0_63] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/07/2016] [Indexed: 12/01/2022] Open
Abstract
The Escherichia coli chaperonin GroEL is an essential molecular chaperone that mediates protein folding in association with its cofactor, GroES. It is widely accepted that GroEL alternates the GroES-sealed folding-active rings during the reaction cycle. In other words, an asymmetric GroEL–GroES complex is formed during the cycle, whereas a symmetric GroEL–(GroES)2 complex is not formed. However, this conventional view has been challenged by the recent reports indicating that such symmetric complexes can be formed in the GroEL–GroES reaction cycle. In this review, we discuss the studies of the symmetric GroEL–(GroES)2 complex, focusing on the molecular mechanism underlying its formation. We also suggest that GroEL can be involved in two types of reaction cycles (asymmetric or symmetric) and the type of cycle used depends on the concentration of non-native substrate proteins.
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Affiliation(s)
- Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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24
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Structural insight into the cooperation of chloroplast chaperonin subunits. BMC Biol 2016; 14:29. [PMID: 27072913 PMCID: PMC4828840 DOI: 10.1186/s12915-016-0251-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background Chloroplast chaperonin, consisting of multiple subunits, mediates folding of the highly abundant protein Rubisco with the assistance of co-chaperonins. ATP hydrolysis drives the chaperonin allosteric cycle to assist substrate folding and promotes disassembly of chloroplast chaperonin. The ways in which the subunits cooperate during this cycle remain unclear. Results Here, we report the first crystal structure of Chlamydomonas chloroplast chaperonin homo-oligomer (CPN60β1) at 3.8 Å, which shares structural topology with typical type I chaperonins but with looser compaction, and possesses a larger central cavity, less contact sites and an enlarged ATP binding pocket compared to GroEL. The overall structure of Cpn60 resembles the GroEL allosteric intermediate state. Moreover, two amino acid (aa) residues (G153, G154) conserved among Cpn60s are involved in ATPase activity regulated by co-chaperonins. Domain swapping analysis revealed that the monomeric state of CPN60α is controlled by its equatorial domain. Furthermore, the C-terminal segment (aa 484–547) of CPN60β influenced oligomer disassembly and allosteric rearrangement driven by ATP hydrolysis. The entire equatorial domain and at least one part of the intermediate domain from CPN60α are indispensable for functional cooperation with CPN60β1, and this functional cooperation is strictly dependent on a conserved aa residue (E461) in the CPN60α subunit. Conclusions The first crystal structure of Chlamydomonas chloroplast chaperonin homo-oligomer (CPN60β1) is reported. The equatorial domain maintained the monomeric state of CPN60α and the C-terminus of CPN60β affected oligomer disassembly driven by ATP. The cooperative roles of CPN60 subunits were also established. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0251-8) contains supplementary material, which is available to authorized users.
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25
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Abstract
Chaperonins are nanomachines that facilitate protein folding by undergoing energy (ATP)-dependent movements that are coordinated in time and space owing to complex allosteric regulation. They consist of two back-to-back stacked oligomeric rings with a cavity at each end where protein substrate folding can take place. Here, we focus on the GroEL/GroES chaperonin system from Escherichia coli and, to a lesser extent, on the more poorly characterized eukaryotic chaperonin CCT/TRiC. We describe their various functional (allosteric) states and how they are affected by substrates and allosteric effectors that include ATP, ADP, nonfolded protein substrates, potassium ions, and GroES (in the case of GroEL). We also discuss the pathways of intra- and inter-ring allosteric communication by which they interconvert and the coupling between allosteric transitions and protein folding reactions.
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Affiliation(s)
- Ranit Gruber
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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26
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Molugu SK, Li J, Bernal RA. Separation of E. coli chaperonin groEL from β-galactosidase without denaturation. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1007:93-9. [PMID: 26590880 DOI: 10.1016/j.jchromb.2015.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/27/2015] [Accepted: 11/03/2015] [Indexed: 11/28/2022]
Abstract
Chaperonins are a class of ubiquitous proteins that assist and accelerate protein folding in the cell. The Escherichia coli groEL is the best known and forms a complex with its co-chaperonin groES in the presence of ATP and assists in the folding of nascent and misfolded substrate proteins. The purification of recombinant groEL results in a nearly homogeneous sample that consistently co-purifies with the major contaminant E. coli β-galactosidase. Removal of β-galactosidase using column chromatography alone is exceedingly difficult. This is due to the fact that the overall size, surface charge, isoelectric point and hydrophobicity of groEL and β-galactosidase are very similar. Therefore purification of groEL chaperonin to homogeneity requires denaturation of the complex into monomers with urea for separating the groEL from contaminating β-galactosidase followed by reassembly of the chaperonin complex. Here, we present a simple procedure for separating β-galactosidase along with many other impurities from groEL preparations under non-denaturing conditions. The groEL is first salted out with 50% ammonium sulfate. This step also precipitates β-galactosidase but this is then salted out by the addition of magnesium chloride which leaves groEL in solution. All remaining contaminants are removed by column chromatography.
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Affiliation(s)
- Sudheer K Molugu
- Department of Chemistry, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Jihui Li
- Department of Chemistry, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Ricardo A Bernal
- Department of Chemistry, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA.
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27
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GroEL2 of Mycobacterium tuberculosis Reveals the Importance of Structural Pliability in Chaperonin Function. J Bacteriol 2015; 198:486-97. [PMID: 26553853 DOI: 10.1128/jb.00844-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Intracellular protein folding is mediated by molecular chaperones, the best studied among which are the chaperonins GroEL and GroES. Conformational changes and allosteric transitions between different metastable states are hallmarks of the chaperonin mechanism. These conformational transitions between three structural domains of GroEL are anchored at two hinges. Although hinges are known to be critical for mediating the communication between different domains of GroEL, the relative importance of hinges on GroEL oligomeric assembly, ATPase activity, conformational changes, and functional activity is not fully characterized. We have exploited the inability of Mycobacterium tuberculosis GroEL2 to functionally complement an Escherichia coli groEL mutant to address the importance of hinge residues in the GroEL mechanism. Various chimeras of M. tuberculosis GroEL2 and E. coli GroEL allowed us to understand the role of hinges and dissect the consequences of oligomerization and substrate binding capability on conformational transitions. The present study explains the concomitant conformational changes observed with GroEL hinge variants and is best supported by the normal mode analysis. IMPORTANCE Conformational changes and allosteric transitions are hallmarks of the chaperonin mechanism. We have exploited the inability of M. tuberculosis GroEL2 to functionally complement a strain of E. coli in which groEL expression is repressed to address the importance of hinges. The significance of conservation at the hinge regions stands out as a prominent feature of the GroEL mechanism in binding to GroES and substrate polypeptides. The hinge residues play a significant role in the chaperonin activity in vivo and in vitro.
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28
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Kim J, Kim JG, Yun G, Lee PS, Kim DN. Toward Modular Analysis of Supramolecular Protein Assemblies. J Chem Theory Comput 2015; 11:4260-72. [PMID: 26575921 DOI: 10.1021/acs.jctc.5b00329] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite recent advances in molecular simulation technologies, analysis of high-molecular-weight structures is still challenging. Here, we propose an automated model reduction procedure aiming to enable modular analysis of these structures. It employs a component mode synthesis for the reduction of finite element protein models. Reduced models may consist of real biological subunits or artificial partitions whose dynamics is described using the degrees of freedom at the substructural interfaces and a small set of dominant vibrational modes only. Notably, the proper number of dominant modes is automatically determined using a novel estimator for eigenvalue errors without calculating the reference eigensolutions of the full model. The performance of the proposed approach is thoroughly investigated by analyzing 50 representative structures including a crystal structure of GroEL and an electron density map of a ribosome.
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Affiliation(s)
| | - Jin-Gyun Kim
- Mechanical Systems Safety Research Division, Korea Institute of Machinery & Materials , Gajeongbuk-ro 156, Yuseong-gu, Daejeon 34103, Republic of Korea
| | | | - Phill-Seung Lee
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology , Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
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29
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Stability and disassembly properties of human naïve Hsp60 and bacterial GroEL chaperonins. Biophys Chem 2015; 208:68-75. [PMID: 26259786 DOI: 10.1016/j.bpc.2015.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/17/2015] [Accepted: 07/19/2015] [Indexed: 02/03/2023]
Abstract
Human Hsp60 chaperonin and its bacterial homolog GroEL, in association with the corresponding co-chaperonins Hsp10 and GroES, constitute important chaperone systems promoting the proper folding of several mitochondrial proteins. Hsp60 is also currently described as a ubiquitous molecule with multiple roles both in health conditions and in several diseases. Naïve Hsp60 bearing the mitochondrial import signal has been recently demonstrated to present different oligomeric organizations with respect to GroEL, suggesting new possible physiological functions. Here we present a combined investigation with circular dichroism and small-angle X-ray scattering of structure, self-organization, and stability of naïve Hsp60 in solution in comparison with bacterial GroEL. Experiments have been performed in different concentrations of guanidine hydrochloride, monitoring the dissociation of tetradecamers into heptamers and monomers, until unfolding. GroEL is proved to be more stable with respect to Hsp60, and the unfolding free energy as well as its dependence on denaturant concentration is obtained.
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Skjærven L, Cuellar J, Martinez A, Valpuesta JM. Dynamics, flexibility, and allostery in molecular chaperonins. FEBS Lett 2015; 589:2522-32. [PMID: 26140986 DOI: 10.1016/j.febslet.2015.06.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 12/26/2022]
Abstract
The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements.
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Affiliation(s)
- Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Jorge Cuellar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Vitlin Gruber A, Zizelski G, Azem A, Weiss C. The Cpn10(1) co-chaperonin of A. thaliana functions only as a hetero-oligomer with Cpn20. PLoS One 2014; 9:e113835. [PMID: 25419702 PMCID: PMC4242682 DOI: 10.1371/journal.pone.0113835] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022] Open
Abstract
The A. thaliana genome encodes five co-chaperonin homologs, three of which are destined to the chloroplast. Two of the proteins, Cpn10(2) and Cpn20, form functional homo-oligomers in vitro. In the current work, we present data on the structure and function of the third A. thaliana co-chaperonin, which exhibits unique properties. We found that purified recombinant Cpn10(1) forms inactive dimers in solution, in contrast to the active heptamers that are formed by canonical Cpn10s. Additionally, our data demonstrate that Cpn10(1) is capable of assembling into active hetero-oligomers together with Cpn20. This finding was reinforced by the formation of active co-chaperonin species upon mixing an inactive Cpn20 mutant with the inactive Cpn10(1). The present study constitutes the first report of a higher plant Cpn10 subunit that is able to function only upon formation of hetero-oligomers with other co-chaperonins.
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Affiliation(s)
- Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Gal Zizelski
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Abdussalam Azem
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Celeste Weiss
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
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Si D, He J. Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions. Structure 2014; 22:1665-76. [DOI: 10.1016/j.str.2014.08.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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Vitlin Gruber A, Nisemblat S, Azem A, Weiss C. The complexity of chloroplast chaperonins. TRENDS IN PLANT SCIENCE 2013; 18:688-94. [PMID: 24035661 DOI: 10.1016/j.tplants.2013.08.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/29/2013] [Accepted: 08/07/2013] [Indexed: 05/07/2023]
Abstract
Type I chaperonins are large oligomeric protein ensembles that are involved in the folding and assembly of other proteins. Chloroplast chaperonins and co-chaperonins exist in multiple copies of two distinct isoforms that can combine to form a range of labile oligomeric structures. This complex system increases the potential number of chaperonin substrates and possibilities for regulation. The incorporation of unique subunits into the oligomer can modify substrate specificity. Some subunits are upregulated in response to heat shock and some show organ-specific expression, whereas others possess additional functions that are unrelated to their role in protein folding. Accumulating evidence suggests that specific subunits have distinct roles in biogenesis of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco).
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Affiliation(s)
- Anna Vitlin Gruber
- The George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Ramat Aviv, Israel
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Fuglebakk E, Reuter N, Hinsen K. Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions. J Chem Theory Comput 2013; 9:5618-28. [PMID: 26592296 DOI: 10.1021/ct400399x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Elastic network models (ENMs) are valuable tools for investigating collective motions of proteins, and a rich variety of simple models have been proposed over the past decade. A good representation of the collective motions requires a good approximation of the covariances between the fluctuations of the individual atoms. Nevertheless, most studies have validated such models only by the magnitudes of the single-atom fluctuations they predict. In the present study, we have quantified the agreement between the covariance structure predicted by molecular dynamics (MD) simulations and those predicted by a representative selection of proposed coarse-grained ENMs. We then contrast this approach with the comparison to MD-predicted atomic fluctuations and comparison to crystallographic B-factors. While all the ENMs yield approximations to the MD-predicted covariance structure, we report large and consistent differences between proposed models. We also find that the ability of the ENMs to predict atomic fluctuations is correlated with their ability to capture the covariance structure. In contrast, we find that the models that agree best with B-factors model collective motions less reliably and recommend against using B-factors as a benchmark.
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Affiliation(s)
- Edvin Fuglebakk
- Computational Biology Unit, UniResearch , 5020 Bergen, Norway
| | - Nathalie Reuter
- Computational Biology Unit, UniResearch , 5020 Bergen, Norway
| | - Konrad Hinsen
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique , 45071 Orléans, France.,Division Expériences, Synchrotron SOLEIL , 91190 Saint Aubin, France
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35
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Cossio P, Hummer G. Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. J Struct Biol 2013; 184:427-37. [PMID: 24161733 DOI: 10.1016/j.jsb.2013.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 10/05/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
Abstract
We develop a method to extract structural information from electron microscopy (EM) images of dynamic and heterogeneous molecular assemblies. To overcome the challenge of disorder in the imaged structures, we analyze each image individually, avoiding information loss through clustering or averaging. The Bayesian inference of EM (BioEM) method uses a likelihood-based probabilistic measure to quantify the consistency between each EM image and given structural models. The likelihood function accounts for uncertainties in the molecular position and orientation, variations in the relative intensities and noise in the experimental images. The BioEM formalism is physically intuitive and mathematically simple. We show that for experimental GroEL images, BioEM correctly identifies structures according to the functional state. The top-ranked structure is the corresponding X-ray crystal structure, followed by an EM structure generated previously from a superset of the EM images used here. To analyze EM images of highly flexible molecules, we propose an ensemble refinement procedure, and validate it with synthetic EM maps of the ESCRT-I-II supercomplex. Both the size of the ensemble and its structural members are identified correctly. BioEM offers an alternative to 3D-reconstruction methods, extracting accurate population distributions for highly flexible structures and their assemblies. We discuss limitations of the method, and possible applications beyond ensemble refinement, including the cross-validation and unbiased post-assessment of model structures, and the structural characterization of systems where traditional approaches fail. Overall, our results suggest that the BioEM framework can be used to analyze EM images of both ordered and disordered molecular systems.
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Affiliation(s)
- Pilar Cossio
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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Crystal structure of a GroEL-ADP complex in the relaxed allosteric state at 2.7 Å resolution. Proc Natl Acad Sci U S A 2013; 110:E2958-66. [PMID: 23861496 DOI: 10.1073/pnas.1311996110] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The chaperonin proteins GroEL and GroES are cellular nanomachines driven by the hydrolysis of ATP that facilitate the folding of structurally diverse substrate proteins. In response to ligand binding, the subunits of a ring cycle in a concerted manner through a series of allosteric states (T, R, and R″), enabling work to be performed on the substrate protein. Removing two salt bridges that ordinarily break during the allosteric transitions of the WT permitted the structure of GroEL-ADP in the R state to be solved to 2.7 Å resolution. Whereas the equatorial domain displays almost perfect sevenfold symmetry, the apical domains, to which substrate proteins bind, and to a lesser extent, the intermediate domains display a remarkable asymmetry. Freed of intersubunit contacts, the apical domain of each subunit adopts a different conformation, suggesting a flexibility that permits interaction with diverse substrate proteins. This result contrasts with a previous cryo-EM study of a related allosteric ATP-bound state at lower resolution. After artificially imposing sevenfold symmetry it was concluded that a GroEL ring in the R-ATP state existed in six homogeneous but slightly different states. By imposing sevenfold symmetry on each of the subunits of the crystal structure of GroEL-ADP, we showed that the synthetic rings of (X-ray) GroEL-ADP and (cryo-EM) GroEL-ATP are structurally closely related. A deterministic model, the click stop mechanism, that implied temporal transitions between these states was proposed. Here, however, these conformational states are shown to exist as a structurally heterogeneous ensemble within a single ring.
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Moriya T, Mio K, Sato C. Novel convergence-oriented approach for evaluation and optimization of workflow in single-particle two-dimensional averaging of electron microscope images. Microscopy (Oxf) 2013; 62:491-513. [PMID: 23625506 DOI: 10.1093/jmicro/dft026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three-dimensional (3D) protein structures facilitate the understanding of their biological functions and provide valuable information for developing medicines. Single-particle analysis (SPA) from electron microscopy (EM) is a structure determination method suitable for macromolecules. To achieve a high resolution using combinations of several SPA software packages, 'workflow' optimization and comparative evaluation by scoring results are essential. Two-dimensional (2D) averaging is a key step for 3D reconstruction. The integrated convergence-evaluation oriented system (IC-EOS) proposed here provides an effective tool for customizing 2D averaging. This assesses the behavior and characteristics of workflows and evaluates the convergence of iteration steps without human intervention. We chose five base measurements for quantifying convergence: resolution, variance, similarity, shift-distance and rotation-angle. Curve fitting to history graphs scored their stability. We call this score 'fluctuation'. The number of particle images discarded from the library and the number of classification groups were examined to see their effects on optimization levels and fluctuation of measurements, allowing the IC-EOS to select the most appropriate workflow for the target. A case study using a bacterial sodium channel and a simulation study using GroEL showed that resolution of 2D averaging improved with relatively stricter particle selection. With fewer groups, resolutions of class averages improved, but similarities between class-averages and their constituent particle images degraded. Fluctuation was useful for selecting adequate conditions, even when achieved values alone were not conclusive. The vote method, using fluctuation, was robust against noise and enabled a decision without exhaustive search trials. Thus, the IC-EOS is a step toward full automation of SPA.
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Affiliation(s)
- Toshio Moriya
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Scheres SHW. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 2012; 180:519-30. [PMID: 23000701 PMCID: PMC3690530 DOI: 10.1016/j.jsb.2012.09.006] [Citation(s) in RCA: 3802] [Impact Index Per Article: 316.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/03/2012] [Accepted: 09/06/2012] [Indexed: 11/17/2022]
Abstract
RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
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Affiliation(s)
- Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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39
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Skjaerven L, Muga A, Reuter N, Martinez A. A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES. Proteins 2012; 80:2333-46. [PMID: 22576372 DOI: 10.1002/prot.24113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/26/2012] [Accepted: 05/04/2012] [Indexed: 11/09/2022]
Abstract
The molecular chaperone, GroEL, essential for correct protein folding in E. coli, is composed of 14 identical subunits organized in two interacting rings, each providing a folding chamber for non-native substrate proteins. The oligomeric assembly shows positive cooperativity within each ring and negative cooperativity between the rings. Although it is well known that ATP and long-range allosteric interactions drive the functional cycle of GroEL, an atomic resolution view of how ligand binding modulates conformational adaptations over long distances remains a major challenge. Moreover, little is known on the relation between equilibrium dynamics at physiological temperatures and the allosteric transitions in GroEL. Here we present multiple all-atom molecular dynamics simulations of the GroEL-GroES assemblies at different stages of the functional cycle. Combined with an extensive analysis of the complete set of experimentally available structures, principal component analysis and conformer plots, we provide an explicit evaluation of the accessible conformational space of unliganded GroEL. Our results suggest the presence of pre-existing conformers at the equatorial domain level, and a shift of the conformational ensemble upon ATP-binding. At the inter-ring interface the simulations capture a remarkable offset motion of helix D triggered by ATP-binding to the folding active ring. The reorientation of helix D, previously only observed upon GroES association, correlates with a change of the internal dynamics in the opposite ring. This work contributes to the understanding of the molecular mechanisms in GroEL and highlights the ability of all-atom MD simulations to model long-range structural changes and allosteric events in large systems.
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Affiliation(s)
- Lars Skjaerven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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40
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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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41
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Selvy PE, Lavieri RR, Lindsley CW, Brown HA. Phospholipase D: enzymology, functionality, and chemical modulation. Chem Rev 2011; 111:6064-119. [PMID: 21936578 PMCID: PMC3233269 DOI: 10.1021/cr200296t] [Citation(s) in RCA: 269] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paige E Selvy
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37064, USA
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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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Pilak O, Harrop SJ, Siddiqui KS, Chong K, De Francisci D, Burg D, Williams TJ, Cavicchioli R, Curmi PMG. Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer. Environ Microbiol 2011; 13:2232-49. [PMID: 21477108 DOI: 10.1111/j.1462-2920.2011.02477.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Archaea are abundant in permanently cold environments. The Antarctic methanogen, Methanococcoides burtonii, has proven an excellent model for studying molecular mechanisms of cold adaptation. Methanococcoides burtonii contains three group II chaperonins that diverged prior to its closest orthologues from mesophilic Methanosarcina spp. The relative abundance of the three chaperonins shows little dependence on organism growth temperature, except at the highest temperatures, where the most thermally stable chaperonin increases in abundance. In vitro and in vivo, the M. burtonii chaperonins are predominantly monomeric, with only 23-33% oligomeric, thereby differing from other archaea where an oligomeric ring form is dominant. The crystal structure of an N-terminally truncated chaperonin reveals a monomeric protein with a fully open nucleotide binding site. When compared with closed state group II chaperonin structures, a large-scale ≈ 30° rotation between the equatorial and intermediate domains is observed resulting in an open nucleotide binding site. This is analogous to the transition observed between open and closed states of group I chaperonins but contrasts with recent archaeal group II chaperonin open state ring structures. The predominance of monomeric form and the ability to adopt a fully open nucleotide site appear to be unique features of the M. burtonii group II chaperonins.
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Affiliation(s)
- Oliver Pilak
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
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44
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Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol 2011; 7:e1002004. [PMID: 21423709 PMCID: PMC3053311 DOI: 10.1371/journal.pcbi.1002004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 12/09/2010] [Indexed: 12/01/2022] Open
Abstract
GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant “opening” of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition. Molecular machines convert chemical energy to mechanical work in the process of carrying out their specific tasks. Often these proteins are fueled by ATP binding and hydrolysis, enabling switching between different conformations. The ATP-dependent chaperone GroEL is a molecular machine that opens and closes its barrel-like structure in order to provide a folding cage for unfolded proteins. The quest to fully understand and control GroEL and other molecular machines is enhanced by complementing experimental work with computational approaches. Here, we provide a description of the molecular basis for the conformational changes in the GroEL subunit by performing extensive molecular dynamics simulations. The simulations sample the conformational population for the different nucleotide-free and bound states in the isolated subunit. The results reveal that the conformations of the subunit when isolated resemble those of the subunit integrated in the GroEL complex. Moreover, the molecular dynamics simulations allow following detailed changes in individual interatomic interactions brought about by ATP-binding.
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Affiliation(s)
- Lars Skjaerven
- Department of Biomedicine, University of Bergen, Bergen, Norway
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van Rooyen J, Abratt V, Belrhali H, Sewell B. Crystallization of recombinant Bacteroides fragilis glutamine synthetase (GlnN) isolated using a novel and rapid purification protocol. Protein Expr Purif 2010; 74:211-6. [DOI: 10.1016/j.pep.2010.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/04/2010] [Accepted: 06/17/2010] [Indexed: 11/15/2022]
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46
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Sielaff B, Lee KS, Tsai FTF. Structural and functional conservation of Mycobacterium tuberculosis GroEL paralogs suggests that GroEL1 Is a chaperonin. J Mol Biol 2010; 405:831-9. [PMID: 21094166 DOI: 10.1016/j.jmb.2010.11.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
GroEL is a group I chaperonin that facilitates protein folding and prevents protein aggregation in the bacterial cytosol. Mycobacteria are unusual in encoding two or more copies of GroEL in their genome. While GroEL2 is essential for viability and likely functions as the general housekeeping chaperonin, GroEL1 is dispensable, but its structure and function remain unclear. Here, we present the 2.2-Å resolution crystal structure of a 23-kDa fragment of Mycobacterium tuberculosis GroEL1 consisting of an extended apical domain. Our X-ray structure of the GroEL1 apical domain closely resembles those of Escherichia coli GroEL and M. tuberculosis GroEL2, thus highlighting the remarkable structural conservation of bacterial chaperonins. Notably, in our structure, the proposed substrate-binding site of GroEL1 interacts with the N-terminal region of a symmetry-related neighboring GroEL1 molecule. The latter is consistent with the known GroEL apical domain function in substrate binding and is supported by results obtained from using peptide array technology. Taken together, these data show that the apical domains of M. tuberculosis GroEL paralogs are conserved in three-dimensional structure, suggesting that GroEL1, like GroEL2, is a chaperonin.
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Affiliation(s)
- Bernhard Sielaff
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Skjaerven L, Martinez A, Reuter N. Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins 2010; 79:232-43. [PMID: 21058295 DOI: 10.1002/prot.22875] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lars Skjaerven
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
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Sielaff B, Lee KS, Tsai FTF. Crystallization and preliminary X-ray crystallographic analysis of a GroEL1 fragment from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:418-20. [PMID: 20383012 PMCID: PMC2852334 DOI: 10.1107/s1744309110004409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 02/03/2010] [Indexed: 12/31/2022]
Abstract
Full-length GroEL1 from Mycobacterium tuberculosis H37Rv was cloned, overexpressed and purified. Crystals were obtained by the hanging-drop vapor-diffusion method and contained a 23 kDa GroEL1 fragment. A complete native data set was collected from a single frozen crystal that belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 75.47, b = 78.67, c = 34.89 A, alpha = beta = gamma = 90 degrees , and diffracted to 2.2 A resolution on a home X-ray source.
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Affiliation(s)
- Bernhard Sielaff
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
| | - Ki Seog Lee
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
| | - Francis T. F. Tsai
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
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Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. Proc Natl Acad Sci U S A 2010; 107:4961-6. [PMID: 20194785 DOI: 10.1073/pnas.0914540107] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys Lett 426:168-175] to sample the conformational space of multidomain proteins in all-atom, explicitly solvated molecular dynamics simulations. The method allows the system to hyperthermally explore the free-energy surface in a set of collective variables computed at the physical temperature. As collective variables, we pick Cartesian coordinates of centers of contiguous subdomains. The method is applied to the GroEL subunit, a 55-kDa, three-domain protein, and HIV-1 gp120. For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t --> r('') transition and are not observed in unaccelerated molecular dynamics: The apical domain is displaced by 30 A, with a twist of 90 degrees relative to the equatorial domain, and the root-mean-squared deviation relative to the r('') conformer is reduced from 13 to 5 A, representing fairly high predictive capability. For gp120, the method predicts both counterrotation of inner and outer domains and disruption of the so-called bridging sheet. In particular, TAMD on gp120 initially in the CD4-bound conformation visits conformations that deviate by 3.6 A from the gp120 conformer in complex with antibody F105, again reflecting good predictive capability. TAMD generates plausible all-atom models of the so-far structurally uncharacterized unliganded conformation of HIV-1 gp120, which may prove useful in the development of inhibitors and immunogens. The fictitious temperature employed also gives a rough estimate of 10 kcal/mol for the free-energy barrier between conformers in both cases.
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Kiser PD, Lorimer GH, Palczewski K. Use of thallium to identify monovalent cation binding sites in GroEL. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:967-71. [PMID: 19851000 PMCID: PMC2765879 DOI: 10.1107/s1744309109032928] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 08/18/2009] [Indexed: 11/10/2022]
Abstract
GroEL is a bacterial chaperone protein that assembles into a homotetradecameric complex exhibiting D(7) symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg(2+) and K(+), to bind and hydrolyze ATP. A K(+)-binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K(+)-binding site may exist within GroEL. Because K(+) has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter-ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K(+) mimetic Tl(+) was incorporated into GroEL crystals, a moderately redundant 3.94 A resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K(+) next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and cooperativity. These findings also demonstrate the general usefulness of Tl(+) for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low.
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