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

ABSTRACT:

Background

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.

Results

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.

Conclusion

This app

SUBMITTER: Qi E 

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

REPOSITORIES: biostudies-literature