Structural Analysis of Macromolecules by Molecular Dynamics Simulation

Abstract

We carried out molecular dynamics simulations of two types of macromolecules, i.e. reverse micelles and, β-1, 3-Dglucans to gain an atomic-level picture of the structure and dynamics.
For reverse micelle simulations, we employed sodium bis (2-ethylhexyl) sulfosuccinate, known as AOT and a new synthesized surfactant, dioleyl phosphoric acid (abbreviated as DOLPA) . After substantial conformational rearrange-ment during the simulations, the final configurations appear to have roughly spherical shapes in the aggregate. Surfactant molecules almost cover the whole core waters. The core of the DOLPA micelle changed from a spherical to an oval shape, while the core remained spherical in an AOT reverse micelle. From the coordination number among micelle components, the difference comes from the interaction between potassium ions and the hydrophilic groups of surfactant, i.e. the phosphoric acid groups of DOLPA and the sulfuric acid groups of AOT.
The β-1, 3-D-glucan forms a right-handed triple helix, and it has been believed that the intermolecular hydrogen bond is present at the center of the helix to maintain the structure. In this hydrogen bond model, three 2nd hydroxyl groups form an inequilateral hexagonal shape perpendicular to the helix axis. We carried out semi-empirical quantum mechanis and ab initio calculations for β-1, 3-D-glucan models, and proposed a new intermolecular hydrogen bond. In our model, the hydrogen bond forms between the O2 atoms on different x-y planes along the helix, hence the hydrogen bond is not perpendicular to the helix axis. The new hydrogen bonds are connected along the helix, traversing three glucan chains to make a left-handed helix. Furthermore, by molecular dynamics simulations for β-1, 3-D-glucan in aqueous solution, the new hydrogen bond we proposed is found to be a major type for most cases.