Videos

Intricate role of water molecules in protein dynamics

Presenter
December 8, 2008
Keywords:
  • molecular biology
MSC:
  • 92C40
Abstract
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.