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Chen J, Zhang Q, Ren W, Li W. Piecing Together the Allosteric Patterns of Chaperonin GroEL. J Phys Chem B 2017; 121:4987-4996. [PMID: 28430446 DOI: 10.1021/acs.jpcb.7b01992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable efforts, elucidating the allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy, and molecular simulations to characterize allosteric patterns of chaperonin GroEL, an ∼800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage. This comprehensive analysis gives a refined resolution down to five residues to pilot the GroEL allosteric determinants, of which the localized dynamics is monitored by tryptophan-mutated GroEL. Furthermore, the GroEL conformational transition is evaluated by molecular dynamics simulations with an atomic-interaction-based coarse-grained model. Collectively, we provide a practical methodology to analyze GroEL allostery in solution.
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Affiliation(s)
- Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences , Okazaki 444-8787, Japan
| | - Qian Zhang
- Department of Chemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Weitong Ren
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
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Chen J, Yagi H, Furutani Y, Nakamura T, Inaguma A, Guo H, Kong Y, Goto Y. Self-assembly of the chaperonin GroEL nanocage induced at submicellar detergent. Sci Rep 2014; 4:5614. [PMID: 25000956 PMCID: PMC4085630 DOI: 10.1038/srep05614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 06/18/2014] [Indexed: 01/08/2023] Open
Abstract
Protein nanoassemblies possess unique advantage in biomedical applications such as drug delivery, biocatalysis and vaccine development. Despite recent accomplishment in atomic structure data, the underlying molecular mechanism of protein self-assembly remains elusive, where considerable heterogeneity is often involved. Here we use E. coli chaperonin GroEL, a tetradecameric protein with a molecular weight of 805 kDa, to probe its transformation from cage-like oligomers to protein nanofibers. We show that sodium dodecyl sulfate (SDS), a widely-used protein denaturant, at submicellar concentration binds to and causes partial distortion of GroEL apical domain. Subsequently, the GroEL apical domain with altered secondary structural content converts the GroEL oligomers into modular structural units which are observed to self-assemble into cylindrical nanofibers under an agitated incubation in a physiological buffer. Interestingly, through targeted mutagenesis where two cysteine residues are introduced at the entry site of GroEL cage, we found that the formation of GroEL nanoassembly could be modulated depending on the redox condition of incubation. Without the need of chemical engineering, tunable GroEL nanofibers built by controlled-assembly are among the largest nanoscale bioassembly with broad applications.
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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
- These authors contributed equally to this work
| | - Hisashi Yagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- These authors contributed equally to this work
- Current address: Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-minami, Tottori 680-8552 and Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-minami, Tottori 680-8552
| | - Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), Myodaiji, Okazaki 444-8585, Japan
| | - Takashi Nakamura
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Asumi Inaguma
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Hao Guo
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), Myodaiji, Okazaki 444-8585, Japan
| | - Yan Kong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009, China
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Romasanta PN, Curto LM, Urtasun N, Sarratea MB, Chiappini S, Miranda MV, Delfino JM, Mariuzza RA, Fernández MM, Malchiodi EL. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies. J Biol Chem 2013; 289:5083-96. [PMID: 24379405 DOI: 10.1074/jbc.m113.532929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Natural killer (NK) cells discriminate between healthy and virally infected or transformed cells using diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 NK receptors, which can adopt two distinct conformations (backfolded and extended), are of particular importance for detecting cells infected with mouse cytomegalovirus (CMV) via recognition of the viral immunoevasin m157. The interaction of m157 with activating (Ly49H) and inhibitory (Ly49I) receptors governs the spread of mouse CMV. We carried out kinetic and thermodynamic experiments to elucidate the Ly49/m157 binding mechanism. Combining surface plasmon resonance, fluorescence anisotropy, and circular dichroism (CD), we determined that the best model to describe both the Ly49H/m157 and Ly49I/m157 interactions is a conformational selection mechanism where only the extended conformation of Ly49 (Ly49*) is able to bind the first m157 ligand followed by binding of the Ly49*/m157 complex to the second m157. The interaction is characterized by strong positive cooperativity such that the second m157 binds the Ly49 homodimer with a 1000-fold higher sequential constant than the first m157 (∼10(8) versus ∼10(5) M(-1)). Using far-UV CD, we obtained evidence for a conformational change in Ly49 upon binding m157 that could explain the positive cooperativity. The rate-limiting step of the overall mechanism is a conformational transition in Ly49 from its backfolded to extended form. The global thermodynamic parameters from the initial state (backfolded Ly49 and m157) to the final state (Ly49*/(m157)2) are characterized by an unfavorable enthalpy that is compensated by a favorable entropy, making the interaction spontaneous.
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Affiliation(s)
- Pablo N Romasanta
- From the Cátedra de Inmunología and Instituto de Estudios de la Inmunidad Humoral (IDEHU), Consejo Nacional de Investigaciones Científicas y técnicas - Universidad de Buenos Aires (CONICET-UBA) and
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Dissection of the ATP-dependent conformational change cycle of a group II chaperonin. J Mol Biol 2013; 426:447-59. [PMID: 24120682 DOI: 10.1016/j.jmb.2013.09.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 09/15/2013] [Accepted: 09/25/2013] [Indexed: 11/21/2022]
Abstract
Group II chaperonin captures an unfolded protein while in its open conformation and then mediates the folding of the protein during ATP-driven conformational change cycle. In this study, we performed kinetic analyses of the group II chaperonin from a hyperthermophilic archaeon, Thermococcus sp. KS-1 (TKS1-Cpn), by stopped-flow fluorometry and stopped-flow small-angle X-ray scattering to reveal the reaction cycle. Two TKS1-Cpn variants containing a Trp residue at position 265 or position 56 exhibit nearly the same fluorescence kinetics induced by rapid mixing with ATP. Fluorescence started to increase immediately after the start of mixing and reached a maximum at 1-2s after mixing. Only in the presence of K(+) that a gradual decrease in fluorescence was observed after the initial peak. Similar results were obtained by stopped-flow small-angle X-ray scattering. A rapid fluorescence increase, which reflects nucleotide binding, was observed for the mutant containing a Trp residue near the ATP binding site (K485W), irrespective of the presence or absence of K(+). Without K(+), a small, rapid fluorescence decrease followed the initial increase, and then a gradual decrease was observed. In contrast, with K(+), a large, rapid fluorescence decrease occurred just after the initial increase, and then the fluorescence gradually increased. Finally, we observed ATP binding signal and also subtle conformational change in an ATPase-deficient mutant with K485W mutation. Based on these results, we propose a reaction cycle model for group II chaperonins.
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Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K. The H/D-exchange kinetics of the Escherichia coli co-chaperonin GroES studied by 2D NMR and DMSO-quenched exchange methods. J Mol Biol 2013; 425:2541-60. [PMID: 23583779 DOI: 10.1016/j.jmb.2013.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022]
Abstract
We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N transverse-optimized NMR spectroscopy and (2) the dimethylsulfoxide-quenched hydrogen-exchange method combined with conventional (1)H-(15)N heteronuclear single quantum coherence spectroscopy. By using these techniques together with direct heteronuclear single quantum coherence experiments, we quantitatively evaluated the exchange rates for 33 out of the 94 peptide amide protons of GroES and their protection factors, and for the remaining 61 residues, we obtained the lower limits of the exchange rates. The protection factors of the most highly protected amide protons were on the order of 10(6)-10(7), and the values were comparable in magnitude to those observed in typical small globular proteins, but the number of the highly protected amide protons with a protection factor larger than 10(6) was only 10, significantly smaller than the numbers reported for the small globular proteins, indicating that significant portions of free heptameric GroES are flexible and natively unfolded. The highly protected amino acid residues with a protection factor larger than 10(5) were mainly located in three β-strands that form the hydrophobic core of GroES, while the residues in a mobile loop (residues 17-34) were not highly protected. The protection factors of the most highly protected amide protons were orders of magnitude larger than the value expected from the equilibrium unfolding parameters previously reported, strongly suggesting that the equilibrium unfolding of GroES is more complicated than a simple two-state or three-state mechanism and may involve more than a single intermediate.
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Affiliation(s)
- Mahesh S Chandak
- 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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Zhang Q, Chen J, Kuwajima K, Zhang HM, Xian F, Young NL, Marshall AG. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry. Sci Rep 2013; 3:1247. [PMID: 23409238 PMCID: PMC3570780 DOI: 10.1038/srep01247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/06/2012] [Indexed: 11/29/2022] Open
Abstract
Here we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) to access E. coli chaperonin GroEL conformation. The ~800 kDa tetradecameric GroEL plays an essential role in the proper folding of many proteins. Previous studies of the structural dynamics of GroEL upon ATP binding have been inconsistent, showing either minimal or major allosteric changes. Our results, based on the native, non-mutated, protein under physiological conditions in solution demonstrate substantial changes in conformation and/or flexibility upon ATP binding. We capture the pivotal step in its functional cycle by use of a non-hydrolyzable ATP analog, ATPγS, to mimic the ATP-bound GroEL state. Comparison of HDX-MS results for apo GroEL and GroEL-ATPγS enables the characterization of the nucleotide-regulated conformational changes throughout the entire protein with high sequence resolution. The 14-mer GroEL complex is the largest protein assembly yet accessed by HDX-MS, with sequence resolution of segments of as few as five amino acids.
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Affiliation(s)
- Qian Zhang
- Florida State University, Department of Chemistry, Tallahassee, FL 32306, USA
- These authors contributed equally to this work
| | - 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
- These authors contributed equally to this work
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (Sokendai), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Hui-Min Zhang
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Feng Xian
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Nicolas L. Young
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Alan G. Marshall
- Florida State University, Department of Chemistry, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
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Chen J, Yagi H, Sormanni P, Vendruscolo M, Makabe K, Nakamura T, Goto Y, Kuwajima K. Fibrillogenic propensity of the GroEL apical domain: a Janus-faced minichaperone. FEBS Lett 2012; 586:1120-7. [PMID: 22575645 DOI: 10.1016/j.febslet.2012.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/21/2012] [Accepted: 03/09/2012] [Indexed: 11/19/2022]
Abstract
The chaperonin GroEL plays an essential role in promoting protein folding and in protecting against misfolding and aggregation in the cellular environment. In this study, we report that both GroEL and its isolated apical domain form amyloid-like fibrils under physiological conditions, and that the fibrillation of the apical domain is accelerated under acidic conditions. We also found, however, that despite its fibrillation propensity, the apical domain exhibits a pronounced inhibitory effect on the fibril growth of β(2)-microglobulin. Thus, the analysis of the behaviour of the apical domain reveals how aggregation and chaperone-mediated anti-aggregation processes can be closely related.
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Affiliation(s)
- Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan.
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Kiselev GG, Naletova IN, Sheval EV, Stroylova YY, Schmalhausen EV, Haertlé T, Muronetz VI. Chaperonins induce an amyloid-like transformation of ovine prion protein: The fundamental difference in action between eukaryotic TRiC and bacterial GroEL. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1730-8. [DOI: 10.1016/j.bbapap.2011.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 01/15/2023]
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