Predicting amino acid residues responsible for enzyme specificity solely from protein sequences

Eudean Shaw, Jonathan S. Dordick

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

We describe a general, modular method for developing protocols to identify the amino acid residues that most likely define the division of a protein superfamily into two subsets. As one possibility, we use PROBE to gather superfamily members and perform an ungapped alignment. We then use a modified BLOSUM62 substitution matrix to determine the discriminating power of each column of aligned residues. The overall method is particularly useful for predicting amino acids responsible for substrate or binding specificity when no structures are available. We apply our method to three pairs of protein classes in three dierent superfamilies, and present our results, some of which have been experimentally verified. This approach may accelerate the elucidation of enzymic substrate specificity, which is critical for both mechanistic insights into biocatalysis and ultimate application.

Original languageEnglish
Pages (from-to)295-300
Number of pages6
JournalBiotechnology and Bioengineering
Volume79
Issue number3
DOIs
StatePublished - 5 Aug 2002
Externally publishedYes

Keywords

  • Bioinformatics
  • Enzymic substrate specificity
  • Multiple sequence alignment
  • Predicting functional residues from protein sequence

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