Modeling and structural analysis of evolutionarily diverse S8 family serine proteases



Aparna Laskar1, Euan James Rodger2, Aniruddha Chatterjee2,3*, Chhabinath Mandal1



1Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata-700032, West Bengal, India; 2Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin-9054, New Zealand; 3National Research Centre for Growth and Development, New Zealand.


Email; *Corresponding author


Article Type




Received October 14, 2011; Accepted October 18, 2011; Published October 31, 2011



Serine proteases are an abundant class of enzymes that are involved in a wide range of physiological processes and are classified into clans sharing structural homology. The active site of the subtilisin-like clan contains a catalytic triad in the order Asp, His, Ser (S8 family) or a catalytic tetrad in the order Glu, Asp and Ser (S53 family). The core structure and active site geometry of these proteases is of interest for many applications. The aim of this study was to investigate the structural properties of different S8 family serine proteases from a diverse range of taxa using molecular modeling techniques. In conjunction with 12 experimentally determined three-dimensional structures of S8 family members, our predicted structures from an archaeon, protozoan and a plant were used for analysis of the catalytic core. Amino acid sequences were obtained from the MEROPS database and submitted to the LOOPP server for threading based structure prediction. The predicted structures were refined and validated using PROCHECK, SCRWL and MODELYN. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S8 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, the analysis presented here is beneficial for future molecular modeling strategies and structure-based rational drug design.



serine protease; SB clan; S8 family; homology; threading; modeling



Laskar et al. Bioinformation 7(5): 239-245 (2011)

Edited by

P Kangueane






Biomedical Informatics



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