Table of Contents
Molecular Biology International
Volume 2012 (2012), Article ID 580965, 9 pages
http://dx.doi.org/10.1155/2012/580965
Research Article

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

1Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, West Bengal, Kolkata 700032, India
2Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand
3National Research Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand

Received 25 July 2012; Revised 17 October 2012; Accepted 17 October 2012

Academic Editor: Alessandro Desideri

Copyright © 2012 Aparna Laskar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases.