How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Olof Stenström; Candide Champion; Marc Lehner; Guillaume Bouvignies; Sereina Riniker; Fabien Ferrage

doi:10.1016/j.sbi.2022.102459

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Curr Opin Struct Biol. 2022 Dec:77:102459. doi: 10.1016/j.sbi.2022.102459. Epub 2022 Sep 20.

Authors

Olof Stenström¹, Candide Champion², Marc Lehner², Guillaume Bouvignies³, Sereina Riniker⁴, Fabien Ferrage⁵

Affiliations

¹ Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
² Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
³ Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. Electronic address: https://twitter.com/@gubouvignies.
⁴ Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland. Electronic address: sriniker@ethz.ch.
⁵ Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. Electronic address: fabien.ferrage@ens.psl.eu.

PMID: 36148743
DOI: 10.1016/j.sbi.2022.102459

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.

Keywords: Molecular dynamics simulations; NMR relaxation; NMR spectroscopy; Protein dynamics.

Publication types

Review

MeSH terms

Magnetic Resonance Spectroscopy
Molecular Dynamics Simulation*
Motion
Nuclear Magnetic Resonance, Biomolecular / methods