Computationally Intensive Research Project

Structure and Recognition in Microbial Membranes, Proteins, and DNA

T. P. Straatsma¹, Mark S. P. Sansom², J. P. Armitage², Michel Dupuis¹, Michael A. Kennedy¹, Martin Zacharias³, John H. Miller⁴, Maciej Gutowski¹, P. Hobza⁵, Erich R. Vorpagel⁶

¹Pacific Northwest National Laboratory, ²University of Oxford, ³International University Bremen, ⁴Washington State University, ⁵Academy of Sciences of the Czech Republic, ⁶Environmental Molecular Sciences Laboratory

FY07 Allocation - 1,050,000

Abstract

Developments in simulation methodologies as well as computer hardware have enabled the molecular simulation of biological systems of increasing size and with increasing accuracy, providing molecular-level detail that is difficult or impossible to obtain experimentally. Computer modeling and simulation studies contribute to our understanding of the behavior of proteins as well as of protein-protein and protein-DNA complexes.

In recent years significant progress has been made in applying molecular simulation methods to the study of biological membranes. However, these applications have focused exclusively on lipid bilayer membranes and on membrane proteins in lipid bilayers. A few simulation studies of outer membrane proteins of Gram-negative bacteria have been reported using simple lipid bilayers, though this is not a realistic representation of the outer membrane environment. This proposal involves more realistic simulation studies of outer membrane proteins of Gram-negative bacteria that include the lipopolysaccharide (LPS) layer. This will make simulations much more complex because of several factors: (1) the limited experimental data available allowing the construction of a molecular model for a single LPS molecule, (2) the need for a parameterization of the oligosaccharide, (3) the complicated setup and equilibration procedure as a result of the highly charged LPS molecules that need to be neutralized by counter ions, and (4) the increase in computational requirements as a result of the much larger molecular systems. This project will focus on generating a library of outer membrane protein simulations to provide an opportunity for large-scale comparative studies of conformational dynamics within a rather disparate family of membrane proteins. The focus on the bacterial cell wall of Gram-negative bacteria is of direct interest to Department of Energy concerns such as the Genomics: GTL program, energy production, and environmental remediation and restoration.

The second component of the proposed project involves modeling studies of damaged cellular DNA as a result of environmental factors including ionizing radiation. The damage resulting from oxidative stress and ionizing radiation is primarily in the form of oxidized bases, single strand breaks, and loss of bases. The goal of this part of the project is to provide, via large-scale computations and simulations, critical information to help characterize the qualitative and quantitative elements that affect structure, stability, and repair characteristics of DNA. This information is important, for example, in understanding the differences between clustered damage sites in DNA formed by ionizing radiation and singly damaged sites produced by endogenous processes. Changes in base-pairing rules can be traced to molecular-level features of the damaged site(s). The premise is that base-pairing and base-stacking interactions are qualitatively and quantitatively different for singly and multiply damaged DNA sites.