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Nucleic Acids Research 2004 32(11):3435-3445; doi:10.1093/nar/gkh653
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Published online 29 June 2004

Nucleic Acids Research, Vol. 32 No. 11 © Oxford University Press 2004; all rights reserved

Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs

Christopher D. Deppmann, Asha Acharya1, Vikas Rishi1, Barry Wobbes2, Sjef Smeekens2, Elizabeth J. Taparowsky and Charles Vinson1,*

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA, 1 Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA and 2 Department Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

* To whom correspondence should be addressed. Tel: +1 301 496 8753; Fax: +1 301 496 8419; Email: vinsonc{at}dc37a.nci.nih.gov
Present addresses: Christopher D. Deppmann, Department of Neuroscience, Johns Hopkins Medical School, Baltimore, MD, USA
Sjef Smeekens, Yacht Biochemistry and Life Sciences, Yacht Technology, Utrecht, The Netherlands
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received March 9, 2004; Revised April 16, 2004; Accepted May 26, 2004

Basic region-leucine zipper (B-ZIP) proteins are a class of dimeric sequence-specific DNA-binding proteins unique to eukaryotes. We have identified 67 B-ZIP proteins in the Arabidopsis thaliana genome. No A.thaliana B-ZIP domains are homologous with any Homo sapiens B-ZIP domains. Here, we predict the dimerization specificity properties of the 67 B-ZIP proteins in the A.thaliana genome based on three structural properties of the dimeric {alpha}-helical leucine zipper coiled coil structure: (i) length of the leucine zipper, (ii) placement of asparagine or a charged amino acid in the hydrophobic interface and (iii) presence of interhelical electrostatic interactions. Many A.thaliana B-ZIP leucine zippers are predicted to be eight or more heptads in length, in contrast to the four or five heptads typically found in H.sapiens, a prediction experimentally verified by circular dichroism analysis. Asparagine in the a position of the coiled coil is typically observed in the second heptad in H.sapiens. In A.thaliana, asparagine is abundant in the a position of both the second and fifth heptads. The particular placement of asparagine in the a position helps define 14 families of homodimerizing B-ZIP proteins in A.thaliana, in contrast to the six families found in H.sapiens. The repulsive interhelical electrostatic interactions that are used to specify heterodimerizing B-ZIP proteins in H.sapiens are not present in A.thaliana. Instead, we predict that plant leucine zippers rely on charged amino acids in the a position to drive heterodimerization. It appears that A.thaliana define many families of homodimerizing B-ZIP proteins by having long leucine zippers with asparagine judiciously placed in the a position of different heptads.


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