2006 Student Research Conference:
19th Annual Student Research Conference


Computational Simulations of the Human Immunodeficiency Virus Rev-RRE Complex
Peri W. Herman
Dr. Maria Nagan, Faculty Mentor

One area of study in computational simulations of the Human Immunodeficiency Virus is the involvement of the Rev-rev response element (RRE) complex. The Rev peptide binds to the RRE sequence of mRNA signaling transport of unspliced and partially spliced RNA out of the nucleus. It is necessary to characterize the arginine side-chain dynamics to understand how Rev binds in vivo. To accomplish this, three models of the complex were simulated using molecular dynamics in the program AMBER. All simulations were begun from NMR structures. Four nanoseconds have been collected on all three models. Root mean square deviation (RMSD) of each model from its starting structure and the average structure indicate convergence. Atomic fluctuations have been calculated on all three models indicating that the system is dynamic. This research will serve as a starting place for the next researcher.

Keywords: Rev, HIV, Arginine side-chains, RRE, mRNA, Molecular Dynamics, NMR structure, Atomic fluctuations


Presentation Type: Oral Paper

Session: 26-1
Location: VH 1432
Time: 9:45

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