Combining Viral Rhodopsin and Retinal Rhodopsin for MD Simulations

Erin Cohan* and Blake Mertz, C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506

Field (Broad Category): Biophysics (Physical Sciences & Engineering) 

Student’s Major: Chemistry 

By separating the chain E and keeping the protonation points of the viral rhodopsin, we can replace the protein with retinal rhodopsin and simulate the integration of the protein into the lipid bilayer. By generating an MD simulation using chain E we can then remove and replace the protein chain with a retinal chain in its place. An individual factor of this viral rhodopsin that makes it unique is that it is inverted in comparison to other rhodopsin function group. Along with the idea that by its shape it can also function as an ion channel. Within the research, the lab uses MD simulations to generate data and graphs measuring lipid concentration and other important factors. By swapping chain E with the retinal protein we hope to merge the two systems successfully. Along with merging the retinal protein, we are about to use the system in a more versatile fashion. By completing the MD simulations we hope to improve the uses for the medical field and alternative energy. 

Funding: 

Program/mechanism supporting research/creative efforts: WVU's Research Apprenticeship Program (RAP) & accompanying HONR 297-level course