RUI: Atomistic Modeling of Membrane Proteins

Wabash College, Crawfordsville IN

Investigators

Abstract

Title: RUI: Atomistic Modeling of Membrane Proteins Many proteins carry out their function within the environment of the cellular membrane. In this project, the investigator will use computer modeling to examine the effect of lipids on the structure and interactions of proteins contained within the cellular membrane. The membrane protein that will be the focus of this work is Rhodopsin, the protein involved in the first steps of the vision process and one that serves as a model for an important class of membrane proteins. Undergraduate students will be trained in this project. In addition to learning computer simulation methods, students will present their results to the campus community and at national and regional scientific meetings. These presentations will prepare them for careers as scientific researchers and will demonstrate exciting opportunities available to prospective science majors. All science majors at the institution will be impacted during undergraduate instruction through the transfer of molecular modeling techniques from the research laboratory to the chemistry curriculum. The primary research tool for this investigation is molecular dynamics (MD) computer simulation. Specific projects include: (1) studies of lipid mediated protein-protein interaction as a function of lipid type with a focus on polyunsaturation, (2) characterization of the annulus of lipids associated with transmembrane proteins in terms of structural, dynamic, and thermodynamic parameters, (3) investigation of retinal-opsin interactions as a function of the Rhodopsin photocycle to understand the extent of reciprocal control between protein and ligand, and (4) refinement of the CHARMM force field for modified retinal ligands to support investigations of their role as agonists. This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Chemical Theory, Models and Computational Methods Program in the Division of Chemistry in the Directorate of Mathematical and Physical Sciences.