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

@article{citeulike:1953909, abstract = {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.}, address = {Department of Neuroscience, Johns Hopkins Medical School, Baltimore, MD, USA.}, author = {Deppmann, C. D. and Acharya, A. and Rishi, V. and Wobbes, B. and Smeekens, S. and Taparowsky, E. J. and Vinson, C.}, citeulike-article-id = {1953909}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkh653}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/32/11/3435}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15226410}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15226410}, doi = {10.1093/nar/gkh653}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {arabidopsis, bzip, dimerization, specificity}, number = {11}, pages = {3435--3445}, posted-at = {2007-11-21 19:45:46}, priority = {2}, title = {Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs.}, url = {http://dx.doi.org/10.1093/nar/gkh653}, volume = {32}, year = {2004} }

TY - JOUR ID - citeulike:1953909 L3 - citeulike-article-id:1953909 N2 - 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. IS - 11 JF - Nucleic Acids Res SN - 1362-4962 AD - Department of Neuroscience, Johns Hopkins Medical School, Baltimore, MD, USA. EP - 3445 TI - Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs. VL - 32 SP - 3435 KW - arabidopsis KW - bzip KW - dimerization KW - specificity AU - Deppmann, CD AU - Acharya, A AU - Rishi, V AU - Wobbes, B AU - Smeekens, S AU - Taparowsky, EJ AU - Vinson, C PY - 2004/// UR - http://dx.doi.org/10.1093/nar/gkh653 ER -