DIMERIZATION SPECIFICITY OF THE LEUCINE ZIPPER-CONTAINING BZIP MOTIF ON DNA-BINDING - PREDICTION AND RATIONAL DESIGN

We propose an interhelical salt bridge rule to explain the dimerizatio n specificity between the two amphipathic alpha-helices in the leucine zipper structure. Using the bZIP class of DNA-binding proteins as a m odel system, we predicted and designed novel dimerization partners. We predicted that ATF4, a member of the ATF/CREB family of transcription factors, would preferentially form heterodimers with IGEBP1, a member of the C/EBP family. We also predicted that neither ATF4 nor IGEBP1 w ould form heterodimers with DBP, a member of the C/EBP superfamily. Th ese predictions were verified using a gel mobility-shift assay. To fur ther test the value of this interhelical salt bridge rule, we modified the bZIP protein C/EBP attempting to design molecules that would form preferentially heterodimers with C/EBP or molecules that would not in teract with C/EBP. These designed molecules behaved as predicted. Ther efore, we conclude that this interhelical salt bridge rule is useful i n understanding the dimerization specificity of bZIP proteins. In addi tion, we suggest that this rule could be used to design novel ''domina nt-negative'' molecules to specifically inhibit the function of target leucine zipper proteins in vivo.