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Presentation

Peri Herman
Truman State University

Subject Listing - Chemistry
Advisor: Dr. Maria Nagan

Thursday, Oral Session 1, Presentation 1, Karpen Hall 035

COMPUTATIONAL SIMULATIONS OF THE HUMAN IMMUNODEFICIENCY VIRUS REV-RRE COMPLEX

Many drugs fight Acquired Immunodeficiency Syndrome but due to its high mutation rate, new and different drugs are needed, requiring a better understanding of how the Human Immunodeficiency Virus works. One area to study is the involvement of the Rev-rev response element (RRE) complex. Rev, which contains an arginine-rich 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-RRE works in vivo. To accomplish this, three models of the complex, were simulated with explicit water and counter ions using molecular dynamics in the program AMBER and visualized with the program VMD. All simulations were begun from NMR structures (Battiste, J. L. et al. Science 1996, 273, 1547) 4.0 ns of data have been collected for all three models. Root mean square deviation of each model from its starting structure and the average structure indicate simulation convergence. Atomic fluctuations have been calculated on all three models indicating that the system is fairly dynamic. Water analysis is currently being run on all three models to find out if ion binding is involved. This research will hopefully serve as a starting place for the next researcher.

Moberly Area Community College
Moberly, MO 65270

Advisor: Dr. Maria Nagan, Assistant Professor, Chemistry, Truman State University, Kirksville, MO