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Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S. The dynamic dimer structure of the chaperone Trigger Factor. Nat Commun 2017; 8:1992. [PMID: 29222465 PMCID: PMC5722895 DOI: 10.1038/s41467-017-02196-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/12/2017] [Indexed: 11/09/2022] Open
Abstract
The chaperone Trigger Factor (TF) from Escherichia coli forms a dimer at cellular concentrations. While the monomer structure of TF is well known, the spatial arrangement of this dimeric chaperone storage form has remained unclear. Here, we determine its structure by a combination of high-resolution NMR spectroscopy and biophysical methods. TF forms a symmetric head-to-tail dimer, where the ribosome binding domain is in contact with the substrate binding domain, while the peptidyl-prolyl isomerase domain contributes only slightly to the dimer affinity. The dimer structure is highly dynamic, with the two ribosome binding domains populating a conformational ensemble in the center. These dynamics result from intermolecular in trans interactions of the TF client-binding site with the ribosome binding domain, which is conformationally frustrated in the absence of the ribosome. The avidity in the dimer structure explains how the dimeric state of TF can be monomerized also by weakly interacting clients.
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Affiliation(s)
- Leonor Morgado
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Department of Chemistry and Molecular Biology, Wallenberg Centre of Molecular and Translational Medicine, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Timothy Sharpe
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Adam Mazur
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.
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Zhuravleva A, Korzhnev DM. Protein folding by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:52-77. [PMID: 28552172 DOI: 10.1016/j.pnmrs.2016.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 06/07/2023]
Abstract
Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these nonnative states may also serve as precursors for protein misfolding and aggregation associated with a range of devastating diseases, including neuro-degeneration, diabetes and cancer. Therefore, in vivo protein folding is often reshaped co- and post-translationally through interactions with the ribosome, molecular chaperones and/or other cellular components. Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes in vitro and in vivo. NMR relaxation dispersion and saturation transfer methods provide the means for a detailed characterization of protein folding kinetics and thermodynamics under native-like conditions, as well as modeling high-resolution structures of weakly populated short-lived conformational states on the protein folding energy landscape. Continuing development of isotope labeling strategies and NMR methods to probe high molecular weight protein assemblies, along with advances of in-cell NMR, have recently allowed protein folding to be studied in the context of ribosome-nascent chain complexes and molecular chaperones, and even inside living cells. Here we review solution NMR approaches to investigate the protein folding energy landscape, and discuss selected applications of NMR methodology to studying protein folding in vitro and in vivo. Together, these examples highlight a vast potential of solution NMR in providing atomistic insights into molecular mechanisms of protein folding and homeostasis in health and disease.
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Affiliation(s)
- Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology and Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA.
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Huang CT, Hsu STD. NMR assignments of the peptidyl-prolyl cis-trans isomerase domain of trigger factor from E. coli. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:149-152. [PMID: 26527152 DOI: 10.1007/s12104-015-9655-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Trigger factor (TF) is a highly conserved multi-domain molecular chaperone in bacteria. It binds via its ribosome binding domain (RBD) to the ribosomal tunnel exit and facilitates co-translational folding of a broad range of protein substrates primarily through interactions with the substrate binding domain (SBD) adjacent to the RBD. Within the SBD, a peptidyl-prolyl cis-trans isomerase (PPIase) domain is inserted leading to an unusual domain insertion, which may provide stabilizing effect to the highly plastic SBD. Here we report the near complete NMR assignments of TF PPIase providing the basis for subsequent structural and folding in the context of the chaperone activity of TF.
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Affiliation(s)
- Chih-Ting Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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Liu CHG, Chien CTH, Lin CH, Hsu STD. NMR assignments of the C-terminal domain of human galectin-8. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:427-430. [PMID: 26126590 DOI: 10.1007/s12104-015-9623-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Galectins recognize β-galectosides to promote a variety of cellular functions. Despite their sequence variations, all galectins share the same carbohydrate recognition domains (CRD) and their modes of ligand recognition at a structural level are essentially identical. Human galectin 8 plays an important role in numerous cancer and immune responses. It consists of two CRDs that are connected via a flexible linker. The substrate affinities and specificities of the N- and C-terminal domains are quite different. In order to investigate the structural basis of their substrate specificities, we complete the NMR (1)H, (13)C, and (15)N chemical shift assignments of C-terminal domain of human galectin-8 (hG8C).
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Affiliation(s)
- Chun-Hao Gerard Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Institue of Bioinformatics and Structural Biology, National Tsin Hua University, Hsinchu, 30013, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Chih-Ta Henry Chien
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei, 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Science, National Taiwan University, Taipei, 106, Taiwan.
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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Barbet-Massin E, Huang CT, Daebel V, Hsu STD, Reif B. Ortsaufgelöste Festkörper-NMR-Studien am “Trigger-Faktor” im Komplex mit der großen ribosomalen 50S-Untereinheit. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Barbet-Massin E, Huang CT, Daebel V, Hsu STD, Reif B. Site-Specific Solid-State NMR Studies of “Trigger Factor” in Complex with the Large Ribosomal Subunit 50S. Angew Chem Int Ed Engl 2015; 54:4367-9. [DOI: 10.1002/anie.201409393] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/09/2015] [Indexed: 02/01/2023]
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Chien CTH, Wang LW, Liu YN, Hsu BD, Lyu PC, Hsu STD. NMR assignments of a hypothetical pseudo-knotted protein HP0242 from Helicobacter pylori. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:287-289. [PMID: 23824732 DOI: 10.1007/s12104-013-9502-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Many knotted proteins have been discovered recently, but the folding process of which remains elusive. HP0242 is a hypothetical protein from Helicobacter pylori, which is a model system for studying the folding pathway of a knotted protein. In this study, we report the (1)H, (13)C, and (15)N chemical shift assignments of HP0242. The results will enable us to further investigate HP0242 by NMR experiments.
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Saio T, Guan X, Rossi P, Economou A, Kalodimos CG. Structural basis for protein antiaggregation activity of the trigger factor chaperone. Science 2014; 344:1250494. [PMID: 24812405 DOI: 10.1126/science.1250494] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular chaperones prevent aggregation and misfolding of proteins, but scarcity of structural data has impeded an understanding of the recognition and antiaggregation mechanisms. We report the solution structure, dynamics, and energetics of three trigger factor (TF) chaperone molecules in complex with alkaline phosphatase (PhoA) captured in the unfolded state. Our data show that TF uses multiple sites to bind to several regions of the PhoA substrate protein primarily through hydrophobic contacts. Nuclear magnetic resonance (NMR) relaxation experiments show that TF interacts with PhoA in a highly dynamic fashion, but as the number and length of the PhoA regions engaged by TF increase, a more stable complex gradually emerges. Multivalent binding keeps the substrate protein in an extended, unfolded conformation. The results show how molecular chaperones recognize unfolded polypeptides and, by acting as unfoldases and holdases, prevent the aggregation and premature (mis)folding of unfolded proteins.
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Affiliation(s)
- Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
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Fusco G, De Simone A, Hsu STD, Bemporad F, Vendruscolo M, Chiti F, Dobson CM. ¹H, ¹³C and ¹⁵N resonance assignments of human muscle acylphosphatase. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:27-9. [PMID: 21643968 DOI: 10.1007/s12104-011-9318-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
Human muscle acylphosphatase (mAcP) is an enzyme with a ferrodoxin-like topology whose primary role is to hydrolyze the carboxyl-phosphate bonds of acylphosphates. The protein has been widely used as a model system for elucidating the molecular determinants of protein folding and misfolding. We present here the full NMR assignments of the backbone and side chains resonances of mAcP complexed with phosphate, thus providing an important resource for future solution-state NMR spectroscopic studies of the structure and dynamics of this protein in the contexts of protein folding and misfolding.
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Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK
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Andersson FI, Jackson SE, Hsu STD. Backbone assignments of the 26 kDa neuron-specific ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1). BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:41-43. [PMID: 20012716 DOI: 10.1007/s12104-009-9203-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 12/02/2009] [Indexed: 05/28/2023]
Abstract
UCH-L1 is a member of the family of ubiquitin C-terminal hydrolases whose primary role is to hydrolyze small C-terminal adducts of ubiquitin to generate free ubiquitin monomers. Expression of UCH-L1 is highly specific to neurons and point mutations in this enzyme are associated with a hereditary form of Parkinson's disease. Herein, we present the NMR backbone assignments of human UCH-L1, thus enabling future solution-state NMR spectroscopic studies on the structure and function of this important protein.
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Affiliation(s)
- Fredrik I Andersson
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
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