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 language | English |
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Pages (from-to) | 295-300 |
Number of pages | 6 |
Journal | Biotechnology and Bioengineering |
Volume | 79 |
Issue number | 3 |
DOIs | |
State | Published - 5 Aug 2002 |
Externally published | Yes |
Keywords
- Bioinformatics
- Enzymic substrate specificity
- Multiple sequence alignment
- Predicting functional residues from protein sequence