title: A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery.
abstract: Quantifying the binding energy in DNA-protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in DNA-protein interactions between the Shewanella oneidensis ArcA two-component transcription factor protein and a systematic set of mutants in an ArcA-P (phosphorylated ArcA) binding site. The binding energies corresponding to each of the 4 nt at each position in the 15-bp binding site were used to construct a position-specific energy matrix (PEM) that allowed a reliable prediction of ArcA-P binding sites not only in Shewanella but also in related bacterial genomes.
authors.affiliation: Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Xiaohu
authors.initials: X
authors.lastname: Wang
authors.forename: Haichun
authors.initials: H
authors.lastname: Gao
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.forename: Timothy
authors.initials: T
authors.lastname: Palzkill
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008957:Models, Genetic; D009154:Mutation; D011401:Promoter Regions, Genetic; D040081:Protein Array Analysis; D011485:Protein Binding; D020592:Shewanella / Q000235:genetics; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D014157:Transcription Factors