Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface

Autor: Laurie M. Franklin, G. Wesley Hatfield, Reuben C. Darlington, Michael L. Opel, Donald F. Senear, J.B. Alexander Ross, Kimberly A. Aeling, Vira Tretyachenko-Ladokhina

Publikováno v: Senear, Donald F.; Tretyachenko-Ladokhina, Vira; Opel, Michael L.; Aeling, Kimberly A.; Wesley Hatfield, G.; Franklin, Laurie M.; et al.(2007). Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface. Nucleic Acids Research, 35(6), 1761-1772. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/6fv9z5d1
Nucleic Acids Research

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6d53b0b981fe5bbba7cd82ac2580c93c
https://doi.org/10.1093/nar/gkl1122

Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism

Autor: G. Wesley Hatfield, Walter M. Holmes, Craig J. Benham, Reid C. Johnson, Michael L. Opel, Kimberly A. Aeling

Publikováno v: Molecular Microbiology. 53:665-674

Summary The leuV operon of Escherichia coli encodes three of the four genes for the tRNA1Leu isoacceptors. Transcription from this and other stable RNA promoters is known to be affected by a cis-acting UP element and by Fis protein interactions with

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::31b7edb13f19a9a151d9708abb914bf1
https://doi.org/10.1111/j.1365-2958.2004.04147.x

Activation and repression of transcription initiation by a distant DNA structural transition

Autor: G. Wesley Hatfield, Steven D. Sheridan, Michael L. Opel

Publikováno v: Molecular Microbiology. 40:684-690

Negative superhelical tension can drive local transitions to alternative DNA structures. Long regions of DNA may contain several sites that are susceptible to forming alternative structures. Their relative propensities to undergo transition are order

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::42be675d8d7873cb3a650652666fe8d5
https://doi.org/10.1046/j.1365-2958.2001.02416.x

Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy

Autor: Kimberly A, Aeling, Michael L, Opel, Nicholas R, Steffen, Vira, Tretyachenko-Ladokhina, G Wesley, Hatfield, Richard H, Lathrop, Donald F, Senear

Publikováno v: The Journal of biological chemistry. 281(51)

Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. Howev

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https://pubmed.ncbi.nlm.nih.gov/17035240

The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites

Autor: Nicholas R, Steffen, Scott D, Murphy, Richard H, Lathrop, Michael L, Opel, Lorenzo, Tolleri, G Wesley, Hatfield

Publikováno v: Genome informatics. International Conference on Genome Informatics. 13

We examine the use of deformation propensity at individual base steps for the identification of DNA-protein binding sites. We have previously demonstrated that estimates of the total energy to bend DNA to its bound conformation can partially explain

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::367d215bc89e4c9b33fc1d8923f2376b
https://pubmed.ncbi.nlm.nih.gov/14571384