2012 Student Research Conference:
25th Annual Student Research Conference

Computational Studies of Protein-RNA Recognition in Viral Leukemia
Shane M. Bernard
Dr. Maria Nagan, Faculty Mentor

Adult T-cell leukemia, caused by a virus called human T-cell leukemia virus type-1 (HTLV-1), infects 10 to 20 million people throughout the world. Rex, a critical viral protein, signals the transition from the early to late phases in the viral life cycle. Rex binds to a specific sequence in viral RNA known as the Rex Response Element (RxRE). The Rex peptide is known to have a higher binding affinity for the aptamer of RexRE than the wild-type RNA, though the source of this difference in affinities is unknown. The purpose of this study is to better understand the roles that arginine-rich motifs and the role of water in Rex recognition of RxRE and its aptamer. Systems have been simulated under 200 mM KCl in the presence of explicit water molecules. Histograms of water positions and measurements of water lifetimes indicate R7 and R13 participate in formation of water networks on the peptide-RNA interface. Systems are being analyzed via thermodynamic integration to determine the free energy of binding of the complex.

Keywords: rna, protein, virus, leukemia, simulation


Presentation Type: Oral Paper

Session: 104-2
Location: MG 2090
Time: 8:15

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