Molecular Dynamics Simulation of Interaction of Histone-like Protein of Mycobacterium Tuberculosis (Hlpmt) and Histone of Clostridium Pasteurianum (DBHclopa) with 35 Based Paired GC Rich U-bend DNA

Abstract Three dimensional structure of the first ninety two residues of histone like protein from Mycobacterium tuberculosis (Hlpmt) and histone of Clostridium pasteurianum (DBHclopa) are obtained here, on the basis of amino acid sequences of the two proteins, making use of secondary structure prediction programs, sequence search and HOMOLOGY based modeling tools available on Internet. The proteins were docked to a 35 base paired GC rich U bend DNA (U35DNA). Structures of proteins Hlpmt and DBHclopa; U35DNA; and complexes: Hlpmt-U35DNA and DBHclopa-U35DNA were optimized by molecular mechanics (MM) and simulated for 260 pico seconds (ps) in vacuum by molecular dynamics (MD) technique using AMBER 4.0 package with Cornell et al force field. The proteins, when simulated alone, showed compaction. DBHclopa showed larger compaction compared with Hlpmt. U35DNA when simulated alone straightened out and assumed a B-form. In the complexes, Hlpmt showed same order of compaction as in absence of DNA, while DBHclopa s...