Molecular dynamics simulations and free energy calculations on protein-nucleic acid complexes

Abstract

We review herein the relevant literature on molecular dynamics simulations of protein-nucleic acid complexes and discuss how the procedure can be employed to gain insight into aspects of the molecular recognition mechanism such as induced fit and the role of solvent, which are not easily forthcoming in experimental studies. We present an overview of the free energy component analysis procedure that can be used in understanding the significance of various physical forces that participate in the complexation process and provide a critical analysis of their applications. © 2006 Springer.