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:

Wall, Michael E.  ^[1]

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1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Publication Date:

Thu Jan 25 00:00:00 EST 2018

Research Org.:

Los Alamos National Laboratory (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; PII: S2052252518000519

Grant/Contract Number:  

AC52-06NA25396

Resource Type:

Published Article

Journal Name:

IUCrJ

Additional Journal Information:

Journal Name: IUCrJ Journal Volume: 5 Journal Issue: 2; Journal ID: ISSN 2052-2525

Publisher:

International Union of Crystallography

Country of Publication:

United Kingdom

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