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Title: Motional displacements in proteins: The origin of wave-vector-dependent values

Abstract

In the case of average mean-square displacement, r 2 , of H atoms in a protein, it is frequently determined using incoherent neutron-scattering experiments. r 2 is obtained from the observed elastic incoherent dynamic structure factor, S i(Q,ω =0), assuming the form S i(Q, ω =0) =exp( -Q 2 r 2 /3). Moreover, this is often referred to as the Gaussian approximation (GA) to S i(Q, ω =0). r 2 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S i(Q, ω =0) deviates from the GA. We investigate the origin of the Q dependence of r 2 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q, ω ) is an accurate approximation and is not the origin of the Q dependence of r 2 . We demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein.more » Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average r 2 . The observed Q dependence of r 2 can be used to provide information on the dynamical heterogeneity in proteins.« less

Authors:
 [1];  [2];  [2];  [1]
  1. Univ. of Delaware, Newark, DE (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1265912
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Additional Journal Information:
Journal Volume: 91; Journal Issue: 5; Journal ID: ISSN 1539-3755
Publisher:
American Physical Society (APS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Vural, Derya, Hong, Liang, Smith, Jeremy C., and Glyde, Henry R. Motional displacements in proteins: The origin of wave-vector-dependent values. United States: N. p., 2015. Web. doi:10.1103/PhysRevE.91.052705.
Vural, Derya, Hong, Liang, Smith, Jeremy C., & Glyde, Henry R. Motional displacements in proteins: The origin of wave-vector-dependent values. United States. doi:10.1103/PhysRevE.91.052705.
Vural, Derya, Hong, Liang, Smith, Jeremy C., and Glyde, Henry R. Thu . "Motional displacements in proteins: The origin of wave-vector-dependent values". United States. doi:10.1103/PhysRevE.91.052705.
@article{osti_1265912,
title = {Motional displacements in proteins: The origin of wave-vector-dependent values},
author = {Vural, Derya and Hong, Liang and Smith, Jeremy C. and Glyde, Henry R.},
abstractNote = {In the case of average mean-square displacement, r2 , of H atoms in a protein, it is frequently determined using incoherent neutron-scattering experiments. r2 is obtained from the observed elastic incoherent dynamic structure factor, Si(Q,ω =0), assuming the form Si(Q, ω =0) =exp( -Q2 r2 /3). Moreover, this is often referred to as the Gaussian approximation (GA) to Si(Q, ω =0). r2 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed Si(Q, ω =0) deviates from the GA. We investigate the origin of the Q dependence of r2 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q, ω ) is an accurate approximation and is not the origin of the Q dependence of r2 . We demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average r2 . The observed Q dependence of r2 can be used to provide information on the dynamical heterogeneity in proteins.},
doi = {10.1103/PhysRevE.91.052705},
journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics},
issn = {1539-3755},
number = 5,
volume = 91,
place = {United States},
year = {2015},
month = {5}
}