MOLECULAR DYNAMICS STUDY OF THE MOTION OF ATOMIC COMPONENTS OF THE DNA MOLECULE AND ITS ENVIRONMENT

PATRICIO PEREZ, Purdue University

Abstract

It is of great interest for us to come to a better understanding of some biological processes through a study of the behavior of the atomic entities involved in them. One of the most important biological molecules in DNA. In the outer part of its helical structure, phosphate groups are known to be present. The natural environment of this molecule is liquid water. Some cations like Na('+) and Mg('2+) are often found in its surroundings. In this work we show results of applying a polarizable water model (the PE model) to the molecular dynamics simulation of hydrated sodium ion microclusters. We found that the PE model with just two adjustable parameters reproduces the experimental enthalpies of formation of the ion-water microclusters better than a number of other methods. We also found that for the case of six water molecules at O K, they do not form a regular octahedron around the sodium ion as predicted by other models. The predicted change in structure appears to be in agreement with experimental observations. We introduced later a phosphate group and performed a molecular dynamics simulation of its interaction with water and a sodium cation. We use polarizable models for both water and the phosphate group. According to our calculation, a potential fitted to quantum mechanical results produces a strong binding between the sodium and the phosphate group. This binding is such that hydration of the sodium is not clearly observed. Regardless of this we can conclude that the effect of assuming the phosphate group polarizable is not significant.

Degree

Ph.D.

Subject Area

Molecules

COinS