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Peptide and Protein

Early stage unwinding mechanism of homo and co-poly peptides

An α-helix is the most important secondary structure among the secondary structures found in proteins and peptides. Also understanding the unwinding mechanism of homopolymeric peptides can help in gaining useful insight in designing stable helical peptides and a priori knowledge of unwinding position in an α-helix made up of various amino acids. Thus, we study the unwinding mechanisms of α-helical homopolymeric peptides under ambient conditions using classical molecular dynamics simulations. In addition to this we are trying to gain insight into the unwinding mechanism of α-helical block copolymers  made by various combination of amino acids. 

Peptide Self assembly

PcrA helicase protein - domain motion 

Computational biology is very fast emerging area nowadays. Many peoples are concerned with studies of very complex biological problems to understand the nature of biological processes like enzyme catalyzed reactions, protein folding, protein-protein and protein-metal interactions etc.; we mainly focus on the mechanistic and protein dynamics studies. Molecular Dynamics simulation is found to be a very efficient tool for understanding the atomistic/molecular picture (structure-property relations, mechanism, dynamical, thermo dynamical properties) of the problems in silico. Many force fields have been developed for last two decades to perform MD simulation more realistically for real biological systems. Multiscale techniques which include quantum chemical, classical molecular dynamics, coarse grained molecular dynamics and mesoscale techniques are used to study the micro scale to meso scale properties of the biological systems. 
We are working on the understanding of basic mechanisms of unwinding of the DNA assisted by the enzyme helicase. We are dealing with the PcrA helicase from Bacillus stereothermophilus, mainly on the process of the unwinding of DNA by the enzyme by the all atomistic Molecular Dynamics study.

PcrA helicase: Monomeric protein consisting of 2 domains with subdomains for each domain, 1A, 2A, 1B, 2B. Experimental studies evidenced that the domain movement of the 1A and 2A involves in the mechanism in the unwinding of DNA. Hence we are mainly focused on the study of these domains motion using Molecular Dynamics Simulation. How the domains displacement can take part in the unwinding of the DNA. Various kinds of analysis were performed to confirm the role of the domain movement in the unwinding of the DNA e.g. distance between domains 1A and 2A, hinge angle between the domains, root mean square displacement, radius of gyration. In addition, we have also elucidating the free energy profiles of binding and unbinding of ATP and as well as local interaction at the active site.