ArticleNucleic acids research2007
DNA sequence-specific recognition by a transcriptional regulator requires indirect readout of A-tracts.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium.Environmental microbiology · 2017Review
- The length of glycine-rich linker in DNA-binding domain is critical for optimal functioning of quorum-sensing master regulatory protein HapR.Molecular genetics and genomics : MGG · 2014Article
- Functional specificity of a protein-DNA complex mediated by two arginines bound to the minor groove.Journal of bacteriology · 2012Article
- Molecular interactions and protein-induced DNA hairpin in the transcriptional control of bacteriophage ø29 DNA.International journal of molecular sciences · 2010Review
- Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system.Nucleic acids research · 2008Article
- Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts.Biophysical journal · 2008Article
Corrections and comments
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Authors and funding
4 authors.
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Abstract
The bacteriophage Ø29 transcriptional regulator p4 binds to promoters of different intrinsic activities. The p4-DNA complex contains two identical protomers that make similar interactions with the target sequence 5'-AACTTTTT-15 bp-AAAATGTT-3'. To define how the various elements in the target sequence contribute to p4's affinity, we studied p4 binding to a series of mutated binding sites. The binding specificity depends critically on base pairs of the target sequence through both direct as well as indirect readout. There is only one specific contact between a base and an amino acid residue; other contacts take place with the phosphate backbone. Alteration of direct amino acid-base contacts, or mutation of non-contacted A.T base pairs at A-tracts abolished binding. We generated three 5 ns molecular dynamics (MD) simulations to investigate the basis for the p4-DNA complex specificity. Recognition is controlled by the protein and depends on DNA dynamic properties. MD results on protein-DNA contacts and the divergence of p4 affinity to modified binding sites reveal an inherent asymmetry, which is required for p4-specific binding and may be crucial for transcription regulation.
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