2007 Student Research Conference:
20th Annual Student Research Conference

Science

Molecular Dynamics Studies of the HIV Rev-RRE Complex
Jessica A. Chenault* and Billy R. Miller III
Dr. Maria Nagan, Faculty Mentor

Binding of the viral protein Rev to the Rev response element (RRE), a sequence found in viral mRNA, is an essential step in the HIV lifecycle. The structure of a minimal peptide-RNA complex has been solved by NMR, but not all of the interactions were resolved. Molecular dynamics simulations of three models of the minimal peptide-RNA complex have been simulated in explicit water, employing the SANDER module of AMBER 8.0 and the Cheatham modifications to the Cornell et al. forcefield. To characterize interactions of the Rev-RRE complex, hydrogen bonding analysis was performed and the results compared to those reported in the NMR structure and biochemical studies. Similar simulations and root mean square calculations were performed on one of these models at salt concentrations of 50 mM, 150 mM, 200 mM, and 500 mM in order to characterize the effect of salt on arginine side chains and Rev-RRE complex stability.

Keywords: HIV, RNA, protein, hydrogen bonding, RMSD, molecular dynamics, biochemistry, computational

Topic(s):Chemistry

Presentation Type: Oral Paper

Session: 63-3
Location: VH 1416
Time: 3:15 pm

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