In silico Study of tertiary structure and binding interaction of Profilin-Schizosaccharomyces pombe

Gangawane A.K¹*, Gomase V.S.², Anjali R.³, Patil C.S.^4
1Department of Biotechnology and Bioinformatics, Padmashree Dr. D. Y. Patil University, Sector 15, CBD Belapur, Navi Mumbai- 400614
²Department of Biotechnology and Bioinformatics, Padmashree Dr. D. Y. Patil University, Sector 15, CBD Belapur, Navi Mumbai- 400614
³Department of Biotechnology and Bioinformatics, Padmashree Dr. D. Y. Patil University, Sector 15, CBD Belapur, Navi Mumbai- 400614
⁴B V Bhoomraddi College of Arts, Sci and Com, Bidar, Dist- Bidar, Karnataka, India-585403
* Corresponding Author : ajganga@yahoo.com

Received : -     Accepted : -     Published : 15-06-2009
Volume : 1     Issue : 1       Pages : 1 - 10
Int J Agr Sci 1.1 (2009):1-10
DOI : http://dx.doi.org/10.9735/0975-3710.1.1.1-10

Keywords : Profilin, Tertiary structure, docking studies, Schizosaccharomyces pombe
Conflict of Interest : None declared
Acknowledgements/Funding : We are thankful to the Department of Biotechnology and Bioinformatics, Padmashree Dr. D. Y. Patil University, Navi Mumbai for providing the financial and technical support

Profilin plays a crucial role by directly linking actin cytoskeleton dynamics to various signal transduction pathways. Profilin has been well conserved during the evolution and can be found throughout the animal and plant kingdom. All known profilin are defined by common structural and biochemical properties and are known to interact with at least three types of ligands: they are complex with the G actin and actin – related proteins; interact with PLP presented either as a peptide or as a sequence motif within specific proteins (with the exception of vaccinia profilin), and bind to polyphosphoinositides. Profilin has different functional roles: Actin binding and membrane refluxes, regulation of phospholipase C-Y1, focal contacts, nuclear transport of proteins, allergen, and tumor suppression. A protein function is tightly linked to its tertiary structure and as a residue located far apart in the sequence can be very close in space, and only few residues are responsible for a proteins function, insights into the tertiary structure of a protein can represent a key component of the functional analysis process. The homology or comparative protein structure of profilin was obtained by optimization of molecular probability density function (pdf) using the software program MODELLER. A stable structure was obtained by fixing the atomic charges by CHARMM 22 force field, and minimizing the energy by conjugate gradient method (1000 iterations) using NAMD software. Protein- protein docking was carried out with Vegazz for profilin dimer formation and profilin –ligand interactions were studied with Auto dock software programs. The in silico studies help in understanding the profilin monomeric interaction and its effect on PLP binding and polyphosphoinositide interactions, the two important processes which regulate number of signaling event.

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