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.  |
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