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. 2017 Oct 3;18(1):438.
doi: 10.1186/s12859-017-1851-1.

Block-based characterization of protease specificity from substrate sequence profile

Enfeng Qi  1 , Dongyu Wang  2 , Bo Gao  1 , Yang Li  1 , Guojun Li  3
Affiliations

Block-based characterization of protease specificity from substrate sequence profile

Enfeng Qi et al. BMC Bioinformatics. .

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

Keywords: Block; Entropy; Protease; Site cooperation.

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Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

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Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
A schematic diagram of construction of different blocks. The blocks of successive amino acids are denoted from N-terminal to C-terminal, so that block B1 represents the P1 site, block B1’ represents the P1’ site, block B2 represents the successive sites of P2 and P1, and block B2’ represents the successive sites of P1’ and P2’ and so on. For example, block B2 LeuLys implies Leu at the site P2 and Lys at the site P1, and block B2’ PheArg implies Phe at the site P1’ and Arg at the site P2’. Other blocks may be deduced similarly
Fig. 2
Fig. 2
Comparisons of eight entropies of proteases with maximum and minimum distance. a Entropy distributions of eight blocks from proteases neurolysin and trypsin 1 with the maximum distance in the distance matrix. b Entropy distributions of eight blocks from proteases PCSK4 and PCSK6 with the minimum distance in the distance matrix
Fig. 3
Fig. 3
Scatter plot of principal component analysis from PC1versus PC2. The selected data is grouped into four types according to the MEROPS database, including aspartic, cysteine, metallo and serine. Coloring according to catalytic types, aspartic protease: blue; cysteine protease: red; metallo protease: green; serine protease: pink
Fig. 4
Fig. 4
Heat map of prominent combinations in each block. Five shades are shown ranging from darkest green (less 20% of substrates) to brightest green (greater 80% of substrates), and black background indicates no prominent combination in the block
Fig. 5
Fig. 5
The proportion of proteases with prominent blocks. The horizontal axis shows eight blocks B4, B3, B2, B1, B1’, B2’, B3’ and B4’. The vertical axis shows the proportions of proteases with significant block in 61 proteases. The proportions from B4 to B4’ are 11.475%, 26.230%, 52.459%, 65.574%, 67.213%, 34.426%, 6.557% and 3.279% respectively
Fig. 6
Fig. 6
Cleavage site sequence logos and the prominent B2 blocks of proteases. a The sequence logos of caspase 3, kexin, furin and PCSK6 peptidase, which have obvious specificity at the site P1. b The sequence logos of HIV-1 retropepsin, MMP 2 and MMP 9, which have multiple preferences at sites P1 and P2
See this image and copyright information in PMC

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