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 pr...

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Bibliographic Details
Published in:Journal of biomolecular structure & dynamics 1998-10, Vol.16 (2), p.223-235
Main Authors: Kothekar, V., Raha, K., Prasad, H. K.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Bacterial Proteins - chemistry
Bacterial Proteins - metabolism
Base Pairing
Clostridium - chemistry
Clostridium pasteurianum
Computer Simulation
DNA - chemistry
DNA - metabolism
Histones - chemistry
Histones - metabolism
Models, Molecular
Molecular Sequence Data
Mycobacterium tuberculosis
Mycobacterium tuberculosis - chemistry
Nucleic Acid Conformation
Protein Structure, Secondary
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Summary: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.
ISSN:0739-1102
1538-0254
DOI:10.1080/07391102.1998.10508241