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Recognition of active and inactive catalytic triads: A template based approach

Gupta, Vikas and Prakash, Udaya NA and Lakshmi, V and Boopathy, R and Jeyakanthan, J and Velmurugan, D and Sekar, K (2010) Recognition of active and inactive catalytic triads: A template based approach. In: International Journal of Biological Macromolecules, 46 (3). pp. 317-323.

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Abstract

It Is well established that a sequence template along with the database is a powerful tool for identifying the biological function of proteins. Here, we describe a method for predicting the catalytic nature of certain proteins among the several protein structures deposited in the Protein Data Bank (PDB) For the present study, we considered a catalytic triad template (Ser-His-Asp) found in serine proteases We found that a geometrically optimized active site template can be used as a highly selective tool for differentiating an active protein among several inactive proteins, based on their Ser-His-Asp interactions. For any protein to be proteolytic in nature, the bond angle between Ser O-gamma-Ser H-gamma His N-epsilon 2 in the catalytic triad needs to be between 115 degrees and 140 degrees The hydrogen bond distance between Ser H-gamma His N-epsilon 2 is more flexible in nature and it varies from 2 0 angstrom to 27 angstrom while in the case of His H-delta 1 Asp O-delta 1, it is from 1.6 angstrom to 2.0 angstrom In terms of solvent accessibility, most of the active proteins lie in the range of 10-16 angstrom(2), which enables easy accessibility to the substrate These observations hold good for most catalytic triads and they can be employed to predict proteolytic nature of these catalytic triads (C) 2010 Elsevier B V All rights reserved.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Elsevier Science.
Keywords: Catalytic triad; Serine protease; Hydrogen bond network; Three-dimensional structure; Solvent accessibility; Intramolecular distances
Department/Centre: Division of Information Sciences > BioInformatics Centre
Date Deposited: 26 Apr 2010 08:29
Last Modified: 19 Sep 2010 06:00
URI: http://eprints.iisc.ernet.in/id/eprint/27254

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