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Asian Journal of Biotechnology
  Year: 2011 | Volume: 3 | Issue: 5 | Page No.: 435-448
DOI: 10.3923/ajbkr.2011.435.448
 
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Molecular Modeling and Structural Analysis of Five SE Clan (S12 Family) Serine Proteases
Aparna Laskar, Sirshendu Chatterjee, Anirban Roy, Sumit Kumar Dey and Chhabinath Mandal

Abstract:
SE clan of serine proteases have Lysine, Serine and Tyrosine residues as catalytic triad in their active site which is an exception to all other serine proteases having conserved residues Serine, Aspartic acid and Histidine in their active sites. The aim of this study was to explore the structural distinctiveness of different S12 family (D-Ala-D-Ala carboxypeptidase B family) serine peptidases from diverse groups of species belonging to SE clan, using molecular modeling techniques. Amino acid sequences of those proteases from each group of organisms, i.e., archean, protozoan, fungal, plant and human were taken from the MEROPS database in FASTA format. Homology and threading modeling approach were used to construct all the structures by SWISS MODEL and LOOPP server respectively. Structural quality assessing validation programs (PROCHECK, MODELYN, MOLPROBITY and PROSA) of the final model have demonstrated its reliability for further studies. A full structural database was constructed starting from bacteria up to human, focusing on the catalytic triad of the proteases. MODELYN study showed statistically that the region of the catalytic triad is highly conserved from bacteria to human. Phylogenetic analysis also supports their evolutionary connection. MOLMOL study showed that the catalytic sites of all the SE Clan proteases exhibit acidic regions in the surface electrostatic potential maps but a few of them contain both large patches of positive and neutral potentials. Hence some of the proteases with predominant positive and neutral regions around the catalytic site can be used as potential drug target against bacterial and protozoan pathogens.
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How to cite this article:

Aparna Laskar, Sirshendu Chatterjee, Anirban Roy, Sumit Kumar Dey and Chhabinath Mandal, 2011. Molecular Modeling and Structural Analysis of Five SE Clan (S12 Family) Serine Proteases. Asian Journal of Biotechnology, 3: 435-448.

DOI: 10.3923/ajbkr.2011.435.448

URL: https://scialert.net/abstract/?doi=ajbkr.2011.435.448

COMMENTS
02 June, 2011
Partha P. Banerjee:
Undoubtedly, its a wonderful theoritical work. I have got many ideas about structural biology from this paper. I would like to congratulate all the authors of this particular paper along with the journal team.
 
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