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Jia M, Wu B, Yang Z, Chen C, Zhao M, Hou X, Niu X, Jin C, Hu Y. Conformational Dynamics of the Periplasmic Chaperone SurA. Biochemistry 2020; 59:3235-3246. [PMID: 32786408 DOI: 10.1021/acs.biochem.0c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The periplasmic protein SurA is the primary chaperone involved in the biogenesis of bacterial outer membrane proteins and is a potential antibacterial drug target. The three-dimensional structure of SurA can be divided into three parts, a core module formed by the N- and C-terminal regions and two peptidyl-prolyl isomerase (PPIase) domains, P1 and P2. Despite the determination of the structures of several SurA-peptide complexes, the functional mechanism of this chaperone remains elusive and the roles of the two PPIase domains are yet unclear. Herein, we characterize the conformational dynamics of SurA by using solution nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer methods. We demonstrate a "closed-to-open" structural transition of the P1 domain that is correlated with both chaperone activity and peptide binding and show that the flexible P2 domain can also occupy conformations that closely contact the NC core module. Our results offer a structural basis for the counteracting roles of the two PPIase domains in regulating the SurA chaperone activity.
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Affiliation(s)
- Moye Jia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Wu
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianhui Hou
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Li G, He C, Bu P, Bi H, Pan S, Sun R, Zhao XS. Single-Molecule Detection Reveals Different Roles of Skp and SurA as Chaperones. ACS Chem Biol 2018. [PMID: 29543429 DOI: 10.1021/acschembio.8b00097] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Skp and SurA are both periplasmic chaperones involved in the biogenesis of Escherichia coli β-barrel outer membrane proteins (OMPs). It is commonly assumed that SurA plays a major role whereas Skp is a minor factor. However, there is no molecular evidence for whether their roles are redundant. Here, by using different dilution methods, we obtained monodisperse and aggregated forms of OmpC and studied their interactions with Skp and SurA by single-molecule fluorescence resonance energy transfer and fluorescence correlation spectroscopy. We found that Skp can dissolve aggregated OmpC while SurA cannot convert aggregated OmpC into the monodisperse form and the conformations of OmpC recognized by the two chaperones as well as their stoichiometries of binding are different. Our study demonstrates the functional distinctions between Skp and SurA. In particular, the role of Skp is not redundant and is probably more significant under stress conditions.
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Affiliation(s)
- Geng Li
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Chenhui He
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Peixuan Bu
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Huimin Bi
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Sichen Pan
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Ronghua Sun
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- Department of Chemical Biology, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
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3
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Banerjee PR, Deniz AA. Shedding light on protein folding landscapes by single-molecule fluorescence. Chem Soc Rev 2014; 43:1172-88. [PMID: 24336839 DOI: 10.1039/c3cs60311c] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule (SM) fluorescence methods have been increasingly instrumental in our current understanding of a number of key aspects of protein folding and aggregation landscapes over the past decade. With the advantage of a model free approach and the power of probing multiple subpopulations and stochastic dynamics directly in a heterogeneous structural ensemble, SM methods have emerged as a principle technique for studying complex systems such as intrinsically disordered proteins (IDPs), globular proteins in the unfolded basin and during folding, and early steps of protein aggregation in amyloidogenesis. This review highlights the application of these methods in investigating the free energy landscapes, folding properties and dynamics of individual protein molecules and their complexes, with an emphasis on inherently flexible systems such as IDPs.
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Affiliation(s)
- Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
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4
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Spencer D, Bertrand GME, Stites WE. The pH dependence of staphylococcal nuclease stability is incompatible with a three-state denaturation model. Biophys Chem 2013; 180-181:86-94. [PMID: 23892194 DOI: 10.1016/j.bpc.2013.06.018] [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] [Received: 04/26/2013] [Revised: 06/14/2013] [Accepted: 06/22/2013] [Indexed: 11/24/2022]
Abstract
Six single substitution mutations, V66F, V66G, V66N, V66Q, V66S, V66T, and V66Y, were made in the background of a highly stable triple mutant (P117G, H124L, and S128A) of staphylococcal nuclease. The thermodynamic stabilities of wild type staphylococcal nuclease, of the stable triple mutant and of its six variants were determined by guanidine hydrochloride denaturation in thirteen different buffers spanning the pH range 4.5 to 10.2. Within experimental error the values of [Formula: see text] and mGuHCl for the various proteins measured over this wide range of pH maintain a constant offset from one another, tracing a series of approximately parallel curves. This data offers an independent means of determining the error of stabilities and slopes determined by guanidine hydrochloride denaturations and shows that previous error estimates are accurate. More importantly, this behavior cannot be reconciled with a three-state denaturation model for staphylococcal nuclease. The large variations in mGuHCl observed in these mutants must therefore arise from other causes.
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Affiliation(s)
- Daniel Spencer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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5
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Wang P, Yang L, Liu P, Gao YQ, Zhao XS. Single-molecule detection reveals knot sliding in TrmD denaturation. Chemistry 2013; 19:5909-16. [PMID: 23512842 DOI: 10.1002/chem.201203809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Indexed: 01/06/2023]
Abstract
An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein-folding process is available. Herein, by combining single-molecule fluorescence resonance energy transfer (smFRET) experiments with molecular dynamics (MD) simulations, we performed a detailed study to characterize the knot in the denatured state of TrmD, a knotted tRNA (guanosine-1) methyltransferase from Escherichia coli, as a model system. We found that the knot still existed in the unfolded state of TrmD, consistent with the results for two other knotted proteins, YibK and YbeA. More interestingly, both smFRET experiments and MD simulations revealed that the knot slid towards the C-terminal during the unfolding process, which could be explained by the relatively strong interactions between the β-sheet core at the N terminal of the native knot region. The size of the knot in the unfolded state is not larger than that in the native state. In addition, the knot slid in a "downhill" mode with simultaneous chain collapse in the denatured state.
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Affiliation(s)
- Peng Wang
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, PR China
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6
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Ge J, Liu Z, Zhao XS. Cocaine Detection in Blood Serum Using Aptamer Biosensor on Gold Nanoparticles and Progressive Dilution. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2011; 22:14-20. [PMID: 22104965 DOI: 10.1016/j.sbi.2011.10.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/25/2022]
Abstract
Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.
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Affiliation(s)
- Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
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8
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Zhi Z, Liu P, Wang P, Huang Y, Zhao XS. Domain-Specific Folding Kinetics of Staphylococcal Nuclease Observed through Single-Molecule FRET in a Microfluidic Mixer. Chemphyschem 2011; 12:3515-8. [DOI: 10.1002/cphc.201100652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/17/2011] [Indexed: 11/07/2022]
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9
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Li X, Zhu R, Yu A, Zhao XS. Ultrafast Photoinduced Electron Transfer between Tetramethylrhodamine and Guanosine in Aqueous Solution. J Phys Chem B 2011; 115:6265-71. [DOI: 10.1021/jp200455b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xun Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, People's Republic of China
| | - Ruixue Zhu
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Republic of China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, People's Republic of China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871, People's Republic of China
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10
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Ferreon ACM, Deniz AA. Protein folding at single-molecule resolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1021-9. [PMID: 21303706 DOI: 10.1016/j.bbapap.2011.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/22/2011] [Accepted: 01/25/2011] [Indexed: 12/15/2022]
Abstract
The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Allan Chris M Ferreon
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines MB-19, La Jolla, CA 92037, USA
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11
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Qu P, Yang X, Li X, Zhou X, Zhao XS. Direct measurement of the rates and barriers on forward and reverse diffusions of intramolecular collision in overhang oligonucleotides. J Phys Chem B 2010; 114:8235-43. [PMID: 20504003 DOI: 10.1021/jp101173y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of end-to-interior (Type I) and end-to-end (Type II) collisions in a dangling overhang anchored on a double-stranded DNA (dsDNA) was studied by monitoring the fluorescence quenching of tetramethylrhodamine (TMR) by guanosine residues through combining photoinduced electron transfer (PET) with fluorescence correlation spectroscopy (FCS) at different temperatures. TMR and guanosine residues are separated by a double helix with dangling bases ranging from 2 to 16. By analyzing the FCS data, we obtained the forward and reverse intrachain diffusion rate constants and respective barriers. For both Type I and Type II collisions, the intrachain diffusion rates followed the scaling law of the Gaussian chain model. Especially, the reverse intrachain diffusion rate was insensitive to the base length of separation. Both the activation enthalpy and activation entropy of the forward and reverse diffusions were length independent. The comparison between Type I and Type II collisions shows that the collision rate of end-to-interior is slower than that of end-to-end. The phenomenon is further checked in detail by a series of dangling DNA with the same separation length but different tail lengths (Type III).
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Affiliation(s)
- Peng Qu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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12
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Pugh SD, Gell C, Smith DA, Radford SE, Brockwell DJ. Single-molecule studies of the Im7 folding landscape. J Mol Biol 2010; 398:132-45. [PMID: 20211187 PMCID: PMC2855442 DOI: 10.1016/j.jmb.2010.02.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 02/20/2010] [Accepted: 02/26/2010] [Indexed: 11/29/2022]
Abstract
Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted Ieqm) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the Ieqm variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na2SO4 in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding.
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Affiliation(s)
- Sara D Pugh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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