Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex

We have performed molecular dynamics (MD) simulations, with particle-mesh E wald, explicit waters, and counterions, and binding specificity analyses us ing combined molecular mechanics and continuum solvent (MM-PBSA) on the bov ine immunodeficiency virus (BIV) Tat peptide-TAR RNA complex. The solution structure for the complex was solved independently by Patel and cc-workers and Puglisi and co-workers. We investigated the differences in both structu res and trajectories, particularly in the formation of the U-A-U base tripl e, the dynamic flexibility of the Tat peptide, and the interactions at the binding interface. We observed a decrease in RMSD in comparing the final av erage RNA structures and initial RNA structures of both trajectories, which suggests the convergence of the RNA structures to a MD equilibrated RNA st ructure. We also calculated the relative binding of different Tat peptide m utants to TAR RNA and found qualitative agreement with experimental studies .