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.
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 showed reduced compaction. In the presence of Hlpmt two ends of helicoidal axis of U35DNA came closer, but slightly out of plane, indicative of its role in overwinding and packaging double stranded DNA. DBHclopa did not give rise to DNA overwinding. The results show architectural role of Hlpmt and DBHclopa in DNA packaging and its sequence dependence.
Kothekar
V
V
Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi. kothekar@medinst.emet.in
Raha
K
K
Prasad
H K
HK
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D020029:Base Pairing; D003013:Clostridium / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006657:Histones / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary
D001426:Bacterial Proteins; D006657:Histones; D004247:DNA