Flexibility of BIV TAR-Tat: Models of Peptide Binding

Flexibility of BIV TAR-Tat: models of peptide binding.

A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database ...

Thermodynamics and solvation dynamics of BIV TAR RNA-Tat peptide interaction.

The interaction of the trans-activation responsive (TAR) region of bovine immunodeficiency virus (BIV) RNA with the Tat peptide is known to play important role in viral replication. Despite being thoroughly studied through a structural point of view, the nature of binding between BIV TAR RNA and the BIV Tat peptide requires information related to its thermodynamics and the nature of hydration a...

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 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-wor...

Translational repression using BIV Tat peptide-TAR RNA interaction in mammalian cells.

We developed a strategy to create novel genetically encoded switches based on translational repression. We illustrated its efficacy by incorporating two copies of an RNA hairpin in the 5'-untranslated region (UTR) of a target mRNA and demonstrating 7-fold translational repression upon expression of a ligand - the BIV Tat peptide.

Peptide models of the Tat-TAR protein-RNA interaction.