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Chen PC, Hologne M, Walker O, Hennig J. Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:1009-1019. [PMID: 29294268 DOI: 10.1021/acs.jctc.7b00750] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1H-15N NMR spin relaxation and relaxation dispersion experiments can reveal the time scale and extent of protein motions across the ps-ms range, where the ps-ns dynamics revealed by fundamental quantities R1, R2, and heteronuclear NOE can be well-sampled by molecular dynamics simulations (MD). Although the principles of relaxation prediction from simulations are well-established, numerous NMR-MD comparisons have hitherto focused upon the aspect of order parameters S2 due to common artifacts in the prediction of transient dynamics. We therefore summarize here all necessary components and highlight existing and proposed solutions, such as the inclusion of quantum mechanical zero-point vibrational corrections and separate MD convergence of global and local motions in coarse-grained and all-atom force fields, respectively. For the accuracy of the MD prediction to be tested, two model proteins GB3 and Ubiquitin are used to validate five atomistic force fields against published NMR data supplemented by the coarse-grained force field MARTINI+EN. In Amber and CHARMM-type force fields, quantitative agreement was achieved for structured elements with minimum adjustment of global parameters. Deviations from experiment occur in flexible loops and termini, indicating differences in both the extent and time scale of backbone motions. The lack of systematic patterns and water model dependence suggests that modeling of the local environment limits prediction accuracy. Nevertheless, qualitative accuracy in a 2 μs CHARMM36m Stam2 VHS domain simulation demonstrates the potential of MD-based interpretation in combination with NMR-measured dynamics, increasing the utility of spin relaxation in integrative structural biology.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280 , 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280 , 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg , Meyerhofstrasse 1, 69117 Heidelberg, Germany
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2
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Hellman M, Tossavainen H, Rappu P, Heino J, Permi P. Characterization of intrinsically disordered prostate associated gene (PAGE5) at single residue resolution by NMR spectroscopy. PLoS One 2011; 6:e26633. [PMID: 22073178 PMCID: PMC3206799 DOI: 10.1371/journal.pone.0026633] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/29/2011] [Indexed: 12/16/2022] Open
Abstract
Background The Cancer-Testis antigens (CTA) are proteins expressed in human germ line and certain cancer cells. CTAs form a large gene family, representing 10% of X-chromosomal genes. They have high potential for cancer-specific immunotherapy. However, their biological functions are currently unknown. Prostate associated genes (PAGE) are characterized as CTAs. PAGE5 is one of six proteins belonging to this protein family, also called CT16. Methodology/Principal findings In this study we show, using bioinformatics, chromatographic and solution state NMR spectroscopic methods, that PAGE5 is an intrinsically disordered protein (IDP). Conclusion/Significance The study stands out as the first time structural characterization of the PAGE family protein and introduces how solution state NMR spectroscopy can be effectively utilized for identification of molecular recognition regions (MoRF) in IDPs, known often as transiently populated secondary structures.
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Affiliation(s)
- Maarit Hellman
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pekka Rappu
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
| | - Jyrki Heino
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail:
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3
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Yao S, Zhang MM, Yoshikami D, Azam L, Olivera BM, Bulaj G, Norton RS. Structure, dynamics, and selectivity of the sodium channel blocker mu-conotoxin SIIIA. Biochemistry 2008; 47:10940-9. [PMID: 18798648 DOI: 10.1021/bi801010u] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
mu-SIIIA, a novel mu-conotoxin from Conus striatus, appeared to be a selective blocker of tetrodotoxin-resistant sodium channels in frog preparations. It also exhibited potent analgesic activity in mice, although its selectivity profile against mammalian sodium channels remains unknown. We have determined the structure of mu-SIIIA in aqueous solution and characterized its backbone dynamics by NMR and its functional properties electrophysiologically. Consistent with the absence of hydroxyprolines, mu-SIIIA adopts a single conformation with all peptide bonds in the trans conformation. The C-terminal region contains a well-defined helix encompassing residues 11-16, while residues 3-5 in the N-terminal region form a helix-like turn resembling 3 10-helix. The Trp12 and His16 side chains are close together, as in the related conotoxin mu-SmIIIA, but Asn2 is more distant. Dynamics measurements show that the N-terminus and Ser9 have larger-magnitude motions on the subnanosecond time scale, while the C-terminus is more rigid. Cys4, Trp12, and Cys13 undergo significant conformational exchange on microsecond to millisecond time scales. mu-SIIIA is a potent, nearly irreversible blocker of Na V1.2 but also blocks Na V1.4 and Na V1.6 with submicromolar potency. The selectivity profile of mu-SIIIA, including poor activity against the cardiac sodium channel, Na V1.5, is similar to that of the closely related mu-KIIIA, suggesting that the C-terminal regions of both are critical for blocking neuronal Na V1.2. The structural and functional characterization described in this paper of an analgesic mu-conotoxin that targets neuronal subtypes of mammalian sodium channels provides a basis for the design of novel analogues with an improved selectivity profile.
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Affiliation(s)
- Shenggen Yao
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
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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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Skrynnikov NR, Millet O, Kay LE. Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions. J Am Chem Soc 2002; 124:6449-60. [PMID: 12033876 DOI: 10.1021/ja012498q] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the previous paper in this issue we have demonstrated that it is possible to measure the five different relaxation rates of a deuteron in (13)CH(2)D methyl groups of (13)C-labeled, fractionally deuterated proteins. The extensive set of data acquired in these experiments provides an opportunity to investigate side-chain dynamics in proteins at a level of detail that heretofore was not possible. The data, acquired on the B1 domain of peptostreptococcal protein L, include 16 (9) relaxation measurements at 4 (2) different magnetic field strengths, 25 degrees C (5 degrees C). These data are shown to be self-consistent and are analyzed using a spectral density mapping procedure which allows extraction of values of the spectral density function at a number of frequencies with no assumptions about the underlying dynamics. Dynamics data from 31 of 35 methyls in the protein for which data could be obtained were well-fitted using the two-parameter Lipari-Szabo model (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546). The data from the remaining 4 methyls can be fitted using a three-parameter version of the Lipari-Szabo model that takes into account, in a simple manner, additional nanosecond time-scale local dynamics. This interpretation is supported by analysis of a molecular dynamics trajectory where spectral density profiles calculated for side-chain methyl sites reflect the influence of slower (nanosecond) time-scale motions involving jumps between rotameric wells. A discussion of the minimum number of relaxation measurements that are necessary to extract the full complement of dynamics information is presented along with an interpretation of the extracted dynamics parameters.
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Affiliation(s)
- Nikolai R Skrynnikov
- Protein Engineering Network Centers of Excellence and Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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Palmer AG. Nmr probes of molecular dynamics: overview and comparison with other techniques. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:129-55. [PMID: 11340055 DOI: 10.1146/annurev.biophys.30.1.129] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.
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Affiliation(s)
- A G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA.
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Hill RB, Bracken C, DeGrado WF, Palmer AG. Molecular Motions and Protein Folding: Characterization of the Backbone Dynamics and Folding Equilibrium of α2D Using 13C NMR Spin Relaxation. J Am Chem Soc 2000. [DOI: 10.1021/ja001129b] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Blake Hill
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Clay Bracken
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - William F. DeGrado
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Arthur G. Palmer
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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Atkinson RA, Kieffer B, Dejaegere A, Sirockin F, Lefèvre JF. Structural and dynamic characterization of omega-conotoxin MVIIA: the binding loop exhibits slow conformational exchange. Biochemistry 2000; 39:3908-19. [PMID: 10747778 DOI: 10.1021/bi992651h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
omega-Conotoxin MVIIA is a 25-residue, disulfide-bridged polypeptide from the venom of the sea snail Conus magus that binds to neuronal N-type calcium channels. It forms a compact folded structure, presenting a loop between Cys8 and Cys15 that contains a set of residues critical for its binding. The loop does not have a unique defined structure, nor is it intrinsically flexible. Broadening of a subset of resonances in the NMR spectrum at low temperature, anomalous temperature dependence of the chemical shifts of some resonances, and exchange contributions to J(0) from (13)C relaxation measurements reveal that conformational exchange affects the residues in this loop. The effects of this exchange on the calculated structure of omega-conotoxin MVIIA are discussed. The exchange appears to be associated with a change in the conformation of the disulfide bridge Cys8-Cys20. The implications for the use of the omega-conotoxins as a scaffold for carrying other functions is discussed.
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Affiliation(s)
- R A Atkinson
- UPR 9003 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Bld. Sébastien Brant, 67400 Illkirch, France.
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