3533435
doi
10.5281/zenodo.3533435
oai:zenodo.org:3533435
user-openforcefield
Using NMR relaxation data to improve the dynamics of methyl groups in AMBER and CHARMM force fields
Hoffmann, Falk
url:https://youtu.be/CkjVspPURFU
url:https://chemrxiv.org/articles/Predicting_NMR_Relaxation_of_Proteins_from_Molecular_Dynamics_Simulations_with_Accurate_Methyl_Rotation_Barriers/8982338/1
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Open Force Field Initiative
force fields
NMR
AMBER
CHARMM
methyl
torsional barrier
molecular dynamics
protein
<p>Falk Hoffmann (Ruhr University Bochum) presented his work on improving torsional barriers associated with methyl group rotations in amino acid side-chains in AMBER and CHARMM force fields by using NMR relaxation rates. This study is available as a <a href="https://chemrxiv.org/articles/Predicting_NMR_Relaxation_of_Proteins_from_Molecular_Dynamics_Simulations_with_Accurate_Methyl_Rotation_Barriers/8982338">preprint</a> on ChemrXiv. This talk is a part of OpenFF Webinars that took place on Sep 20, 2019.</p>
<p><br>
<strong>Abstract:</strong> The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates. In this talk I will present how we used NMR relaxation rates to identify disagreements between simulation and experiment for these energy barriers. The corresponding dihedral angle terms in AMBER and CHARMM force fields which are responsible for these energy barriers are subsequently improved and correspondence between experiment and simulation could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Improved methyl group rotation barriers were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Furthermore, I will show how these energy barriers influence the validity of the Lipari-Szabo model for protein side-chains which is used to extract generalized order parameters from NMR relaxation experiments and MD simulations.</p>
Zenodo
2019-11-08
info:eu-repo/semantics/lecture
3533434
user-openforcefield
1579540902.153153
23953870
md5:71114fc9b3a35ae2d7ba04e25e1bae4e
https://zenodo.org/records/3533435/files/FalkHoffmann-OFFWebinar-Slides.pdf
35157172
md5:ece907b201f92a6865c233b9016173f4
https://zenodo.org/records/3533435/files/FalkHoffmann-2019-09-20.mp4
public
https://youtu.be/CkjVspPURFU
Is part of
url
https://chemrxiv.org/articles/Predicting_NMR_Relaxation_of_Proteins_from_Molecular_Dynamics_Simulations_with_Accurate_Methyl_Rotation_Barriers/8982338/1
Cites
url
10.5281/zenodo.3533434
isVersionOf
doi