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

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 increase...

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Autor principal: Wall, Michael E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947722/
https://www.ncbi.nlm.nih.gov/pubmed/29765607
http://dx.doi.org/10.1107/S2052252518000519
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author Wall, Michael E.
author_facet Wall, Michael E.
author_sort Wall, Michael E.
collection PubMed
description 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.
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spelling pubmed-59477222018-05-15 Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering Wall, Michael E. IUCrJ Research Papers 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. International Union of Crystallography 2018-01-25 /pmc/articles/PMC5947722/ /pubmed/29765607 http://dx.doi.org/10.1107/S2052252518000519 Text en © Michael E. Wall 2018 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/2.0/uk/
spellingShingle Research Papers
Wall, Michael E.
Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title_full Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title_fullStr Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title_full_unstemmed Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title_short Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
title_sort internal protein motions in molecular-dynamics simulations of bragg and diffuse x-ray scattering
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947722/
https://www.ncbi.nlm.nih.gov/pubmed/29765607
http://dx.doi.org/10.1107/S2052252518000519
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