REVEALING CORRELATED AMINO-ACID POSITIONS IN THE DNA-BINDING REGIONS OF THE CREB AND AP-1 TRANSCRIPTION FACTOR FAMILIES

A method is proposed for analyzing multiple alignments of amino acid s equences to reveal pairs of positions for residues with correlated phy sicochemical properties. The technique estimates the direct dependence within the pair, eliminating the influence of other residues. Examina tion of the DNA-binding regions in the CREB and AP-1 transcription fac tor families demonstrates a negative correlation of isoelectric points for the N- and the C-flanking positions. The observed pattern is inte rpreted within the framework of a simplified electrostatic model of DN A-protein interaction.