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Marchenkov V, Ivashina T, Marchenko N, Ryabova N, Selivanova O, Timchenko A, Kihara H, Ksenzenko V, Semisotnov G. In Vivo Incorporation of Photoproteins into GroEL Chaperonin Retaining Major Structural and Functional Properties. Molecules 2023; 28:molecules28041901. [PMID: 36838891 PMCID: PMC9965216 DOI: 10.3390/molecules28041901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The incorporation of photoproteins into proteins of interest allows the study of either their localization or intermolecular interactions in the cell. Here we demonstrate the possibility of in vivo incorporating the photoprotein Aequorea victoria enhanced green fluorescent protein (EGFP) or Gaussia princeps luciferase (GLuc) into the tetradecameric quaternary structure of GroEL chaperonin and describe some physicochemical properties of the labeled chaperonin. Using size-exclusion and affinity chromatography, electrophoresis, fluorescent and electron transmission microscopy (ETM), small-angle X-ray scattering (SAXS), and bioluminescence resonance energy transfer (BRET), we show the following: (i) The GroEL14-EGFP is evenly distributed within normally divided E. coli cells, while gigantic undivided cells are characterized by the uneven distribution of the labeled GroEL14 which is mainly localized close to the cellular periplasm; (ii) EGFP and likely GLuc are located within the inner cavity of one of the two GroEL chaperonin rings and do not essentially influence the protein oligomeric structure; (iii) GroEL14 containing either EGFP or GLuc is capable of interacting with non-native proteins and the cochaperonin GroES.
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Affiliation(s)
- Victor Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Tanya Ivashina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, 142290 Pushchino, Russia
| | - Natalia Marchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Natalya Ryabova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Olga Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Alexander Timchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Hiroshi Kihara
- Department of Physics, Kansai Medical University, Shin-Machi 2-5-1, Hirakata 573-1010, Japan
| | - Vladimir Ksenzenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Gennady Semisotnov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
- Correspondence: ; Tel.: +7-(496)-731-8409
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Wälti MA, Canagarajah B, Schwieters CD, Clore GM. Visualization of Sparsely-populated Lower-order Oligomeric States of Human Mitochondrial Hsp60 by Cryo-electron Microscopy. J Mol Biol 2021; 433:167322. [PMID: 34688687 PMCID: PMC8627483 DOI: 10.1016/j.jmb.2021.167322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022]
Abstract
Human mitochondrial Hsp60 (mtHsp60) is a class I chaperonin, 51% identical in sequence to the prototypical E. coli chaperonin GroEL. mtHsp60 maintains the proteome within the mitochondrion and is associated with various neurodegenerative diseases and cancers. The oligomeric assembly of mtHsp60 into heptameric ring structures that enclose a folding chamber only occurs upon addition of ATP and is significantly more labile than that of GroEL, where the only oligomeric species is a tetradecamer. The lability of the mtHsp60 heptamer provides an opportunity to detect and visualize lower-order oligomeric states that may represent intermediates along the assembly/disassembly pathway. Using cryo-electron microscopy we show that, in addition to the fully-formed heptamer and an "inverted" tetradecamer in which the two heptamers associate via their apical domains, thereby blocking protein substrate access, well-defined lower-order oligomeric species, populated at less than 6% of the total particles, are observed. Specifically, we observe open trimers, tetramers, pentamers and hexamers (comprising ∼4% of the total particles) with rigid body rotations from one subunit to the next within ∼1.5-3.5° of that for the heptamer, indicating that these may lie directly on the assembly/disassembly pathway. We also observe a closed-ring hexamer (∼2% of the particles) which may represent an off-pathway species in the assembly/disassembly process in so far that conversion to the mature heptamer would require the closed-ring hexamer to open to accept an additional subunit. Lastly, we observe several classes of tetramers where additional subunits characterized by fuzzy electron density are caught in the act of oligomer extension.
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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, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, and National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Computational Biomolecular Nuclear Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - G Marius Clore
- 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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Panina IS, Mamchur AA, Yaroshevich IA, Zlenko DV, Pichkur EB, Kudryavtseva SS, Muronetz VI, Sokolova OS, Stanishneva-Konovalova TB. Study of GroEL Conformational Mobility by Cryo-Electron Microscopy and Molecular Dynamics. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL apo-form was obtained by cryo-electron microscopy (cryo-EM) with a resolution of 3.02 Å and supplemented by molecular dynamics (MD) calculations. The results of cryo-EM and MD are in good agreement and demonstrate a diverse mobility of the protein subunit domains. The MD results predict the dynamics and the network of intramolecular contacts of the C-terminal sections of the protein. These results are of great importance for the subsequent study of the mechanism of protein folding in the GroEL cavity.
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Novel cryo-EM structure of an ADP-bound GroEL-GroES complex. Sci Rep 2021; 11:18241. [PMID: 34521893 PMCID: PMC8440773 DOI: 10.1038/s41598-021-97657-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/23/2021] [Indexed: 11/11/2022] Open
Abstract
The GroEL–GroES chaperonin complex is a bacterial protein folding system, functioning in an ATP-dependent manner. Upon ATP binding and hydrolysis, it undergoes multiple stages linked to substrate protein binding, folding and release. Structural methods helped to reveal several conformational states and provide more information about the chaperonin functional cycle. Here, using cryo-EM we resolved two nucleotide-bound structures of the bullet-shaped GroEL–GroES1 complex at 3.4 Å resolution. The main difference between them is the relative orientation of their apical domains. Both structures contain nucleotides in cis and trans GroEL rings; in contrast to previously reported bullet-shaped complexes where nucleotides were only present in the cis ring. Our results suggest that the bound nucleotides correspond to ADP, and that such a state appears at low ATP:ADP ratios.
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Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin. Nat Commun 2020; 11:1916. [PMID: 32317635 PMCID: PMC7174398 DOI: 10.1038/s41467-020-15698-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF3-bound) ground-state mimic double-ring mHsp6014-(mHsp107)2 football complex, and the cryo-EM structures of the ADP-bound successor mHsp6014-(mHsp107)2 complex, and a single-ring mHsp607-mHsp107 half-football. The structures explain the nucleotide dependence of mHsp60 ring formation, and reveal an inter-ring nucleotide symmetry consistent with the absence of negative cooperativity. In the ground-state a two-fold symmetric H-bond and a salt bridge stitch the double-rings together, whereas only the H-bond remains as the equatorial gap increases in an ADP football poised to split into half-footballs. Refolding assays demonstrate obligate single- and double-ring mHsp60 variants are active, and complementation analysis in bacteria shows the single-ring variant is as efficient as wild-type mHsp60. Our work provides a structural basis for active single- and double-ring complexes coexisting in the mHsp60-mHsp10 chaperonin reaction cycle.
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Lorimer GH, Horovitz A, McLeish T. Allostery and molecular machines. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0173. [PMID: 29735727 DOI: 10.1098/rstb.2017.0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 27042, USA
| | - Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom McLeish
- Department of Physics, University of York, Heslington, York YO10 5DD, UK
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Conway de Macario E, Yohda M, Macario AJL, Robb FT. Bridging human chaperonopathies and microbial chaperonins. Commun Biol 2019; 2:103. [PMID: 30911678 PMCID: PMC6420498 DOI: 10.1038/s42003-019-0318-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022] Open
Abstract
Chaperonins are molecular chaperones that play critical physiological roles, but they can be pathogenic. Malfunctional chaperonins cause chaperonopathies of great interest within various medical specialties. Although the clinical-genetic aspects of many chaperonopathies are known, the molecular mechanisms causing chaperonin failure and tissue lesions are poorly understood. Progress is necessary to improve treatment, and experimental models that mimic the human situation provide a promising solution. We present two models: one prokaryotic (the archaeon Pyrococcus furiosus) with eukaryotic-like chaperonins and one eukaryotic (Chaetomium thermophilum), both convenient for isolation-study of chaperonins, and report illustrative results pertaining to a pathogenic mutation of CCT5.
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Affiliation(s)
- Everly Conway de Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo Japan
| | - Alberto J. L. Macario
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Frank T. Robb
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Columbus Center, Baltimore, MD USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD USA
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