Paper Citing NAMD - Abstract
Wedberg, Rasmus; Abildskov, Jens; Peters, Gunther H.
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2575-2585, MAR 1 2012
In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.
