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A vector projection approach to predicting HIV protease cleavage sites in proteins
Author(s) -
Chou KuoChen,
Zhang ChunTing,
Kézdy Ferenc J
Publication year - 1993
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340160206
Subject(s) - protease , proteases , hiv 1 protease , oligopeptide , projection (relational algebra) , substrate specificity , cleavage (geology) , human immunodeficiency virus (hiv) , enzyme , biology , computational biology , mathematics , biochemistry , peptide , algorithm , virology , paleontology , fracture (geology)
Abstract A vector projection method is proposed to predict the cleavability of oligopeptides by extended‐specificity site proteases. For an enzyme with eight specificity subsites the substrate octapeptide can be uniquely expressed as a vector in an 8‐dimensional space, whose eight bases correspond to the amino acids at the eight subsites, P 1 , P 1′ , P 2′ , P 3′ and P 4′ , respectively. The component of such a characteristic vector on each of the eight bases is defined as the frequency of an amino acid occurring at a given site. These frequencies were derived from a set of octapeptides known to be cleaved by HIV protease. The cleavability of an octapeptide can then be estimated from the projection of its characteristic vector on an idealized, optimally cleavable vector. The high ratio of correct prediction vs. total prediction for the data in both the training and the testing sets indicates that the new method is self‐consistent and efficient. It provides a rapid and accurate algorithm for analyzing the specificity of any multisubsite enzyme for which there is no coupling between subsites. In particular, it is useful for predicting the cleavability of an oligopeptide by either HIV‐1 or HIV‐2 protease, and hence offers a supplementary means for finding effective inhibitors of HIV protease as potential drugs against AIDS. © Wiley‐Liss, Inc.