Related ArticlesPredicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers.
J Chem Phys. 2020 Feb 28;152(8):084102
Authors: Hoffmann F, Mulder FAA, Schäfer LV
Abstract
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, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations even now display very good agreement with the experiment. Results herein showcase the performance of present-day MD force fields and manifest their refined ability to accurately describe internal protein dynamics.
[NMR paper] Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Related Articles Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
J Phys Chem B. 2019 Apr 11;:
Authors: Rashid S, Lee BL, Wajda B, Spyracopoulos L
Abstract
19F NMR spectroscopy is a powerful tool for the study of the structures, dynamics, and interactions of proteins bearing cysteine residues chemically...
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[ASAP] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations
Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations
https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00195/20180430/images/medium/bi-2018-001959_0008.gif
Biochemistry
DOI: 10.1021/acs.biochem.8b00195
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[NMR paper] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Biochemistry. 2018 Apr 17;:
Authors: Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is...
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04-18-2018 01:41 PM
[NMR paper] Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Biochemistry. 2018 Feb 07;:
Authors: Solomentsev G, Diehl C, Akke M
Abstract
FKBP12 (FK506 binding protein 12 kDa) is an important drug target that attracts a great deal of interest as a model system for computational drug design and studies on the role of protein dynamics in ligand binding. NMR...
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NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
Publication date: 2 February 2018
Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br>
Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br>
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[NMR paper] Ab-initio Prediction of NMR Spin-Relaxation Parameters from Molecular Dynamics Simulations.
Ab-initio Prediction of NMR Spin-Relaxation Parameters from Molecular Dynamics Simulations.
Related Articles Ab-initio Prediction of NMR Spin-Relaxation Parameters from Molecular Dynamics Simulations.
J Chem Theory Comput. 2018 Jan 02;:
Authors: Chen PC, Hologne M, Walker O, Hennig J
Abstract
1H-15N NMR spin relaxation and relaxation dispersion experiments can reveal the time scale and extent of protein motions across the ps-ms range, where the ps-ns dynamics revealed by fundamental quantities R1, R2, and heteronuclear NOE can be...
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[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
J Phys Chem B. 2014 Oct 28;
Authors: Allnér O, Foloppe N, Nilsson L
Abstract
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...
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Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja1083656
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