Connecting protein structure with predictions of regulatory sites Export

@article{citeulike:1240104, abstract = {10.1073/pnas.0701356104 A common task posed by microarray experiments is to infer the binding site preferences for a known transcription factor from a collection of genes that it regulates and to ascertain whether the factor acts alone or in a complex. The converse problem can also be posed: Given a collection of binding sites, can the regulatory factor or complex of factors be inferred? Both tasks are substantially facilitated by using relatively simple homology models for protein\^{a}€“DNA interactions, as well as the rapidly expanding protein structure database. For budding yeast, we are able to construct reliable structural models for 67 transcription factors and with them redetermine factor binding sites by using a Bayesian Gibbs sampling algorithm and an extensive protein localization data set. For 49 factors in common with a prior analysis of this data set (based largely on phylogenetic conservation), we find that half of the previously predicted binding motifs are in need of some revision. We also solve the inverse problem of ascertaining the factors from the binding sites by assigning a correct protein fold to 25 of the 49 cases from a previous study. Our approach is easily extended to other organisms, including higher eukaryotes. Our study highlights the utility of enlarging current structural genomics projects that exhaustively sample fold structure space to include all factors with significantly different DNA-binding specificities.}, address = {Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021.}, author = {Morozov, Alexandre V. and Siggia, Eric D.}, citeulike-article-id = {1240104}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0701356104}, citeulike-linkout-1 = {http://www.pnas.org/content/104/17/7068.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/104/17/7068.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/104/17/7068}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17438293}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17438293}, day = {24}, doi = {10.1073/pnas.0701356104}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {3dstructure, site-prediction}, month = {April}, number = {17}, pages = {7068--7073}, posted-at = {2009-03-23 16:34:54}, priority = {2}, title = {Connecting protein structure with predictions of regulatory sites}, url = {http://dx.doi.org/10.1073/pnas.0701356104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:1240104 L3 - citeulike-article-id:1240104 N2 - 10.1073/pnas.0701356104 A common task posed by microarray experiments is to infer the binding site preferences for a known transcription factor from a collection of genes that it regulates and to ascertain whether the factor acts alone or in a complex. The converse problem can also be posed: Given a collection of binding sites, can the regulatory factor or complex of factors be inferred? Both tasks are substantially facilitated by using relatively simple homology models for protein–DNA interactions, as well as the rapidly expanding protein structure database. For budding yeast, we are able to construct reliable structural models for 67 transcription factors and with them redetermine factor binding sites by using a Bayesian Gibbs sampling algorithm and an extensive protein localization data set. For 49 factors in common with a prior analysis of this data set (based largely on phylogenetic conservation), we find that half of the previously predicted binding motifs are in need of some revision. We also solve the inverse problem of ascertaining the factors from the binding sites by assigning a correct protein fold to 25 of the 49 cases from a previous study. Our approach is easily extended to other organisms, including higher eukaryotes. Our study highlights the utility of enlarging current structural genomics projects that exhaustively sample fold structure space to include all factors with significantly different DNA-binding specificities. IS - 17 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 AD - Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021. EP - 7073 TI - Connecting protein structure with predictions of regulatory sites VL - 104 SP - 7068 KW - 3dstructure KW - site-prediction AU - Morozov, Alexandre AU - Siggia, Eric PY - 2007/04/24/ UR - http://dx.doi.org/10.1073/pnas.0701356104 ER -