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. 2001 Jun;80(6):2833–2842. doi: 10.1016/S0006-3495(01)76250-9

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

C M Reyes 1, R Nifosì 1, A D Frankel 1, P A Kollman 1
PMCID: PMC1301468  PMID: 11371457

Abstract

We have performed molecular dynamics (MD) simulations, with particle-mesh Ewald, explicit waters, and counterions, and binding specificity analyses using combined molecular mechanics and continuum solvent (MM-PBSA) on the bovine immunodeficiency virus (BIV) Tat peptide-TAR RNA complex. The solution structure for the complex was solved independently by Patel and co-workers and Puglisi and co-workers. We investigated the differences in both structures and trajectories, particularly in the formation of the U-A-U base triple, the dynamic flexibility of the Tat peptide, and the interactions at the binding interface. We observed a decrease in RMSD in comparing the final average RNA structures and initial RNA structures of both trajectories, which suggests the convergence of the RNA structures to a MD equilibrated RNA structure. We also calculated the relative binding of different Tat peptide mutants to TAR RNA and found qualitative agreement with experimental studies.

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Selected References

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