Predicting Transcription Factor Specificity with All-Atom Models

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dc.creatorRahi, Sahand Jamal
dc.creatorVirnau, Peter
dc.creatorMirny, Leonid A.
dc.creatorKardar, Mehran
dc.date2008-09-24
dc.date.accessioned2026-07-07T10:16:46Z
dc.date.available2026-07-07T10:16:46Z
dc.descriptionThe binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR E. coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and non-cognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and weakly influenced by bending of DNA.
dc.description26 pages, 3 figures
dc.identifierhttps://arxiv.org/abs/0809.4080
dc.identifierhttp://arxiv.org/abs/0809.4080
dc.identifierNucleic Acids Res. 36, 6209-6217 (2008)
dc.identifierdoi:10.1093/nar/gkn589
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/173622
dc.subjectBiomolecules
dc.subjectBiological Physics
dc.subjectQuantitative Methods
dc.titlePredicting Transcription Factor Specificity with All-Atom Models
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