Theoretical indicators of enzyme reaction specificity from conserved information in amino acid sidechains

Amino acid sequences for 11 acetohydroxy acid synthase (EC 4.1.3.18; AHS) polypeptides with experimentally established activity were chosen for computational comparisons to detect conserved local information associated with reaction specificity for each sequence. Windowed analysis by Pearson product moment cross-correlation of six amino acid sidechain properties revealed locally conserved segments common to all proteins with AHS activity. Seven information segments were detected in the same arrangement in sequences for the large subunit polypeptides of prokaryotes, and in the sequences for single polypeptides of eukaryotic AHS. The information segments were numbered 1-7 according to sequential position, and sequence features such as cofactor binding sites were defined for specific segments. Extension of the information segment analysis to seven other proteins of the pyruvate decarboxylase superfamily permitted use of the content and organization of information segments to recognize four classes of enzyme reaction specificity. Estimates of information entropy, based upon a state space defined by reaction specificity, directly reflected the known reaction complexity for all but one enzyme examined. Our data suggest that development of information-segment models for enzyme superfamilies may improve the accuracy of inferring protein activity from sequence.