Friday, 27 October 2006
OLCC-McClain (Oakley-Lindsay Center)
249

Molecular Dynamics Studies of the Human Immunodeficiency Virus Rev-RRE Complex under Varying Salt Concentrations

Billy Ray Miller III, Truman State University, Kirksville, MO

Acquired Immunodeficiency Syndrome (AIDS) and the virus that causes the disease, Human Immunodeficiency Virus (HIV), have been responsible for millions of deaths around the world. In an attempt to understand HIV and its life an essential component of the life cycle, recognition of the Rev Response Element (RRE) by the Rev protein is examined computationally. The Rev-RRE complex signals a cascade of events that eventually allows the unspliced and partially spliced viral RNA to exit the host nucleus. It has been previously documented that varying salt concentrations have an effect on the dynamics and binding of the Rev-RRE complex. Molecular dynamics simulations of the complex were collected and examined under various NaCl concentrations (50 mM, 150mM, 500mM, and 1M) in a truncated octahedron box of water. Root Mean Square (RMS) fluctuations on all protein side chains were determined. These preliminary results suggest that several side chains are behaving contrary to previous proton NMR studies performed by Wilkinson et al. (2000). Further analysis will include characterization of salt effects on the free energy of binding.

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