Intricate role of water molecules in protein dynamics

Monday, December 8, 2008 - 10:00am - 10:40am
EE/CS 3-180
Donald Hamelberg (Georgia State University)
Water molecules are ubiquitous in living organisms and have therefore been
viewed more as an environment for biomolecules rather than as a collection
of interacting molecules. Water molecules make up an integral part of
protein structures, while assisting in catalysis, providing stability and
controlling the plasticity of binding sites. In order to realistically mimic
the environment of biomolecules, molecular dynamics simulations are
routinely done in explicit water. Unfortunately, most of the computational
resources go into computing the interactions between these water molecules.
Therefore, many implicit solvation models pursued over the years have only
viewed the presence of water as a continuum dielectric. However, critical
questions do arise about the inherent faster dynamics that are usually
obtained with implicit solvation models. We show that explicit water does
not only slow down protein dynamics by increasing the frictional drag, but
also by increasing the local energetic roughness of the energy landscape by
as much as 1.0 kcal/mol, an effect which is lacking in typical implicit
solvation models. The possible implications of this effect in catalysis will
also be discussed.
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