2007 Student Research Conference:
20th Annual Student Research Conference


Molecular Dynamics Studies of Human Immunodeficiency Virus RSG-1.2-RRE Recognition
Lauren A. Michael
Dr. Maria Nagan, Faculty Mentor

Binding of the human immunodeficiency virus (HIV) protein, Rev, is an essential step to the HIV life cycle. A synthetic peptide, RSG-1.2, has been found to bind with the Rev Response Element (RRE) of HIV RNA with much greater affinity and specificity than the Rev peptide. Molecular Dynamics (MD) simulations have been used to characterize specific interactions of RSG-1.2 with RRE and to examine the effects of salt concentrations on these interactions. The lowest-energy model of RSG-1.2 has being simulated with explicit water and salt ions using the AMBER 8.0 molecular dynamics suite. Each trajectory is propagated for 10.0 ns using a 2.0 fs time step at constant pressure and temperature, then visualized with VMD 1.8.4b6. Intermolecular hydrogen bonding is assessed and electrostatic surface potentials will be generated. As arginine residues in Rev are known to be important for binding, contacts of arginine residues in RSG-1.2 will also be evaluated.

Keywords: biochemistry, computational, molecular dynamics, HIV, RNA, protein, RSG-1.2, hydrogen bonding


Presentation Type: Oral Paper

Session: 63-4
Location: VH 1416
Time: 3:30 pm

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