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Title: Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

Abstract

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations canmore » be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Authors:
ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE National Nuclear Security Administration (NNSA); Univ. of California, Los Angeles, CA (United States)
OSTI Identifier:
1418076
Alternate Identifier(s):
OSTI ID: 1427377
Report Number(s):
LA-UR-17-27716
Journal ID: ISSN 2052-2525; IUCRAJ
Grant/Contract Number:
AC52-06NA25396
Resource Type:
Journal Article: Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 5; Journal Issue: 2; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biological Science; diffuse scattering; protein crystallography; X-ray diffraction; molecular dynamics simulation; protein conformational ensemble; staphylococcal nuclease

Citation Formats

Wall, Michael E. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering. United States: N. p., 2018. Web. doi:10.1107/S2052252518000519.
Wall, Michael E. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering. United States. doi:10.1107/S2052252518000519.
Wall, Michael E. Thu . "Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering". United States. doi:10.1107/S2052252518000519.
@article{osti_1418076,
title = {Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering},
author = {Wall, Michael E.},
abstractNote = {Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.},
doi = {10.1107/S2052252518000519},
journal = {IUCrJ},
number = 2,
volume = 5,
place = {United States},
year = {Thu Jan 25 00:00:00 EST 2018},
month = {Thu Jan 25 00:00:00 EST 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1107/S2052252518000519

Citation Metrics:
Cited by: 1 work
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