1
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NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophys Rev 2019; 12:155-174. [PMID: 31838649 DOI: 10.1007/s12551-019-00609-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
Allostery is a ubiquitous biological mechanism in which a distant binding site is coupled to and drastically alters the function of a catalytic site in a protein. Allostery provides a high level of spatial and temporal control of the integrity and activity of biomolecular assembles composed of proteins, nucleic acids, or small molecules. Understanding the physical forces that drive allosteric coupling is critical to harnessing this process for use in bioengineering, de novo protein design, and drug discovery. Current microscopic models of allostery highlight the importance of energetics, structural rearrangements, and conformational fluctuations, and in this review, we discuss the synergistic use of solution NMR spectroscopy and computational methods to probe these phenomena in allosteric systems, particularly protein-nucleic acid complexes. This combination of experimental and theoretical techniques facilitates an unparalleled detection of subtle changes to structural and dynamic equilibria in biomolecules with atomic resolution, and we provide a detailed discussion of specialized NMR experiments as well as the complementary methods that provide valuable insight into allosteric pathways in silico. Lastly, we highlight two case studies to demonstrate the adaptability of this approach to enzymes of varying size and mechanistic complexity.
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2
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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3
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Xie S, Wen K, Peng T, Wang J, Yao K, Jiang H. A novel variable antibody fragment dimerized by the dHLX peptide with enhanced affinity against amantadine compared to its corresponding scFv antibody. FOOD AGR IMMUNOL 2017. [DOI: 10.1080/09540105.2017.1368459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sanlei Xie
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Tao Peng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianyi Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Yao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Haiyang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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4
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Anderson JS, Hernández G, LeMaster DM. Prediction of Bond Vector Autocorrelation Functions from Larmor Frequency-Selective Order Parameter Analysis of NMR Relaxation Data. J Chem Theory Comput 2017; 13:3276-3289. [DOI: 10.1021/acs.jctc.7b00387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Janet S. Anderson
- Department
of Chemistry, Union College, Schenectady, New York 12308, United States
| | - Griselda Hernández
- Wadsworth
Center, New York State Department of Health and Department of Biomedical
Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York 12201, United States
| | - David M. LeMaster
- Wadsworth
Center, New York State Department of Health and Department of Biomedical
Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York 12201, United States
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5
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Rennella E, Sekhar A, Kay LE. Self-Assembly of Human Profilin-1 Detected by Carr-Purcell-Meiboom-Gill Nuclear Magnetic Resonance (CPMG NMR) Spectroscopy. Biochemistry 2017; 56:692-703. [PMID: 28052669 DOI: 10.1021/acs.biochem.6b01263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein oligomerization in the cell has important implications for both health and disease, and an understanding of the mechanisms by which proteins can self-associate is, therefore, of critical interest. Initial stages of the oligomerization process can be hard to detect, as they often involve the formation of sparsely populated and transient states that are difficult to characterize by standard biophysical approaches. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we study the oligomerization of human profilin-1, a protein that regulates the polymerization of actin. We show that in solution and at millimolar concentrations profilin-1 is predominantly monomeric. However, fits of concentration-dependent relaxation data are consistent with the formation of a higher-order oligomer that is generated via a multistep process. Together with crystallographic data for profilin-2, a homologue of the protein studied here, our results suggest that profilin-1 forms a sparsely populated tetrameric conformer in solution.
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Affiliation(s)
- Enrico Rennella
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto , Toronto, Ontario M5S 1A8, Canada.,Program in Molecular Structure and Function, Hospital for Sick Children , 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
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6
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Abstract
Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following Review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery.
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Affiliation(s)
- George P. Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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7
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Khan SN, Charlier C, Augustyniak R, Salvi N, Déjean V, Bodenhausen G, Lequin O, Pelupessy P, Ferrage F. Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation. Biophys J 2016; 109:988-99. [PMID: 26331256 PMCID: PMC4564687 DOI: 10.1016/j.bpj.2015.06.069] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach.
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Affiliation(s)
- Shahid N Khan
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Cyril Charlier
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Rafal Augustyniak
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Nicola Salvi
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Victoire Déjean
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Geoffrey Bodenhausen
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France; Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, BCH, Lausanne, Switzerland
| | - Olivier Lequin
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Philippe Pelupessy
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France
| | - Fabien Ferrage
- Département de Chimie, École Normale Supérieure-PSL Research University, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, LBM, Paris, France; Centre National de la Recherche Scientifique, UMR 7203 LBM, Paris, France.
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8
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Kadeřávek P, Zapletal V, Fiala R, Srb P, Padrta P, Přecechtělová JP, Šoltésová M, Kowalewski J, Widmalm G, Chmelík J, Sklenář V, Žídek L. Spectral density mapping at multiple magnetic fields suitable for (13)C NMR relaxation studies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:23-40. [PMID: 27003380 DOI: 10.1016/j.jmr.2016.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 06/05/2023]
Abstract
Standard spectral density mapping protocols, well suited for the analysis of (15)N relaxation rates, introduce significant systematic errors when applied to (13)C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and (13)C frequencies can be obtained from data acquired at three magnetic fields for uniformly (13)C-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.
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Affiliation(s)
- Pavel Kadeřávek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Institute of Biophysics of Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
| | - Radovan Fiala
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
| | - Pavel Srb
- Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
| | - Petr Padrta
- Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
| | | | - Mária Šoltésová
- Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, CZ-180 00 Prague, Czech Republic.
| | - Jozef Kowalewski
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Josef Chmelík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 00 Prague 4 - Krč, Czech Republic.
| | - Vladimír Sklenář
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.
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9
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Lisi GP, Loria JP. Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:1-17. [PMID: 26952190 PMCID: PMC4785347 DOI: 10.1016/j.pnmrs.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 05/04/2023]
Abstract
Conformational motions play an essential role in enzyme function, often facilitating the formation of enzyme-substrate complexes and/or product release. Although considerable debate remains regarding the role of molecular motions in the conversion of enzymatic substrates to products, numerous examples have found motions to be crucial for optimization of enzyme scaffolds, effective substrate binding, and product dissociation. Conformational fluctuations are often rate-limiting to enzyme catalysis, primarily through product release, with the chemical reaction occurring much more quickly. As a result, the direct involvement of motions at various stages along the enzyme reaction coordinate remains largely unknown and untested. In the following review, we describe the use of solution NMR techniques designed to probe various timescales of molecular motions and detail examples in which motions play a role in propagating catalytic effects from the active site and directly participate in essential aspects of enzyme function.
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Affiliation(s)
- George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States.
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10
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Hoang J, Prosser RS. Conformational Selection and Functional Dynamics of Calmodulin: A 19F Nuclear Magnetic Resonance Study. Biochemistry 2014; 53:5727-36. [DOI: 10.1021/bi500679c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua Hoang
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department
of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S
1A8, Canada
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11
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Weininger U, Brath U, Modig K, Teilum K, Akke M. Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection. JOURNAL OF BIOMOLECULAR NMR 2014; 59:23-9. [PMID: 24706175 PMCID: PMC4003406 DOI: 10.1007/s10858-014-9826-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/25/2014] [Indexed: 05/04/2023]
Abstract
Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimization. Using selective excitation and inversion of the narrow component of the (13)C doublet, the experiment achieves significant sensitivity enhancement in terms of both signal intensity and the fractional contribution from exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-selected R 1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor at a temperature of 328 K, where the ring flip is in the fast exchange regime with a mean waiting time between flips of 320 μs. The determined chemical shift difference matches perfectly with that measured from the NMR spectrum at lower temperatures, where separate peaks are observed for the two sites. We further show that potentially complicating effects of strong scalar coupling between protons (Weininger et al. in J Phys Chem B 117: 9241-9247, 2013b) can be accounted for using a simple expression, and provide recommendations for data acquisition when the studied system exhibits this behavior. The present method extends the repertoire of relaxation methods tailored for aromatic side chains by enabling studies of faster processes and improved control over artifacts due to strong coupling.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Ulrika Brath
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
- Present Address: Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Göteborg, Sweden
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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12
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Nováček J, Žídek L, Sklenář V. Toward optimal-resolution NMR of intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:41-52. [PMID: 24656079 DOI: 10.1016/j.jmr.2013.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their important roles in fundamental cellular processes, there is an urgent need to characterize the conformational behavior of IDPs at the highest possible level. The unique feature of NMR spectroscopy in the context of IDPs is its ability to supply details of their structural and temporal alterations at atomic-level resolution. Here, we briefly review recently proposed NMR-based strategies to characterize transient states populated by IDPs and summarize the latest achievements and future prospects in methodological development. Because low chemical shift dispersion represents the major obstacle encountered when studying IDPs by nuclear magnetic resonance, particular attention is paid to techniques allowing one to approach the physical limits of attainable resolution.
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Affiliation(s)
- Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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13
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Weininger U, Blissing AT, Hennig J, Ahlner A, Liu Z, Vogel HJ, Akke M, Lundström P. Protein conformational exchange measured by 1H R1ρ relaxation dispersion of methyl groups. JOURNAL OF BIOMOLECULAR NMR 2013; 57:47-55. [PMID: 23904100 DOI: 10.1007/s10858-013-9764-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/17/2013] [Indexed: 06/02/2023]
Abstract
Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations by NMR relaxation dispersion experiments. Processes at the faster end of this range are more challenging to study, because higher RF field strengths are required to achieve refocusing of the exchanging magnetization. Here we describe a rotating-frame relaxation dispersion experiment for (1)H spins in methyl (13)CHD2 groups, which improves the characterization of fast exchange processes. The influence of (1)H-(1)H rotating-frame nuclear Overhauser effects (ROE) is shown to be negligible, based on a comparison of R 1ρ relaxation data acquired with tilt angles of 90° and 35°, in which the ROE is maximal and minimal, respectively, and on samples containing different (1)H densities surrounding the monitored methyl groups. The method was applied to ubiquitin and the apo form of calmodulin. We find that ubiquitin does not exhibit any (1)H relaxation dispersion of its methyl groups at 10 or 25 °C. By contrast, calmodulin shows significant conformational exchange of the methionine methyl groups in its C-terminal domain, as previously demonstrated by (1)H and (13)C CPMG experiments. The present R 1ρ experiment extends the relaxation dispersion profile towards higher refocusing frequencies, which improves the definition of the exchange correlation time, compared to previous results.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100, Lund, Sweden
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14
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Manley G, Rivalta I, Loria JP. Solution NMR and computational methods for understanding protein allostery. J Phys Chem B 2013; 117:3063-73. [PMID: 23445323 DOI: 10.1021/jp312576v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Allosterism is an essential biological regulatory mechanism. In enzymes, allosteric regulation results in an activation or inhibition of catalytic turnover. The mechanisms by which this is accomplished are unclear and vary significantly depending on the enzyme. It is commonly the case that a metabolite binds to the enzyme at a site distant from the catalytic site, yet its binding is coupled to and sensed by the active site. This coupling can manifest in changes in structure, dynamics, or both at the active site. These interactions between the allosteric and active site, which are often quite distant from one another, involve numerous atoms as well as complex conformational rearrangements of the protein secondary and tertiary structure. Interrogation of this complex biological phenomenon necessitates multiple experimental approaches. In this article, we outline a combined solution NMR spectroscopic and computational approach using molecular dynamics and network models to uncover mechanistic aspects of allostery in the enzyme imidazole glycerol phosphate synthase.
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Affiliation(s)
- Gregory Manley
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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15
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Weininger U, Liu Z, McIntyre DD, Vogel HJ, Akke M. Specific 12CβD(2)12CγD(2)S13CεHD(2) isotopomer labeling of methionine to characterize protein dynamics by 1H and 13C NMR relaxation dispersion. J Am Chem Soc 2012; 134:18562-5. [PMID: 23106551 PMCID: PMC3497853 DOI: 10.1021/ja309294u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Protein dynamics on the micro- to millisecond time scale
is increasingly
found to be critical for biological function, as demonstrated by numerous
NMR relaxation dispersion studies. Methyl groups are excellent probes
of protein interactions and dynamics because of their favorable NMR
relaxation properties, which lead to sharp signals in the 1H and 13C NMR spectra. Out of the six different methyl-bearing
amino acid residue types in proteins, methionine plays a special role
because of its extensive side-chain flexibility and the high polarizability
of the sulfur atom. Methionine is over-represented in many protein–protein
recognition sites, making the methyl group of this residue type an
important probe of the relationships among dynamics, interactions,
and biological function. Here we present a straightforward method
to label methionine residues with specific 13CHD2 methyl isotopomers against a deuterated background. The resulting
protein samples yield NMR spectra with improved sensitivity due to
the essentially 100% population of the desired 13CHD2 methyl isotopomer, which is ideal for 1H and 13C spin relaxation experiments to investigate protein dynamics
in general and conformational exchange in particular. We demonstrate
the approach by measuring 1H and 13C CPMG relaxation
dispersion for the nine methionines in calcium-free calmodulin (apo-CaM).
The results show that the C-terminal domain, but not the N-terminal
domain, of apo-CaM undergoes fast exchange between the ground state
and a high-energy state. Since target proteins are known to bind specifically
to the C-terminal domain of apo-CaM, we speculate that the high-energy
state might be involved in target binding through conformational selection.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, Sweden
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16
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Weininger U, Respondek M, Akke M. Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2012; 54:9-14. [PMID: 22833056 PMCID: PMC3427480 DOI: 10.1007/s10858-012-9656-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 07/12/2012] [Indexed: 05/12/2023]
Abstract
Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Michal Respondek
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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17
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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18
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Otten R, Villali J, Kern D, Mulder FAA. Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r). J Am Chem Soc 2010; 132:17004-14. [PMID: 21058670 PMCID: PMC2991065 DOI: 10.1021/ja107410x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Indexed: 11/29/2022]
Abstract
To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ (1)H Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [(1)H, (13)C]-d-glucose in ∼100% D(2)O, which yields CHD(2) methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using (13)C TOCSY NMR spectroscopy, as was recently demonstrated (Otten, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure (1)H CPMG relaxation dispersion profiles for CHD(2) methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-δ1 and Thr-γ2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong (13)C scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone (15)N CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the (1)H line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 ± 0.5) × 10(3) per second (i.e., τ(ex) = 64.7 ± 1.9 μs). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by (1)H CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone (15)N relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins.
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19
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McNaughton L, Li Z, Van Roey P, Hanes SD, LeMaster DM. Restricted domain mobility in the Candida albicans Ess1 prolyl isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1537-41. [PMID: 20304107 DOI: 10.1016/j.bbapap.2010.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/09/2010] [Accepted: 03/12/2010] [Indexed: 01/08/2023]
Abstract
Ess1 is a peptidyl prolyl cis/trans isomerase that is required for virulence of the pathogenic fungi Candida albicans and Cryptococcus neoformans. The enzyme isomerizes the phospho-Ser-Pro linkages in the C-terminal domain of RNA polymerase II. Its human homolog, Pin1, has been implicated in a wide range of human diseases, including cancer and Alzheimer's disease. Crystallographic and NMR studies have demonstrated that the sequence linking the catalytic isomerase domain and the substrate binding WW domain of Pin1 is unstructured and that the two domains are only loosely associated in the absence of the substrate. In contrast, the crystal structure of C. albicans Ess1 revealed a highly ordered linker that contains a three turn alpha-helix and extensive association between the two tightly juxtaposed domains. In part to address the concern that the marked differences in the domain interactions for the human and fungal structures might reflect crystal lattice effects, NMR chemical shift analysis and 15N relaxation measurements have been employed to confirm that the linker of the fungal protein is highly ordered in solution. With the exception of two loops within the active site of the isomerase domain, the local backbone geometry observed in the crystal structure appears to be well preserved throughout the protein chain. The marked differences in interdomain interactions and linker flexibility between the human and fungal enzymes provide a structural basis for therapeutic targeting of the fungal enzymes.
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Affiliation(s)
- Lynn McNaughton
- Wadsworth Center, New York State Department of Health, School of Public Health, University at Albany, Empire State Plaza, Albany, NY 12201, USA
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20
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Abstract
Molecular dynamics are essential for protein function. In some cases these dynamics involve the interconversion between ground state, highly populated conformers and less populated higher energy structures ('excited states') that play critical roles in biochemical processes. Here we describe recent advances in NMR spectroscopy methods that enable studies of these otherwise invisible excited states at an atomic level and that help elucidate their important relation to function. We discuss a range of examples from molecular recognition, ligand binding, enzyme catalysis and protein folding that illustrate the role that motion plays in 'funneling' conformers along preferred pathways that facilitate their biological function.
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Affiliation(s)
- Andrew J Baldwin
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada
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21
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Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling. J Mol Biol 2009; 396:178-94. [PMID: 19931284 DOI: 10.1016/j.jmb.2009.11.032] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 11/11/2009] [Accepted: 11/12/2009] [Indexed: 11/24/2022]
Abstract
The ubiquitin (Ub)-binding p62 scaffold protein (encoded by the SQSTM1 gene) regulates a diverse range of signalling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors and is an important regulator of macroautophagy. Mutations within the gene encoding p62 are commonly found in patients with Paget's disease of bone and largely cluster within the C-terminal ubiquitin-associated (UBA) domain, impairing its ability to bind Ub, resulting in dysregulated NF-kappaB signalling. However, precisely how Ub-binding is regulated at the molecular level is unclear. NMR relaxation dispersion experiments, coupled with concentration-dependent NMR, CD, isothermal titration calorimetry and fluorescence kinetic measurements, reveal that the p62 UBA domain forms a highly stable dimer (K(dim) approximately 4-12 microM at 298 K). NMR analysis shows that the dimer interface partially occludes the Ub-binding surface, particularly at the C-terminus of helix 3, making UBA dimerisation and Ub-binding mutually exclusive processes. Somewhat unusually, the monomeric UBA appears to be the biologically active form and the dimer appears to be the inactive one. Engineered point mutations in loop 1 (E409K and G410K) are shown to destabilise the dimer interface, lead to a higher proportion of the bound monomer and, in NF-kappaB luciferase reporter assays, are associated with reduced NF-kappaB activity compared with wt-p62.
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22
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Lundström P, Vallurupalli P, Hansen DF, Kay LE. Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy. Nat Protoc 2009; 4:1641-8. [PMID: 19876024 DOI: 10.1038/nprot.2009.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The utility of nuclear magnetic resonance (NMR) spectroscopy as a tool for the study of biomolecular structure and dynamics has benefited from the development of facile labeling methods that incorporate NMR active probes at key positions in the molecule. Here we describe a protocol for the labeling of proteins that facilitates their study using a technique that is sensitive to millisecond conformational exchange processes. The samples necessary for an analysis of exchange dynamics are discussed, using the Abp1p SH3 domain from Saccharomyces cerevisiae as an example. For this system, the time frame for production of each sample, including in vitro refolding, is about 80 h. The samples so produced facilitate the measurement of accurate chemical shifts of low populated, invisible conformers that are part of the exchange pathway. The accuracy of the methodology has been established experimentally and the chemical shifts that are obtained provide important restraints in structure calculations of the excited state.
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Affiliation(s)
- Patrik Lundström
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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23
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O’Connell NE, Grey MJ, Tang Y, Kosuri P, Miloushev VZ, Raleigh DP, Palmer AG. Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2009; 45:85-98. [PMID: 19644656 PMCID: PMC2810208 DOI: 10.1007/s10858-009-9340-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 06/30/2009] [Indexed: 05/12/2023]
Abstract
Identification and characterization of ensembles of intermediate states remains an important objective in describing protein folding in atomic detail. The 67-residue villin headpiece, HP67, consists of an N-terminal subdomain (residues 10-42) that transiently unfolds at equilibrium under native-like conditions and a highly stable C-terminal subdomain (residues 43-76). The transition between folded and unfolded states of the N-terminal domain has been characterized previously by (15)N NMR relaxation dispersion measurements (Grey et al. in J Mol Biol 355:1078, 2006). In the present work, (13)C spin relaxation was used to further characterize backbone and hydrophobic core contributions to the unfolding process. Relaxation of (13)C(alpha) spins was measured using the Hahn echo technique at five static magnetic fields (11.7, 14.1, 16.4, 18.8, and 21.1 T) and the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion method at a static magnetic field of 14.1 T. Relaxation of methyl (13)C spins was measured using CPMG relaxation dispersion experiments at static magnetic fields of 14.1 and 18.8 T. Results for (13)C and (15)N spins yielded a consistent model in which the partially unfolded intermediate state of the N-terminal subdomain maintains residual structure for residues near the unprotonated His41 imidazole ring and in the interface between the N- and C-terminal subdomains. In addition, a second faster process was detected that appears to represent local dynamics within the folded state of the molecule and is largely confined to the hydrophobic interface between the N- and C-terminal subdomains.
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Affiliation(s)
- Nichole E. O’Connell
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Michael J. Grey
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Yuefeng Tang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Pallav Kosuri
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Vesselin Z. Miloushev
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Daniel P. Raleigh
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794
- Address correspondence to: A. G. P.: Voice: (212) 305-8675, Fax: (212) 305-6949, ; D. P. R. Voice: (631) 632-9547,
| | - Arthur G. Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032
- Address correspondence to: A. G. P.: Voice: (212) 305-8675, Fax: (212) 305-6949, ; D. P. R. Voice: (631) 632-9547,
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24
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Picton LK, Casares S, Monahan AC, Majumdar A, Hill RB. Evidence for conformational heterogeneity of fission protein Fis1 from Saccharomyces cerevisiae. Biochemistry 2009; 48:6598-609. [PMID: 19522466 DOI: 10.1021/bi802221h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Fission 1 (Fis1) is an evolutionarily conserved, type II integral membrane protein implicated in maintaining the proper morphology of mitochondria and peroxisomes. A concave surface on the cytosolic domain of Fis1 from Saccharomyces cerevisiae is implicated in binding other fission proteins, yet structural studies reveal that this surface is sterically occluded by its N-terminal arm. Here we address the question of whether the N-terminal arm of yeast Fis1 exists in a dynamic equilibrium that would allow access to this functionally important surface. NMR measurements sensitive to dynamics occurring on a wide range of time scales (picoseconds to minutes) were used to assess whether the Fis1 arm is dynamic. Hydrogen-deuterium exchange experiments revealed that the Fis1 arm, alpha-helix 6, and proximal loops were not protected from solvent exchange, consistent with motions on the second to minute time scale. An engineered cysteine, I85C, located on the concave surface that lies underneath the Fis1 arm, was readily modified by a fluorescent probe, revealing more solvent accessibility of this position than would be predicted from the structure. Chemical denaturation, NMR chemical shift perturbation, and residual dipolar coupling experiments support the idea that the dynamic equilibrium can be shifted on the basis of changing pH and temperature, with the changes primarily localizing to the Fis1 arm and proximal regions. The data as a whole are consistent with the Fis1 arm adopting a primarily "closed" conformational state able to undergo dynamic excursions that reveal the concave surface and therefore may be important for binding other fission factors and for Fis1 function.
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Affiliation(s)
- Lora K Picton
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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25
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Lundström P, Lin H, Kay LE. Measuring 13Cbeta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 44:139-155. [PMID: 19448976 DOI: 10.1007/s10858-009-9321-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/20/2009] [Indexed: 05/26/2023]
Abstract
A labeling scheme is introduced that facilitates the measurement of accurate (13)C(beta) chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of (13)C enrichment (30-40%) at C(beta) side-chain carbon positions for 15 of the amino acids with little (13)C label at positions one bond removed (approximately 5%). A pair of samples are produced using [1-(13)C]-glucose/NaH(12)CO(3) or [2-(13)C]-glucose as carbon sources with isolated and enriched (>30%) (13)C(beta) positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of (13)C(beta) chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples.
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Affiliation(s)
- Patrik Lundström
- Molecular Biotechnology/IFM, Linköping University, 581 83, Linköping, Sweden
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26
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Lundström P, Hansen DF, Vallurupalli P, Kay LE. Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. J Am Chem Soc 2009; 131:1915-26. [PMID: 19152327 DOI: 10.1021/ja807796a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carr-Purcell-Meiboom-Gill relaxation dispersion NMR spectroscopy can provide detailed information about low populated, invisible states of protein molecules, including backbone chemical shifts of the invisible conformer and bond vector orientations that can be used as structural constraints. Notably, the measurement of 1Halpha chemical shifts in excited protein states has not been possible to date because, in the absence of suitable labeling, the homonuclear proton scalar coupling network in side chains of proteins leads to a significant degradation in the performance of proton-based relaxation dispersion experiments. Here we have overcome this problem through a labeling scheme in which proteins are prepared with U-2H glucose and 50% D2O/50% H2O that results in deuteration levels of between 50-88% at the Cbeta carbon. Effects from residual 1Halpha-1Hbeta scalar couplings can be suppressed through a new NMR experiment that is presented here. The utility of the methodology is demonstrated on a ligand binding exchanging system and it is shown that 1Halpha chemical shifts extracted from dispersion profiles are, on average, accurate to 0.03 ppm, an order of magnitude better than they can be predicted from structure using a database approach. The ability to measure 1Halpha chemical shifts of invisible conformers is particularly important because such shifts are sensitive to both secondary and tertiary structure. Thus, the methodology presented is a valuable addition to a growing list of experiments for characterizing excited protein states that are difficult to study using the traditional techniques of structural biology.
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Affiliation(s)
- Patrik Lundström
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario, Canada, M5S 1A8
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27
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Zintsmaster JS, Wilson BD, Peng JW. Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance. J Am Chem Soc 2008; 130:14060-1. [PMID: 18834120 DOI: 10.1021/ja805839y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We show that Carr-Purcell-Meiboom-Gill (CPMG) 13Calpha NMR relaxation dispersion measurements are a viable means for profiling mus-ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Calpha nuclei that experience mus-ms modulation of their chemical shifts due to binding. 13Calpha shifts are dominated by local torsion angles , psi, chi1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The mus-ms dynamic information gained helps establish flexibility-activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
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Affiliation(s)
- John S Zintsmaster
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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28
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Lundström P, Hansen DF, Kay LE. Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively (13)C labeled samples. JOURNAL OF BIOMOLECULAR NMR 2008; 42:35-47. [PMID: 18762869 DOI: 10.1007/s10858-008-9260-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 07/18/2008] [Accepted: 07/18/2008] [Indexed: 05/26/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy has emerged as a powerful method for quantifying chemical shifts of excited protein states. For many applications of the technique that involve the measurement of relaxation rates of carbon magnetization it is necessary to prepare samples with isolated (13)C spins so that experiments do not suffer from magnetization transfer between coupled carbon spins that would otherwise occur during the CPMG pulse train. In the case of (13)CO experiments however the large separation between (13)CO and (13)C(alpha) chemical shifts offers hope that robust (13)CO dispersion profiles can be recorded on uniformly (13)C labeled samples, leading to the extraction of accurate (13)CO chemical shifts of the invisible, excited state. Here we compare such chemical shifts recorded on samples that are selectively labeled, prepared using [1-(13)C]-pyruvate and NaH(13)CO(3,) or uniformly labeled, generated from (13)C-glucose. Very similar (13)CO chemical shifts are obtained from analysis of CPMG experiments recorded on both samples, and comparison with chemical shifts measured using a second approach establishes that the shifts measured from relaxation dispersion are very accurate.
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Affiliation(s)
- Patrik Lundström
- Department of Medical Genetics, The University of Toronto, Toronto, ON, Canada, M5S 1A8
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29
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Markin CJ, Saltibus LF, Spyracopoulos L. Dynamics of the RING domain from human TRAF6 by 15N NMR spectroscopy: implications for biological function. Biochemistry 2008; 47:10010-7. [PMID: 18759459 DOI: 10.1021/bi800252x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Activation of transcription factor NF-kappaB requires Lys63-linked polyubiquitination of the E3 ubiquitin ligase TRAF6 via protein-protein interactions mediated by a RING domain. In this study, intra- and intermolecular chemical exchange processes of the TRAF6 RING domain were analyzed by (15)N NMR spectroscopy. Micro- to millisecond time scale motions were assessed through R 1, R 2, NOE, and cross-correlated relaxation measurements, and the kinetics of these motions were quantified with relaxation dispersion. The relaxation experiments indicate that the protein core is rigid, consistent with the functional requirement that RING domains form a binding scaffold for E2 ubiquitin conjugation enzymes. Chemical exchange is observed at the C-terminal end of the main alpha-helix of the RING domain. The C-terminal end of the main alpha-helix from the RING domain is involved in E2-E3 interactions, and modulation of slow motions for this region of the helix may be a general mechanism by which these interactions achieve ubiquitin transfer. Chemical shift mapping indicates that the TRAF6 RING domain does not self-associate in solution. Numerous RING domains are homo- or heterodimeric, and this is thought to be a functional necessity for recruitment of substrates for ubiquitination, or recruitment of multiple E2 enzymes for efficient substrate ubiquitination. However, lack of self-association for the RING domain from TRAF6, and the observation that the intact protein is a trimer, suggests that close association of RING domains within a homodimeric scaffold may not be a fundamental requirement for biological function.
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Affiliation(s)
- Craig J Markin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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30
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Hansen DF, Vallurupalli P, Kay LE. Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states. JOURNAL OF BIOMOLECULAR NMR 2008; 41:113-20. [PMID: 18574698 DOI: 10.1007/s10858-008-9251-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 05/26/2008] [Indexed: 05/12/2023]
Abstract
Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers are populated to only low levels and are often only transiently formed their study is not amenable to many of the tools of structural biology. In this perspective we discuss the role of CPMG-based relaxation dispersion NMR spectroscopy in characterizing these low populated, invisible states. It is shown that robust methods for measuring both backbone chemical shifts and residual anisotropic interactions in the excited state are in place and that these data provide valuable restraints for structural studies of invisible conformers.
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Affiliation(s)
- D Flemming Hansen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada
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31
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Korzhnev DM, Kay LE. Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc Chem Res 2008; 41:442-51. [PMID: 18275162 DOI: 10.1021/ar700189y] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological function depends on molecular dynamics that lead to excursions from highly populated ground states to much less populated excited states. The low populations and the transient formation of such excited states render them invisible to the conventional methods of structural biology. Thus, while detailed pictures of ground-state structures of biomolecules have emerged over the years, largely through X-ray diffraction and solution nuclear magnetic resonance (NMR) spectroscopy studies, much less structural data has been accumulated on the conformational properties of the invisible excited states that are necessary to fully explain function. NMR spectroscopy is a powerful tool for studying conformational dynamics because it is sensitive to dynamics over a wide range of time scales, extending from picoseconds to seconds and because information is, in principle, available at nearly every position in the molecule. Here an NMR method for quantifying millisecond time scale dynamics that involve transitions between different molecular conformations is described. The basic experimental approach, termed relaxation dispersion NMR spectroscopy, is outlined to provide the reader with an intuitive feel for the technology. A variety of different experiments that probe conformational exchange at different sites in proteins are described, including a brief summary of data-fitting procedures to extract both the kinetic and thermodynamic properties of the exchange process and the structural features of the invisible excited states along the exchange pathway. It is shown that the methodology facilitates detection of intermediates and other excited states that are populated at low levels, 0.5% or higher, that cannot be observed directly in spectra, so long as they exchange with the observable ground state of the protein on the millisecond time scale. The power of the methodology is illustrated by a detailed application to the study of protein folding of the small modular SH3 domain. The kinetics and thermodynamics that describe the folding of this domain have been characterized through the effects of temperature, pressure, side-chain deuteration, and mutation, and the structural features of a low-populated folding intermediate have been assessed. Despite the fact that many previous studies have shown that SH3 domains fold via a two-state mechanism, the NMR methods presented unequivocally establish the presence of an on-pathway folding intermediate. The unique capabilities of NMR relaxation dispersion follow from the fact that large numbers of residues can be probed individually in a single experiment. By contrast, many other forms of spectroscopy monitor properties that are averaged over all residues in the molecule or that make use of only one or two reporters. The NMR methodology is not limited to protein folding, and applications to enzymatic catalysis, binding, and molecular recognition are beginning to emerge.
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Affiliation(s)
- Dmitry M. Korzhnev
- Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lewis E. Kay
- Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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32
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Loria JP, Berlow RB, Watt ED. Characterization of enzyme motions by solution NMR relaxation dispersion. Acc Chem Res 2008; 41:214-21. [PMID: 18281945 DOI: 10.1021/ar700132n] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In many enzymes, conformational changes that occur along the reaction coordinate can pose a bottleneck to the rate of conversion of substrates to products. Characterization of these rate-limiting protein motions is essential for obtaining a full understanding of enzyme-catalyzed reactions. Solution NMR experiments such as the Carr-Purcell-Meiboom-Gill (CPMG) spin-echo or off-resonance R 1rho pulse sequences enable quantitation of protein motions in the time range of microseconds to milliseconds. These experiments allow characterization of the conformational exchange rate constant, k ex, the equilibrium populations of the relevant conformations, and the chemical shift differences (Deltaomega) between the conformations. The CPMG experiments were applied to the backbone N-H positions of ribonuclease A (RNase A). To probe the role of dynamic processes in the catalytic cycle of RNase A, stable mimics of the apo enzyme (E), enzyme-substrate (ES) complex, and enzyme-product (EP) complex were formed. The results indicate that the ligand has relatively little influence on the kinetics of motion, which occurs at 1700 s (-1) and is the same as both k cat, and the product dissociation rate constant. Instead, the effect of ligand is to stabilize one of the pre-existing conformations. Thus, these NMR experiments indicate that the conformational change in RNase A is ligand-stabilized and does not appear to be ligand-induced. Further evidence for the coupling of motion and enzyme function comes from the similar solvent deuterium kinetic isotope effect on k ex derived from the NMR measurements and k cat from enzyme kinetic studies. This isotope effect of approximately 2 depends linearly on solvent deuterium content suggesting the involvement of a single proton in RNase A motion and function. Moreover, mutation of His48 to alanine eliminates motion in RNase A and decreases the catalytic turnover rate indicating the involvement of His48, which is far from the active site, in coupling motion and function. For the enzyme triosephosphate isomerase (TIM), the opening and closing motion of a highly conserved active site loop (loop 6) has been implicated in many studies to play an important role in the catalytic cycle of the enzyme. Off-resonance R 1rho experiments were performed on TIM, and results were obtained for amino acid residues in the N-terminal (Val167), and C-terminal (Lys174, Thr177) portions of loop 6. The results indicate that all three loop residues move between the open and closed conformation at about 10,000 s (-1), which is the same as the catalytic rate constant. The O (eta) atom of Tyr208 provides a hydrogen bond to stabilize the closed form of loop 6 by interacting with the amide nitrogen of Ala176; these atoms are outside of hydrogen bonding distance in the open form of the enzyme. Mutation of Tyr208 to phenylalanine results in significant loss of catalytic activity but does not appear to alter the kex value of the N-terminal part of loop 6. Instead, removal of this hydrogen bond appears to result in an increase in the equilibrium population of the open conformer of loop 6, thereby resulting in a loss of activity through a shift in the conformational equilibrium of loop 6. Solution NMR relaxation dispersion experiments are powerful experimental tools that can elucidate protein motions with atomic resolution and can provide insight into the role of these motions in biological function.
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Affiliation(s)
- J. Patrick Loria
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
| | - Rebecca B. Berlow
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Eric D. Watt
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
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33
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Affiliation(s)
- David D Boehr
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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34
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Lundström P, Vallurupalli P, Religa TL, Dahlquist FW, Kay LE. A single-quantum methyl 13C-relaxation dispersion experiment with improved sensitivity. JOURNAL OF BIOMOLECULAR NMR 2007; 38:79-88. [PMID: 17464570 DOI: 10.1007/s10858-007-9149-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 02/07/2007] [Accepted: 02/12/2007] [Indexed: 05/15/2023]
Abstract
A pulse sequence is described for recording single-quantum (13)C-methyl relaxation dispersion profiles of (13)C-selectively labeled methyl groups in proteins that offers significant improvements in sensitivity relative to existing approaches where initial magnetization derives from (13)C polarization. Sensitivity gains in the new experiment are achieved by making use of polarization from (1)H spins and (1)H --> (13)C --> (1)H type magnetization transfers. Its utility has been established by applications involving three different protein systems ranging in molecular weight from 8 to 28 kDa, produced using a number of different selective labeling approaches. In all cases exchange parameters from both (13)C-->(1)H and (1)H --> (13)C --> (1)H classes of experiment are in good agreement, with gains in sensitivity of between 1.7 and 4-fold realized using the new scheme.
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Affiliation(s)
- Patrik Lundström
- Department of Medical Genetics, The University of Toronto, Toronto, ON, Canada, M5S 1A8
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35
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Vallurupalli P, Scott L, Williamson JR, Kay LE. Strong coupling effects during X-pulse CPMG experiments recorded on heteronuclear ABX spin systems: artifacts and a simple solution. JOURNAL OF BIOMOLECULAR NMR 2007; 38:41-6. [PMID: 17334825 DOI: 10.1007/s10858-006-9139-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 12/15/2006] [Accepted: 12/18/2006] [Indexed: 05/14/2023]
Abstract
Simulation and experiment have been used to establish that significant artifacts can be generated in X-pulse CPMG relaxation dispersion experiments recorded on heteronuclear ABX spin-systems, such as (13)C( i )-(13)C( j )-(1)H, where (13)C( i ) and (13)C( j ) are strongly coupled. A qualitative explanation of the origin of these artifacts is presented along with a simple method to significantly reduce them. An application to the measurement of (1)H CPMG relaxation dispersion profiles in an HIV-2 TAR RNA molecule where all ribose sugars are protonated at the 2' position, deuterated at all other sugar positions and (13)C labeled at all sugar carbons is presented to illustrate the problems that strong (13)C-(13)C coupling introduces and a simple solution is proposed.
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Affiliation(s)
- Pramodh Vallurupalli
- Department of Medical Genetics, The University of Toronto, Toronto, ON, Canada, M5S 1A8
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36
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Eichmüller C, Skrynnikov NR. Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C. JOURNAL OF BIOMOLECULAR NMR 2007; 37:79-95. [PMID: 17180551 DOI: 10.1007/s10858-006-9105-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 10/02/2006] [Indexed: 05/13/2023]
Abstract
The microsecond time-scale motions in the N-terminal domain of cardiac troponin C (NcTnC) loaded with lanthanide ions have been investigated by means of a (1)H(N) off-resonance spin-lock experiment. The observed relaxation dispersion effects strongly increase along the series of NcTnC samples containing La(3+), Ce(3+), and Pr(3+) ions. This rise in dispersion effects is due to modulation of long-range pseudocontact shifts by micros time-scale dynamics. Specifically, the motion in the coordination sphere of the lanthanide ion (i.e. in the NcTnC EF-hand motif) causes modulation of the paramagnetic susceptibility tensor which, in turn, causes modulation of pseudocontact shifts. It is also probable that opening/closing dynamics, previously identified in Ca(2+)-NcTnC, contributes to some of the observed dispersions. On the other hand, it is unlikely that monomer-dimer exchange in the solution of NcTnC is directly responsible for the dispersion effects. Finally, on-off exchange of the lanthanide ion does not seem to play any significant role. The amplification of dispersion effects by Ln(3+) ions is a potentially useful tool for studies of micros-ms motions in proteins. This approach makes it possible to observe the dispersions even when the local environment of the reporting spin does not change. This happens, for example, when the motion involves a 'rigid' structural unit such as individual alpha-helix. Even more significantly, the dispersions based on pseudocontact shifts offer better chances for structural characterization of the dynamic species. This method can be generalized for a large class of applications via the use of specially designed lanthanide-binding tags.
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37
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Slupsky CM, Spyracopoulos L, Booth VK, Sykes BD, Crump MP. Probing nascent structures in peptides using natural abundance 13C NMR relaxation and reduced spectral density mapping. Proteins 2007; 67:18-30. [PMID: 17256768 DOI: 10.1002/prot.21294] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The main chain motional properties for a series of peptides that appear to have preferred conformations in solution have been systematically studied using solution-state nuclear magnetic resonance spectroscopy. The series of peptides were derived from the N-termini of pro-inflammatory chemokine proteins and HoxB1, a transcriptional regulator. As an unstructured control, a ten residue peptide was designed, synthesized, and found to be minimally structured from solution NMR data. The dynamic properties of the main chain for the peptides were assessed through longitudinal and transverse main chain (13)Calpha relaxation rates and the heteronuclear nuclear Overhauser effect. Motional parameters were interpreted using reduced spectral density mapping and compared with those derived from an extended Lipari-Szabo model in which the rotational correlation time was calculated for each main chain site of the peptide. Comparison of spectral density and Lipari-Szabo analyses for the peptides to those of the unstructured control peptide reveals significant differences in the dynamic behavior of the peptides. The amplitude of picosecond to nanosecond timescale motions for the main chain is observed to decrease for all of the chemokine peptides and HoxB1 over the regions that show partial structure at low temperatures. Comparatively, changes in picosecond to nanosecond timescale motions for the unstructured control peptide show no correlation with sequence position. These results indicate that there are distinguishable low temperature motional differences between an intrinsically unstructured peptide and peptides that have an inherent propensity to structure.
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Affiliation(s)
- Carolyn M Slupsky
- Protein Engineering Network Centres of Excellence, University of Alberta, Edmonton, Alberta, Canada
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38
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Scian M, Marin M, Bellanda M, Tou L, Alexander JM, Rosenblatt M, Chorev M, Peggion E, Mammi S. Backbone dynamics of human parathyroid hormone (1-34): flexibility of the central region under different environmental conditions. Biopolymers 2006; 84:147-60. [PMID: 16123988 DOI: 10.1002/bip.20355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The presence of a stable tertiary structure in the bioactive N-terminal portion of parathyroid hormone (PTH), a major hormone in the maintenance of extracellular calcium homeostasis, is still debated. In this work, 15N relaxation parameters of the 33 backbone amides of human PTH(1-34) were determined in phosphate-buffered saline solution (PBS) and in the presence of dodecylphosphocholine (DPC) micelles. The relaxation parameters were analyzed using both the model-free formalism (G. Lipari and A. Szabo, Journal of the American Chemical Society, 1982, Vol. 104, pp. 4546-4549) and the reduced spectral density functions approach (J.-F. Lefevre, K. T. Dayie, J. W. Peng, and G. Wagner, Biochemistry, 1996, Vol. 35, pp. 2674-2686). In PBS, the region around Gly12 possesses a high degree of flexibility and the C-terminal helix is less flexible than the N-terminal one. In the presence of DPC micelles, the mobility of the entire molecule is reduced, but the stability of the N-terminal helix increases relative to the C-terminal one. A point of relatively higher mobility at residue Gly12 is still present and a new site of local mobility at residues 16-17 is generated. These results justify the lack of experimental nuclear Overhauser effect (NOE) restraints with lack of tertiary structure and support the hypothesis that, in the absence of the receptor, the relative spatial orientation of the two N- and C-terminal helices is undefined. The flexibility in the midregion of PTH(1-34), maintained in the presence of the membrane-mimetic environment, may enable the correct relative disposition of the two helices, favoring a productive interaction with the receptor.
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Affiliation(s)
- Michele Scian
- Institute of Biomolecular Chemistry, CNR, Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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39
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Kovrigin EL, Kempf JG, Grey MJ, Loria JP. Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 180:93-104. [PMID: 16458551 DOI: 10.1016/j.jmr.2006.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 01/12/2006] [Accepted: 01/17/2006] [Indexed: 05/06/2023]
Abstract
This work examines the robustness of fitting of parameters describing conformational exchange (k(ex), p(a/b), and Deltaomega) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of k(ex), p(a/b), and Deltaomega to quantitatively assess the degree of the parameter inter-dependence. The demonstrated high correlation between parameters can preclude accurate dynamics parameter estimation from NMR spin-relaxation data obtained at a single static magnetic field. The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties.
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Affiliation(s)
- Evgenii L Kovrigin
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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40
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Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG. Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain. J Mol Biol 2006; 355:1078-94. [PMID: 16332376 DOI: 10.1016/j.jmb.2005.11.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 11/01/2005] [Accepted: 11/02/2005] [Indexed: 12/29/2022]
Abstract
The contribution of interactions involving the imidazole ring of His41 to the pH-dependent stability of the villin headpiece (HP67) N-terminal subdomain has been investigated by nuclear magnetic resonance (NMR) spin relaxation. NMR-derived backbone N-H order parameters (S2) for wild-type (WT) HP67 and H41Y HP67 indicate that reduced conformational flexibility of the N-terminal subdomain in WT HP67 is due to intramolecular interactions with the His41 imidazole ring. These interactions, together with desolvation effects, contribute to significantly depress the pKa of the buried imidazole ring in the native state. 15N R1rho relaxation dispersion data indicate that WT HP67 populates a partially folded intermediate state that is 10.9 kJ mol(-1) higher in free energy than the native state under non-denaturing conditions at neutral pH. The partially folded intermediate is characterized as having an unfolded N-terminal subdomain while the C-terminal subdomain retains a native-like fold. Although the majority of the residues in the N-terminal subdomain sample a random-coil distribution of conformations, deviations of backbone amide 1H and 15N chemical shifts from canonical random-coil values for residues within 5A of the His41 imidazole ring indicate that a significant degree of residual structure is maintained in the partially folded ensemble. The pH-dependence of exchange broadening is consistent with a linear three-state exchange model whereby unfolding of the N-terminal subdomain is coupled to titration of His41 in the partially folded intermediate with a pKa,I=5.69+/-0.07. Although maintenance of residual interactions with the imidazole ring in the unfolded N-terminal subdomain appears to reduce pKa,I compared to model histidine compounds, protonation of His41 disrupts these interactions and reduces the difference in free energy between the native state and partially folded intermediate under acidic conditions. In addition, chemical shift changes for residues Lys70-Phe76 in the C-terminal subdomain suggest that the HP67 actin binding site is disrupted upon unfolding of the N-terminal subdomain, providing a potential mechanism for regulating the villin-dependent bundling of actin filaments.
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Affiliation(s)
- Michael J Grey
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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41
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Pawley NH, Clark MD, Michalczyk R. Rectifying system-specific errors in NMR relaxation measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:77-87. [PMID: 16213172 DOI: 10.1016/j.jmr.2005.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 08/11/2005] [Accepted: 08/30/2005] [Indexed: 05/04/2023]
Abstract
15N spin relaxation parameters provide a powerful tool for probing the internal dynamics and thermodynamics of proteins. The biological insight provided by these experiments often involves interpretation of small changes in relaxation parameters. This, in turn, requires careful data analysis, especially in the identification and treatment of systematic error. While progress continues on reduction of experiment-specific errors associated with pulse sequences, system-specific sources of error have received far less attention. The impact of these errors varies between facilities, spectrometers, and biological samples. We demonstrate that performing a series of control experiments along with relaxation measurements can help identify, quantify, and isolate sources of system-specific error, and, in some cases, correct for systematic changes. We further demonstrate that control experiments can be performed without significant loss of spectrometer time, and lead to more accurate relaxation parameter values.
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Affiliation(s)
- Norma H Pawley
- Bioscience Division, B-3, MS G758, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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42
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Lundström P, Akke M. Microsecond Protein Dynamics Measured by 13Cα Rotating-Frame Spin Relaxation. Chembiochem 2005; 6:1685-92. [PMID: 16028301 DOI: 10.1002/cbic.200500086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
NMR spin relaxation in the rotating frame (R1rho) is a unique method for atomic-resolution characterization of conformational (chemical) exchange processes occurring on the microsecond timescale. We present a rotating-frame 13C(alpha) relaxation dispersion experiment for measuring conformational dynamics in uniformly 13C-labeled proteins. The experiment was validated by using the E140Q mutant of the C-terminal fragment of calmodulin, which exhibits significant conformational exchange between two major conformations, as gauged from previous 15N and 1H relaxation studies. Consistent with previous work, the present 13C(alpha) R1rho experiment detects conformational-exchange dynamics throughout the protein. The average correlation time of <tau(ex)>=25+/-8 micros is in excellent agreement with those determined previously from 1H and 15N R1rho relaxation data: <tau(ex)>=19+/-7 and 21+/-3 micros, respectively. The extracted chemical-shift differences between the exchanging states reveal significant fluctuations in dihedral angles within single regions of Ramachandran phi-psi space, that were not identified from the 1H and 15N relaxation data. The present results underscore the advantage of using several types of nuclei to probe exchange dynamics in biomolecules.
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Affiliation(s)
- Patrik Lundström
- Department of Biophysical Chemistry, Lund University, P.O.Box 124, 22100 Lund, Sweden
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43
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Korzhnev DM, Mittermaier AK, Kay LE. Cross-correlated spin relaxation effects in methyl 1H CPMG-based relaxation dispersion experiments: complications and a simple solution. JOURNAL OF BIOMOLECULAR NMR 2005; 31:337-42. [PMID: 15929000 DOI: 10.1007/s10858-005-2468-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 02/10/2005] [Indexed: 05/02/2023]
Abstract
Artifacts associated with the measurement of methyl (1)H single quantum CPMG-based relaxation dispersion profiles are described. These artifacts arise due to the combination of cross-correlated spin relaxation effects involving intra-methyl (1)H-(1)H dipolar interactions and imperfections in (1)H refocusing pulses that are applied during CPMG intervals that quantify the effects of chemical exchange on measured transverse relaxation rates. As a result substantial errors in extracted exchange parameters can be obtained. A simple 'work-around' is presented where the (1)H chemical shift difference between the exchanging states is extracted from a combination of (13)C single quantum and (13)C-(1)H multiple quantum dispersion profiles. The approach is demonstrated with an application to a folding/unfolding reaction involving a G48M mutant Fyn SH3 domain.
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Affiliation(s)
- Dmitry M Korzhnev
- Contribution from the Protein Engineering Network Centers of Excellence and the Department of Medical Genetics, The University of Toronto, Ontario, Canada
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44
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Palmer AG, Grey MJ, Wang C. Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular-weight systems. Methods Enzymol 2005; 394:430-65. [PMID: 15808232 DOI: 10.1016/s0076-6879(05)94018-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Transverse relaxation optimized NMR spectroscopy (TROSY) techniques for (1)H-(15)N backbone amide moieties and for (13)CH(3) methyl groups have permitted the development of Hahn spin echo and Carr-Purcell-Meiboom-Gill (CPMG) experiments for characterizing chemical exchange kinetic phenomena on microsecond-millisecond time scales in proteins with molecular masses >50 kDa. This chapter surveys the theoretical bases for TROSY in spin systems subject to chemical exchange linebroadening, the experimental methods that have been developed to quantitatively characterize chemical exchange in large proteins, and the emerging applications to triose phosphate isomerase, hemoglobin, and malate synthase G, with molecular masses ranging from 54 to 82 kDa.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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45
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Abstract
The fastest simple, kinetically two-state protein folds a million times more rapidly than the slowest. Here we review many recent theories of protein folding kinetics in terms of their ability to qualitatively rationalize, if not quantitatively predict, this fundamental experimental observation.
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Affiliation(s)
- Blake Gillespie
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA.
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46
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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47
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Podkorytov IS, Skrynnikov NR. Microsecond time-scale dynamics from relaxation in the rotating frame: experiments using spin lock with alternating phase. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 169:164-173. [PMID: 15183365 DOI: 10.1016/j.jmr.2004.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 04/13/2004] [Indexed: 05/24/2023]
Abstract
A spin lock comprised of radiofrequency pulses with alternating phase, (x) (-x)(x) (-x) , is proposed as a new technique to probe microsecond time-scale dynamics. A series of R1rho measurements using different pulse duration tp allows one to determine exchange rate, kex, the product p(a)p(b)(Delta omega(ab))2 involving populations of the exchanging species, p(a) and p(b), together with chemical shift difference, (Delta omega(ab)), and the strength of the spin-lock field, B1. The interpretation is based on simple analytical expression for R1rho derived on the basis of Redfield theory. The application of the method is demonstrated for partially deuterated molecule of cyclohexane undergoing chair-to-chair interconversion at -9 degrees C.
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Affiliation(s)
- Ivan S Podkorytov
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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48
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Abstract
Globular proteins are characterized by the specific and tight packing of hydrophobic side-chains in the so-called "hydrophobic core." Formation of the core is key in folding, stabilization, and conformational specificity. The critical role of hydrophobic cores in maintaining the highly ordered structures present in natural proteins justifies the tremendous efforts devoted to their redesign. Both experimental and computational combinatorial-based approaches have been reported in the last years as powerful protein design tools. These manage to explore large regions of the sequence/conformational space, allowing the search for alternative protein core arrangements displaying native-like properties. The overall results obtained from core design projects have contributed significantly to our present knowledge of protein folding and function. In addition, core design has worked as a benchmark for the development of ambitious protein design projects that nowadays are allowing the de novo design of novel protein structures and functions.
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Affiliation(s)
- Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, Barcelona, Spain.
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49
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Thuduppathy GR, Hill RB. Applications of NMR spin relaxation methods for measuring biological motions. Methods Enzymol 2004; 384:243-64. [PMID: 15081691 PMCID: PMC3061832 DOI: 10.1016/s0076-6879(04)84015-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gillespie B, Vu DM, Shah PS, Marshall SA, Dyer RB, Mayo SL, Plaxco KW. NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics. J Mol Biol 2003; 330:813-9. [PMID: 12850149 DOI: 10.1016/s0022-2836(03)00616-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We address the importance of natural selection in the origin and maintenance of rapid protein folding by experimentally characterizing the folding kinetics of two de novo designed proteins, NC3-NCAP and ENH-FSM1. These 51 residue proteins, which adopt the helix-turn-helix homeodomain fold, share as few as 12 residues in common with their most closely related natural analog. Despite the replacement of up to 3/4 of their residues by a computer algorithm optimizing only thermodynamic properties, the designed proteins fold as fast or faster than the 35,000 s(-1) observed for the closest natural analog. Thus these de novo designed proteins, which were produced in the complete absence of selective pressures or design constraints explicitly aimed at ensuring rapid folding, are among the most rapidly folding proteins reported to date.
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Affiliation(s)
- Blake Gillespie
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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