hide
Free keywords:
Protein dynamics; Molecular dynamics; Conformational sampling;
Collective coordinates; Collective degrees of freedom; Enhanced sampling; Replica exchange; Principal component analysis/PCA;
Essential dynamics; TEE-REX; CONCOORD/tCONCOORD; Geometrical constraints
Abstract:
Understanding protein function requires detailed knowledge about protein
dynamics, i.e. the different conformational states the system can adopt. Despite
substantial experimental progress, simulation techniques such as molecular
dynamics (MD) currently provide the only routine means to obtain dynamical
information at an atomic level on timescales of nano- to microseconds. Even with the
current development of computational power, sampling techniques beyond MD are
necessary to enhance conformational sampling of large proteins and assemblies
thereof. The use of collective coordinates has proven to be a promising means in this
respect, either as a tool for analysis or as part of new sampling algorithms. Starting
from MD simulations, several enhanced sampling algorithms for biomolecular
simulations are reviewed in this chapter. Examples are given throughout illustrating
how consideration of the dynamic properties of a protein sheds light on its function.
