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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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Hoffmann F, Mulder FAA, Schäfer LV. How Much Entropy Is Contained in NMR Relaxation Parameters? J Phys Chem B 2021; 126:54-68. [PMID: 34936366 DOI: 10.1021/acs.jpcb.1c07786] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solution-state NMR relaxation experiments are the cornerstone to study internal protein dynamics at an atomic resolution on time scales that are faster than the overall rotational tumbling time τR. Since the motions described by NMR relaxation parameters are connected to thermodynamic quantities like conformational entropies, the question arises how much of the total entropy is contained within this tumbling time. Using all-atom molecular dynamics simulations of the T4 lysozyme, we found that entropy buildup is rather fast for the backbone, such that the majority of the entropy is indeed contained in the short-time dynamics. In contrast, the contribution of the slow dynamics of side chains on time scales beyond τR on the side-chain conformational entropy is significant and should be taken into account for the extraction of accurate thermodynamic properties.
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Affiliation(s)
- Falk Hoffmann
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44 780 Bochum, Germany
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44 780 Bochum, Germany
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Xie M, Yu L, Bruschweiler-Li L, Xiang X, Hansen AL, Brüschweiler R. Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation. SCIENCE ADVANCES 2019; 5:eaax5560. [PMID: 31453342 PMCID: PMC6693908 DOI: 10.1126/sciadv.aax5560] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/09/2019] [Indexed: 05/03/2023]
Abstract
Protein function depends critically on intrinsic internal dynamics, which is manifested in distinct ways, such as loop motions that regulate protein recognition and catalysis. Under physiological conditions, dynamic processes occur on a wide range of time scales from subpicoseconds to seconds. Commonly used NMR spin relaxation in solution provides valuable information on very fast and slow motions but is insensitive to the intermediate nanosecond to microsecond range that exceeds the protein tumbling correlation time. Presently, very little is known about the nature and functional role of these motions. It is demonstrated here how transverse spin relaxation becomes exquisitely sensitive to these motions at atomic resolution when studying proteins in the presence of nanoparticles. Application of this novel cross-disciplinary approach reveals large-scale dynamics of loops involved in functionally critical protein-protein interactions and protein-calcium ion recognition that were previously unobservable.
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Affiliation(s)
- Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
| | - Xinyao Xiang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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Sekhar A, Vallurupalli P, Kay LE. Defining a length scale for millisecond-timescale protein conformational exchange. Proc Natl Acad Sci U S A 2013; 110:11391-6. [PMID: 23801755 PMCID: PMC3710843 DOI: 10.1073/pnas.1303273110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Although atomic resolution 3D structures of protein native states and some folding intermediates are available, the mechanism of interconversion between such states remains poorly understood. Here we study the four-helix bundle FF module, which folds via a transiently formed and sparsely populated compact on-pathway intermediate, I. Relaxation dispersion NMR spectroscopy has previously been used to elucidate the 3D structure of this intermediate and to establish that the conformational exchange between the I and the native, N, states of the FF domain is driven predominantly by water dynamics. In the present study we use NMR methods to define a length scale for the FF I-N transition, namely the effective hydrodynamic radius (EHR) that provides an average measure of the size of the structural units participating in the transition at any given time. Our experiments establish that the EHR is less than 4 Å, on the order of the size of one to two amino acid side chains, much smaller than the FF domain hydrodynamic radius (13 Å). The small magnitude of the EHR provides strong evidence that the I-N interconversion does not proceed via the synchronous motion of large clusters of amino acid residues, but rather by the exposure/burial of one or two side chains from solvent at any given time. Because the hydration of small hydrophobic solutes (< 4 Å) does not involve considerable dewetting or disruption of the water-hydrogen bonding network, the FF domain I-N transition does not require appreciable changes to the structure of the surrounding water.
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Affiliation(s)
- Ashok Sekhar
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Pramodh Vallurupalli
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Lewis E. Kay
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
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Liao X, Long D, Li DW, Brüschweiler R, Tugarinov V. Probing side-chain dynamics in proteins by the measurement of nine deuterium relaxation rates per methyl group. J Phys Chem B 2011; 116:606-20. [PMID: 22098066 DOI: 10.1021/jp209304c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate the feasibility of the measurement of up to nine deuterium spin relaxation rates in 13CHD2 and 13CH2D methyl isotopomers of small proteins. In addition to five measurable 2H relaxation rates in a 13CH2D methyl group (Millet, O.; Muhandiram, D. R.; Skrynnikov, N. R.; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6439-48), the measurement of additional four rates of (nearly) single-exponentially decaying magnetization terms in methyl groups of the 13CHD2 variety is reported. Consistency relationships between 2H spin relaxation rates measured in the two different types of methyl groups are derived and verified experimentally for a subset of methyl-containing side chains in the protein ubiquitin. A detailed comparison of methyl-bearing side-chain dynamics parameters obtained from relaxation measurements in 13CH2D and 13CHD2 methyls of ubiquitin at 10, 27, and 40 °C reveals that transverse 2H relaxation rates in 13CHD2 groups are reliable and accurate reporters of the amplitudes of methyl 3-fold axis motions (S(axis)2) for protein molecules with global molecular tumbling times τ(C) >~9 ns. For smaller molecules, simple correction of transverse 2H relaxation rates in 13CHD2 groups is sufficient for the derivation of robust measures of order. Residue-specific distributions of S(axis)2 are consistent with atomic-detail molecular dynamics (MD) results. Both 13CHD2- and 13CH2D-derived S(axis)2 values are in good overall agreement with those obtained from 1 μs MD simulations at all the three temperatures, although some differences in the site-specific temperature dependence between MD- and 2H-relaxation-derived S(axis)2 values are observed.
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Affiliation(s)
- Xinli Liao
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Shapiro YE, Polimeno A, Freed JH, Meirovitch E. Methyl dynamics of a Ca2+-calmodulin-peptide complex from NMR/SRLS. J Phys Chem B 2011; 115:354-65. [PMID: 21166433 PMCID: PMC3062514 DOI: 10.1021/jp107130m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS accounts for dynamical coupling between the tumbling of the protein and the local motion of the probe and for general tensorial properties. It is the generalization of the traditional model-free (MF) method, which does not account for mode-coupling and treats only simple tensorial properties. SRLS is applied herein to ²H relaxation of ¹³CDH₂ groups in the complex of Ca(2+)-calmodulin with the peptide smMLCKp. Literature data comprising ²H T₁ and T₂ acquired at 14.1 and 17.6 T, and 288, 295, 308, and 320 K, are used. We find that mode-coupling is a small effect for methyl dynamics. On the other hand, general tensorial properties are important. In particular, it is important to allow for the asymmetry of the local spatial restrictions, which can be represented in SRLS by a rhombic local ordering tensor with components S(0)(2) and S(2)(2). The principal axes frame of this tensor is obviously different from the axial frames of the magnetic tensors. Here, we find that -0.2 ≤ S(0)(2) ≤ 0.5 and -0.4 ≤ S(2)(2) ≤ 0. MF features a single "generalized" order parameter, S, confined to the 0-0.316 range; the local geometry is inherently simple. The parameter S is inaccurate, having absorbed unaccounted for effects, notably S(2)(2) ≠ 0. We find that the methionine methyls (the other methyl types) reorient with rates of 8.6 × 10⁹ to 21.4 × 10⁹ (0.67 × 10⁹ to 6.5 × 10⁹) 1/s. The corresponding activation energies are 10 (10-27) kJ/mol. By contrast, MF yields inaccurate effective local motional correlation times, τ(e), with nonphysical temperature dependence. Thus, the problematic S- and τ(e)-based MF picture of methyl dynamics has been replaced with an insightful physical picture based on a local ordering tensor related to structural features, and a local diffusion tensor that yields accurate activation energies.
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Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:360-405. [PMID: 20625480 PMCID: PMC2899824 DOI: 10.1016/j.pnmrs.2010.03.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
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Vögeli B, Riek R. Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation. JOURNAL OF BIOMOLECULAR NMR 2010; 46:135-147. [PMID: 19904498 DOI: 10.1007/s10858-009-9387-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/22/2009] [Indexed: 05/28/2023]
Abstract
The measurements of cross-correlated relaxation rates between H(N)-N and C(beta)-C(gamma) intraresidual and sequential dipolar interactions is demonstrated in ASN, ASP and aromatic residues. The experiment can be used for deuterated samples and no additional knowledge such as Karplus parametrizations is required for the analysis. The data constitutes a new type of information since no other method relates the C(beta)-C(gamma) bond to H(N)-N. Using this method the dominant populations of rotamer states of chi 1 can be readily cross checked provided that phi or psi are known. In addition, dynamics on all timescales can be probed. As opposed to standard dynamics analysis of isolated bonds, the presented observables depend on relative dynamics with an interesting prospect to analyze correlated fluctuations of the two torsion angles phi or psi with chi 1. Experimental rates are compared to single conformer and ensemble representations of GB3 and ubiquitin. In particular, it is found that the recently published ubiquitin ensemble 2k39 improves the agreement obtained for 1UBQ. In general, however, input data restricting ASX and aromatic side chains in structure calculation is sparse highlighting the need for new NMR observables.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zurich, Switzerland.
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Chevelkov V, Fink U, Reif B. Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 45:197-206. [PMID: 19629713 DOI: 10.1007/s10858-009-9348-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 06/26/2009] [Indexed: 05/13/2023]
Abstract
We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include (15)N T (1) relaxation times measured at two different magnetic fields as well as (1)H-(15)N dipole, (15)N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T (2) in the solid-state. In addition, global order parameters are included from a (1)H,(15)N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 degrees for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken alpha-spectrin SH3 domain.
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Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin, Germany
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Palmer AG. A topical issue: NMR investigations of molecular dynamics. JOURNAL OF BIOMOLECULAR NMR 2009; 45:1-4. [PMID: 19669621 PMCID: PMC7087731 DOI: 10.1007/s10858-009-9345-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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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