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 c

SUBMITTER: Wall ME 

PROVIDER: S-EPMC5947722 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature