Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

Research output: Contribution to journal › Journal article › Research › peer-review

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.

In: Journal of Chemical Theory and Computation, Vol. 17, No. 8, 2021, p. 5262-5275.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Kümmerer, F, Orioli, S, Harding-Larsen, D, Hoffmann, F, Gavrilov, Y, Teilum, K & Lindorff-Larsen, K 2021, 'Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations', Journal of Chemical Theory and Computation, vol. 17, no. 8, pp. 5262-5275. https://doi.org/10.1021/acs.jctc.0c01338

APA

Kümmerer, F., Orioli, S., Harding-Larsen, D., Hoffmann, F., Gavrilov, Y., Teilum, K., & Lindorff-Larsen, K. (2021). Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations. Journal of Chemical Theory and Computation, 17(8), 5262-5275. https://doi.org/10.1021/acs.jctc.0c01338

Vancouver

Kümmerer F, Orioli S, Harding-Larsen D, Hoffmann F, Gavrilov Y, Teilum K et al. Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations. Journal of Chemical Theory and Computation. 2021;17(8):5262-5275. https://doi.org/10.1021/acs.jctc.0c01338

Author

Kümmerer, Felix ; Orioli, Simone ; Harding-Larsen, David ; Hoffmann, Falk ; Gavrilov, Yulian ; Teilum, Kaare ; Lindorff-Larsen, Kresten. / Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations. In: Journal of Chemical Theory and Computation. 2021 ; Vol. 17, No. 8. pp. 5262-5275.

Bibtex

@article{00bd733a402349288e546de4ab894ce8,

title = "Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations",

abstract = "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. ",

author = "Felix K{\"u}mmerer and Simone Orioli and David Harding-Larsen and Falk Hoffmann and Yulian Gavrilov and Kaare Teilum and Kresten Lindorff-Larsen",

note = "Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

doi = "10.1021/acs.jctc.0c01338",

language = "English",

volume = "17",

pages = "5262--5275",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

publisher = "American Chemical Society",

number = "8",

}

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

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

Department of Biology