Probing Side-Chain Dynamics in Proteins by NMR Relaxation of Isolated C Magnetization Modes in CH Methyl Groups

Overview

Journal J Phys Chem B

Publisher American Chemical Society

Specialty Chemistry

Date 2021 Mar 26

PMID 33769060

Citations 6

Authors

Vitali Tugarinov

Alberto Ceccon

G Marius Clore

Affiliations

Soon will be listed here.

Abstract

The dynamics of methyl-bearing side chains in proteins were probed by C relaxation measurements of a number of C magnetization modes in selectively CH-labeled methyl groups of proteins. We first show how C magnetization modes in a CH spin-system can be isolated using acute-angle H radio-frequency pulses. The parameters of methyl-axis dynamics, a measure of methyl-axis ordering () and the correlation time of fast local methyl-axis motions (τ), derived from C relaxation in CH groups are compared with their counterparts obtained from C relaxation in CHD methyl isotopomers. We show that in high-molecular-weight proteins, excellent correlations are obtained between the [CHD]-derived values and those extracted from relaxation of the C magnetization of the = 1/2 manifold in CH methyls. In smaller proteins, a certain degree of anticorrelation is observed between the and τ values obtained from C relaxation of the = 1/2 manifold magnetization in CH methyls. These parameters can be partially decorrelated by inclusion in the analysis of relaxation data of the = 3/2 manifold C magnetization.

Citing Articles

The utility of small nutation angle H pulses for NMR studies of methyl-containing side-chain dynamics in proteins.

Tugarinov V, Clore G Prog Nucl Magn Reson Spectrosc. 2024; 144-145:40-62.

PMID: 39645350 PMC: 11625180. DOI: 10.1016/j.pnmrs.2024.05.004.

Precision measurements of relaxation rates of degenerate H transitions in methyl groups of small proteins.

Tugarinov V, Clore G J Magn Reson. 2023; 357:107584.

PMID: 37939502 PMC: 10753654. DOI: 10.1016/j.jmr.2023.107584.

Protein dynamics: The future is bright and complicated!.

Nam K, Wolf-Watz M Struct Dyn. 2023; 10(1):014301.

PMID: 36865927 PMC: 9974214. DOI: 10.1063/4.0000179.

Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements.

Vugmeyster L, Nichols P, Ostrovsky D, McKnight C, Vogeli B Magnetochemistry. 2023; 9(1).

PMID: 36776538 PMC: 9910280. DOI: 10.3390/magnetochemistry9010033.

Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy.

Karamanos T, Clore G Annu Rev Biophys. 2022; 51:223-246.

PMID: 35044800 PMC: 9358445. DOI: 10.1146/annurev-biophys-090921-120150.

References

Sheppard D, Sprangers R, Tugarinov V . Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins. Prog Nucl Magn Reson Spectrosc. 2010; 56(1):1-45. DOI: 10.1016/j.pnmrs.2009.07.004. View

Tugarinov V, Kay L . Quantitative 13C and 2H NMR relaxation studies of the 723-residue enzyme malate synthase G reveal a dynamic binding interface. Biochemistry. 2005; 44(49):15970-7. DOI: 10.1021/bi0519809. View

Ollerenshaw J, Tugarinov V, Skrynnikov N, Kay L . Comparison of 13CH3, 13CH2D, and 13CHD2 methyl labeling strategies in proteins. J Biomol NMR. 2005; 33(1):25-41. DOI: 10.1007/s10858-005-2614-2. View

Tugarinov V, Karamanos T, Clore G . Optimized selection of slow-relaxing C transitions in methyl groups of proteins: application to relaxation dispersion. J Biomol NMR. 2020; 74(12):673-680. PMC: 7704780. DOI: 10.1007/s10858-020-00349-3. View

Igumenova T, Frederick K, Wand A . Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev. 2006; 106(5):1672-99. PMC: 2547146. DOI: 10.1021/cr040422h. View

Yuwen T, Huang R, Vallurupalli P, Kay L . A Methyl-TROSY-Based H Relaxation Dispersion Experiment for Studies of Conformational Exchange in High Molecular Weight Proteins. Angew Chem Int Ed Engl. 2019; 58(19):6250-6254. DOI: 10.1002/anie.201900241. View

Schutz S, Sprangers R . Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. Prog Nucl Magn Reson Spectrosc. 2020; 116:56-84. DOI: 10.1016/j.pnmrs.2019.09.004. View

Millet O, Muhandiram D, Skrynnikov N, Kay L . Deuterium spin probes of side-chain dynamics in proteins. 1. Measurement of five relaxation rates per deuteron in (13)C-labeled and fractionally (2)H-enriched proteins in solution. J Am Chem Soc. 2002; 124(22):6439-48. DOI: 10.1021/ja012497y. View

Tugarinov V, Karamanos T, Clore G . Magic-Angle-Pulse Driven Separation of Degenerate H Transitions in Methyl Groups of Proteins: Application to Studies of Methyl Axis Dynamics. Chemphyschem. 2020; 21(11):1087-1091. PMC: 8855707. DOI: 10.1002/cphc.202000200. View

10.

Sprangers R, Kay L . Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature. 2007; 445(7128):618-22. DOI: 10.1038/nature05512. View

11.

Tugarinov V, Karamanos T, Ceccon A, Clore G . Optimized NMR Experiments for the Isolation of I=1/2 Manifold Transitions in Methyl Groups of Proteins. Chemphyschem. 2019; 21(1):13-19. PMC: 8855706. DOI: 10.1002/cphc.201900959. View

12.

Tugarinov V, Ollerenshaw J, Kay L . Probing side-chain dynamics in high molecular weight proteins by deuterium NMR spin relaxation: an application to an 82-kDa enzyme. J Am Chem Soc. 2005; 127(22):8214-25. DOI: 10.1021/ja0508830. View

13.

Ishima R, Petkova A, Louis J, Torchia D . Comparison of methyl rotation axis order parameters derived from model-free analyses of (2)H and (13)C longitudinal and transverse relaxation rates measured in the same protein sample. J Am Chem Soc. 2001; 123(25):6164-71. DOI: 10.1021/ja0104711. View

14.

Rosenzweig R, Kay L . Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Annu Rev Biochem. 2014; 83:291-315. DOI: 10.1146/annurev-biochem-060713-035829. View

15.

Tugarinov V, Kay L . A 2H NMR relaxation experiment for the measurement of the time scale of methyl side-chain dynamics in large proteins. J Am Chem Soc. 2006; 128(38):12484-9. DOI: 10.1021/ja063071s. View

16.

Frederick K, Marlow M, Valentine K, Wand A . Conformational entropy in molecular recognition by proteins. Nature. 2007; 448(7151):325-9. PMC: 4156320. DOI: 10.1038/nature05959. View