Applications of statistical criteria in protein sequence analysis: case study of yeast RNA polymerase II subunits.

We have recently proposed statistical techniques to identify unusual protein sequence features. Extensive mapping of these features to particular groups of proteins may afford new ways of protein classification. Here we present a case study of such analysis by discussing special features of the amino acid sequences of yeast RNA polymerase II, the first eukaryotic RNA polymerase for which all subunits have been sequenced. Specific new suggestions derived from this analysis include: (i) based on unusual charge configurations in some of the sequences, electrostatic forces may play a significant role in subunit interactions; (ii) RPB4, on account of similar charge distribution, may well be grouped together with RNA polymerase II transcription initiation factors.