Protein Dynamics: From Structure to Function
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.
KeywordsProtein 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
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