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

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(epsilon2) in the catalytic triad needs to be between 115 degrees and 140 degrees. The hydrogen bond distance between Ser H(gamma)...His N(epsilon2) is more flexible in nature and it varies from 2.0 A to 2.7 A while in the case of His H(delta1)...Asp O(delta1), it is from 1.6A to 2.0 A. In terms of solvent accessibility, most of the active proteins lie in the range of 10-16 A(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.

journal_name

Int J Biol Macromol

journal_title

International journal of biological macromolecules

authors

Gupta V,Prakash NA,Lakshmi V,Boopathy R,Jeyakanthan J,Velmurugan D,Sekar K

doi

10.1016/j.ijbiomac.2010.01.011

subject

Has Abstract

pub_date

2010-04-01 00:00:00

pages

317-23

issue

3

eissn

0141-8130

issn

1879-0003

pii

S0141-8130(10)00021-8

journal_volume

46

pub_type

杂志文章

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