Block-based characterization of protease specificity from substrate sequence profile

BMC Bioinformatics

Research Article

Yang Li¹  Bo Gao¹  Guojun Li¹  Enfeng Qi¹  Dongyu Wang² 

[1] School of Mathematics, Shandong University, 250100, Jinan, China;The State Key Laboratory of Microbial Technology, Shandong University, 250100, Jinan, China;

关键词: Protease;    Block;    Entropy;    Site cooperation;   

DOI  :  10.1186/s12859-017-1851-1

 received in 2017-06-15, accepted in 2017-09-26,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionThis approach will help in the discovery of specific substrate sequences which may bridge between proteases and cleavage substrate as more substrate information becomes available.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

Fig. 6