Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding : prediction and rational design

• Published in: Genes & development Vol. 7; no. 6; pp. 1047 - 1058
• Main Authors: VINSON, C. R, TSONWIN HAI, BOYD, S. M
• Format: Journal Article
• Language: English
• Published: Cold Spring Harbor, NY Cold Spring Harbor Laboratory 01.06.1993
• Subjects: Activating Transcription Factor 4; Activating Transcription Factors; Amino Acid Sequence; Animals; Basic-Leucine Zipper Transcription Factors; Biological and medical sciences; Blood Proteins - chemistry; Blood Proteins - genetics; Blood Proteins - metabolism; Cyclic AMP Response Element-Binding Protein - chemistry; Cyclic AMP Response Element-Binding Protein - genetics; Cyclic AMP Response Element-Binding Protein - metabolism; DNA - chemistry; DNA - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Fundamental and applied biological sciences. Psychology; G-Box Binding Factors; Leucine Zippers; Lymphokines - chemistry; Lymphokines - genetics; Lymphokines - metabolism; Mammals; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Mutation; Plant Proteins - chemistry; Plant Proteins - genetics; Prostatic Secretory Proteins; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription. Transcription factor. Splicing. Rna processing; Vertebrata; Leucine zipper structure; Mammalia; Structural unit; Molecular structure; DNA binding protein; Molecular interaction; Dimerization; Structure function relationship
• ISSN: 0890-9369; 1549-5477
• DOI: 10.1101/gad.7.6.1047

We propose an interhelical salt bridge rule to explain the dimerization specificity between the two amphipathic alpha-helices in the leucine zipper structure. Using the bZIP class of DNA-binding proteins as a model 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 superfamily. These predictions were verified using a gel mobility-shift assay. To further 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 interact with C/EBP. These designed molecules behaved as predicted. Therefore, we conclude that this interhelical salt bridge rule is useful in understanding the dimerization specificity of bZIP proteins. In addition, we suggest that this rule could be used to design novel "dominant-negative" molecules to specifically inhibit the function of target leucine zipper proteins in vivo.