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Block-based characterization of protease specificity from substrate sequence profile.

ABSTRACT: The mechanism of action of proteases has been widely studied based on substrate specificity. Prior research has been focused on the amino acids at a single amino acid site, but rarely on combinations of amino acids around the cleavage bond.We propose a novel block-based approach to reveal the potential combinations of amino acids which may regulate the action of proteases. Using the entropies of eight blocks centered at a cleavage bond, we created a distance matrix for 61 proteases to compare their specificities. After quantitative analysis, we discovered a number of prominent blocks, each of which consists of successive amino acids near a cleavage bond, intuitively characterizing the site cooperation of the substrate sequences.This approach will help in the discovery of specific substrate sequences which may bridge between proteases and cleavage substrate as more substrate information becomes available.

SUBMITTER: Qi E

PROVIDER: S-EPMC5627433 | biostudies-other | 2017 Oct

REPOSITORIES: biostudies-other

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Block-based characterization of protease specificity from substrate sequence profile.

Qi Enfeng E Wang Dongyu D Gao Bo B Li Yang Y Li Guojun G

BMC bioinformatics 20171003 1

<h4>Background</h4>The mechanism of action of proteases has been widely studied based on substrate specificity. Prior research has been focused on the amino acids at a single amino acid site, but rarely on combinations of amino acids around the cleavage bond.<h4>Results</h4>We propose a novel block-based approach to reveal the potential combinations of amino acids which may regulate the action of proteases. Using the entropies of eight blocks centered at a cleavage bond, we created a distance ma ...[more]

PMID: 28974219

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