Assignment of Enzyme Substrate Specificity by Principal Component Analysis of Aligned Protein Sequences: An Experimental Test Using DNA Glycosylase Homologues

Published

January 1, 2000

Author(s)

A Gogos, D Jantz, K. J. Tuerk, D Richardson, M. Dizdaroglu, N D. Clarke

Abstract

We have studied the relationship between amino acid sequence and substrate specificity in a DNA glycosylase family by characterizing experimentally the specificity of four new members of the family. We show that principal component analysis (PCA) of the sequence family correctly predicts the substrate specificity of one of the novel homologs even though conventional sequence analysis methods fail to group this homolog with other sequences of the same specificity. PCA also suggested, correctly, that another homolog characterized previously differs in its specificity from those sequences with which it clusters by conventional criteria. These results suggest that principal component analysis of sequence families can be a useful tool in annotating genome sequences when there is ambiguity concerning which subfamily a new homolog belongs to.

Citation

Proteins-Structure Function And Genetics

Volume

40

Pub Type

Journals

Keywords

DNA glycosylase, genome annotation, principal component analysis, specificity, substrate

Citation

Gogos, A. , Jantz, D. , Tuerk, K. , Richardson, D. , Dizdaroglu, M. and Clarke, N. (2000), Assignment of Enzyme Substrate Specificity by Principal Component Analysis of Aligned Protein Sequences: An Experimental Test Using DNA Glycosylase Homologues, Proteins-Structure Function And Genetics (Accessed May 18, 2024)