Comparative modeling and molecular dynamics studies on TAR RNA
binding properties of human immunodeficiency virus TAT protein

Abstract

Macromolecules undergo changes with time and condition thereby affecting the structural and functional properties. These sequential and structural changes can be enumerated by
comparative methods using the sequences and structural models. Molecular dynamics simulations are used to investigate dynamics and interactions of proteins in aqueous solution. We have studied the sequential variations in HIV-1 Trans-activating regulatory protein (Tat) among different strains and isolates taken from different geographical areas. Then these variations are modeled in consensus structures, so that each of the disparity can be suitably studied. Molecular dynamics simulation is carried out on each of these models to study the residual motions and interaction fluctuations. The results are compared and the functional implications of each of these transforms are studied. We have identified intra molecular interactions of importance for structure stabilization. The results show the functional characteristics of the protein or part of it is precisely reflected in its structural interactions and molecular dynamics flexibility.