Title

Authors

Affiliation

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

aniruddha.chatterjee@otago.ac.nz; *Corresponding author

Article Type

Hypothesis

Date

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.

Keywords

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

Citation

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

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.