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

2001
2001
Inglese
80
6
2833
2842
2-s2.0-0034999080
Sì, ma tipo non specificato
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.
4
info:eu-repo/semantics/article
262
Carolina, M Reyes; Nifosì, Riccardo; Alan, D Frankel; Peter, A Kollman
01 Contributo su Rivista::01.01 Articolo in rivista
none
01.01 Articolo in rivista
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.14243/195848
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