Biochemistry Seminar: David A. Case, "MD simulations of total X-ray scattering in protein crystals"
City College of New York<br />
85 Saint Nicholas Terrace
David A. Case, Distinguished Professor, Department of Chemistry and Chemical Biology, Rutgers University, NJ, will give a talk on "MD simulations of total X-ray scattering in protein crystals"
The adaption of graphical processing units (GPUs) to biomolecular simulations has made microsecond-scale simulations of biomolecular
crystals available on a nearly-routine basis. Typically, a super-cell consisting of several crystallographic unit cells becomes
the periodically-repeating unit in the simulation.
Straightforward comparisons between computed and experimental average structures and atomic displacement parameters can be used to identify problems in biomolecular force fields. The high accuracy and precision crystallography (compared to NMR or other solution methods)
makes such comparisons uniquely informative, and the statistics of such comparisons benefit from having many copies of chains in equivalent
environments in the simulation.
Structural fluctuations in the simulations can be used to estimate diffuse scattering intensities, which can be compared to measurements
using modern detectors. Both simulations and experiments allow one to place Bragg and non-Bragg intensities on a common, "absolute",
scale, showing that a surpisingly large fraction of scattered X-rays occur between the Bragg peaks, and are usually ignored.