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

IUCrJ
Michael E Wall

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 do...Continue Reading

References

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Citations

May 17, 2018·IUCrJ·Michael E Wall
Jun 27, 2019·Journal of Applied Crystallography·Andrew R McCluskeyKaren J Edler
Oct 31, 2019·Wiley Interdisciplinary Reviews. Computational Molecular Science·David S Cerutti, David A Case
Jul 18, 2020·F1000Research·Michael C ThompsonJose A Rodriguez
Mar 11, 2020·Nature Communications·Steve P MeisburgerNozomi Ando
Mar 6, 2019·Journal of the American Chemical Society·Michael E WallGregory L Warren

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Methods Mentioned

BETA
X-ray
Bragg diffraction
NMR

Software Mentioned

Lunus Python script
phenix
Computational Crystallography Toolbox ( cctbx
simulate
MOLREP
MolProbity
AmberTools
NVT
Lunus
CHARMM27

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