title: Cleavage entropy as quantitative measure of protease specificity.
abstract: A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity.
authors: Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria.
authors: Julian E
authors: JE
authors: Fuchs
authors: Susanne
authors: S
authors: von Grafenstein
authors: Roland G
authors: RG
authors: Huber
authors: Michael A
authors: MA
authors: Margreiter
authors: Gudrun M
authors: GM
authors: Spitzer
authors: Hannes G
authors: HG
authors: Wallnoefer
authors: Klaus R
authors: KR
authors: Liedl
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D010450:Endopeptidases / Q000737:chemistry*; D019277:Entropy; D019143:Evolution, Molecular; D006801:Humans; D009154:Mutation; D010447:Peptide Hydrolases / Q000737:chemistry*; D010802:Phylogeny; D057057:Serine Proteases / Q000737:chemistry; D015398:Signal Transduction; D013379:Substrate Specificity; D013917:Thrombin / Q000737:chemistry; D014357:Trypsin / Q000737:chemistry
chemical_list: D010450:Endopeptidases; D010447:Peptide Hydrolases; D057057:Serine Proteases; D014357:Trypsin; D013917:Thrombin
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