Biophysical Society Annual Meeting 2020
Date:
As science becomes increasingly interdisciplinary, the Biophysical Society Annual Meeting continues its long-held reputation for bringing together leading scientists from the all over the world who work at the interface of the life, physical, and computational sciences. The dynamic five-day Meeting provides attendees with opportunities to share their latest unpublished findings and learn the newest emerging techniques and applications. More information about the conference here
I presented a poster EF-X IN SILICO: MODELING PROTEIN DYNAMICS IN AN ELECTRIC FIELD.
ABSTRACT:
Protein functions result from local and collective atomic motions that span a wide range of time scales. An integrated analysis of experimental and simulation data can shed light on the detailed mechanism of these motions. Applying a high electric field to protein crystals enables conformational changes that can be captured by time-resolved X-ray crystallography. Such an experiment (referred to as EF-X) carried out on a human PDZ domain obtained a series of atomistic “snapshots” of ensemble averages protein dynamics at 50 to 100 ns time intervals. Here, we present a molecular dynamics (MD) study of the same system and provide a detailed picture of the protein dynamics in between the experimental “snapshots”. We replicated the experimental conditions and system geometry in the presence and absence of an electric field. By constructing a model of the protein crystal as a 3x3x3 supercell with a total of 108 individual proteins, we achieved extensive sampling of the protein conformational ensemble at the sub-millisecond time scale. In the study, we quantify the effects of the electric field on the protein structure and crystal symmetry. This work demonstrates how MD simulations can complement information obtained in EF-X experiments by providing the higher spatial and temporal resolution of underlying dynamical processes.