Specificity in protein-DNA interactions: TATA box-binding protein recognition of promoter sequences.
Item
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Title
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Specificity in protein-DNA interactions: TATA box-binding protein recognition of promoter sequences.
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Identifier
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AAI9807980
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identifier
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9807980
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Creator
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Pastor Colon, Nina.
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Contributor
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Adviser: Harel Weinstein
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Date
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1997
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Language
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English
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Publisher
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City University of New York.
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Subject
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Biophysics, General | Biology, Molecular
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Abstract
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The TATA box-binding protein (TBP) is an ancient basal transcription factor absolutely required for transcription in archaea and eukaryotes. In order to understand at the molecular level the mechanisms that might be used by TBP to select its binding sites (the TATA boxes), molecular dynamics simulations were carried out to explore the conformations of DNA oligomers that contain TATA boxes, of TBP, and of a TBP/DNA complex, all in aqueous solution. The free DNA sequences were chosen to include known binding sites for wild type TBP, binding sites for mutant TBPs, one inverted TATA box, and a sequence that is not bound by TBP and serves as a negative control. An inosine variant of the Major Late Promoter was included to test the equivalence of IC and AT basepairs. Direct comparison to experimental data showed that the simulation protocol is capable of reproducing known structural and dynamic properties of the systems studied. The counterion distribution around the DNA oligomers showed some sequence dependence, but the interpretation could be complicated as different measures indicate varying degrees of temporal convergence.;A TATA box sequence ideal for TBP binding was derived from the analysis of specific average and transient structural properties of the free DNA oligomers that resemble the conformation imposed on DNA in complexes with TBP. Comparison to experimental data showed that the stronger the adherence to this ideal sequence, the greater the measured affinity of TBP for the particular DNA sequence. The simulations of TBP revealed little change in the backbone structure, but flexibility evidenced by the sampling of various rotamers by the side chains of internal residues. The distribution of the rotating side chains is different in the free protein and in the complex, and their location on the protein could be related to the directionality of TBP binding to DNA. Analysis of the water structure surrounding the macromolecules allowed for the quantification of the changes in the structure of water in the first hydration layer. These changes in the solvent structure are related to the measured decrease in heat capacity upon TBP binding to TATA sequences.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
