当前位置： SCI文献检索 > BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS期刊下所有文献 > General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations.

Abstract：

:Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner.

journal_name

Biochem Biophys Res Commun

journal_title

Biochemical and biophysical research communications

authors

Liu Q,Shi C,Yu L,Zhang L,Xiong Y,Tian C

doi

10.1016/j.bbrc.2015.01.018

subject

Has Abstract

pub_date

2015-02-13 00:00:00

pages

467-72

issue

3

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(15)00040-6

journal_volume

457

pub_type

杂志文章

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