ArticleNucleic acids research2008
A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 23 citations in OpenAlex.
- ArcA modulates multidrug resistance and compound susceptibility inMicrobiology spectrum · 2025Article
- The ArcAB Two-Component System: Function in Metabolism, Redox Control, and Infection.Microbiology and molecular biology reviews : MMBR · 2022Review
- Article
- Lipopolysaccharide Transport System Links Physiological Roles of σMicrobiology spectrum · 2021Article
- Tools to map target genes of bacterial two-component system response regulators.Environmental microbiology reports · 2020Review
- Transcriptional regulator ArcA mediates expression of oligopeptide transport systems both directly and indirectly in Shewanella oneidensis.Scientific reports · 2019Article
- Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors.Quantitative biology (Beijing, China) · 2018Article
- Impaired cell envelope resulting from arcA mutation largely accounts for enhanced sensitivity to hydrogen peroxide in Shewanella oneidensis.Scientific reports · 2015Article
- Evolutionary meandering of intermolecular interactions along the drift barrier.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Endogenous generation of hydrogen sulfide and its regulation in Shewanella oneidensis.Frontiers in microbiology · 2015Article
- Article
- Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium.BMC genomics · 2013Article
- The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.PLoS genetics · 2013Article
- Inference of self-regulated transcriptional networks by comparative genomics.Evolutionary bioinformatics online · 2012Article
- Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.PloS one · 2011Article
- Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis.PloS one · 2010Article
- Modeling the quantitative specificity of DNA-binding proteins from example binding sites.PloS one · 2009Article
- Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.PLoS computational biology · 2009Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.