Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Standard
Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations. / Kümmerer, Felix; Orioli, Simone; Harding-Larsen, David; Hoffmann, Falk; Gavrilov, Yulian; Teilum, Kaare; Lindorff-Larsen, Kresten.
I: Journal of Chemical Theory and Computation, Bind 17, Nr. 8, 2021, s. 5262-5275.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
AU - Kümmerer, Felix
AU - Orioli, Simone
AU - Harding-Larsen, David
AU - Hoffmann, Falk
AU - Gavrilov, Yulian
AU - Teilum, Kaare
AU - Lindorff-Larsen, Kresten
N1 - Publisher Copyright: © 2021 American Chemical Society.
PY - 2021
Y1 - 2021
N2 - Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side-chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (average block selection using relaxation data with entropy restraints), can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties and highlight areas needed for further improvements of the approach.
AB - Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side-chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (average block selection using relaxation data with entropy restraints), can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties and highlight areas needed for further improvements of the approach.
U2 - 10.1021/acs.jctc.0c01338
DO - 10.1021/acs.jctc.0c01338
M3 - Journal article
C2 - 34291646
AN - SCOPUS:85112342975
VL - 17
SP - 5262
EP - 5275
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 8
ER -
ID: 276166008