MOLECULAR SIMULATIONS OF PROTEIN STRUCTURE AND DYNAMICS

Synopsis

Molecular dynamics (MD) simulations offer a powerful tool to investigate the structure and dynamics of proteins because they can provide an all-atom view of their complex conformational landscapes. Using simulations, we study biomolecular systems consisting of hundreds of thousands to millions of atoms on a nanosecond to microsecond timescale. These system sizes and timescales are relevant to functionally important processes, such as ligand binding, protein allostery, and protein aggregation. With recent advances in both simulation and experiment, it is now possible to make direct comparisons between data obtained in silico and in vitro. MD offers a useful tool to elucidate the molecular basis for effects observed using experimental methods, and to quantitatively describe differences in protein ensembles. I will present recent and ongoing simulation studies of proteins across the continuum of protein disorder, from ordered states of proteins in crystals to intrinsically disordered regions.