Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor

Abstract

Solvent interactions, especially solvent-mediated dielectric screening and Debye-Hückel screening, are thought to be essential determinants of the structure and function of proteins and nucleic acids. These interactions guide the polypeptide chain towards a protein's native conformation [2, 3, 4], stabilize the B structure of DNA, govern transitions to its A form [5] and play an important role in substrate binding and enzymatic activity [6, 7, 8]. The proper description of solvent-mediated electrostatic interactions of biopolymers have received increased attention and methods have been developed to determine the electrostatic potential around biopolymers. Some of the efforts have presented water external to biopolymers by discrete descriptions either involving molecular dynamics models of water [9, 10, 11] or its representation by Langevin dipoles [12]. Other efforts have described water by a continuum model [13, 7, 14, 15].