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Interplay of protein and DNA structure revealed in simulations of the lac operon.

The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gen... Full description

Journal Title: PloS one 2013, Vol.8(2), p.e56548
Main Author: Czapla, Luke
Other Authors: Grosner, Michael A , Swigon, David , Olson, Wilma K
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0056548
Link: http://search.proquest.com/docview/1314708009/?pq-origsite=primo
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title: Interplay of protein and DNA structure revealed in simulations of the lac operon.
format: Article
creator:
  • Czapla, Luke
  • Grosner, Michael A
  • Swigon, David
  • Olson, Wilma K
subjects:
  • DNA, Bacterial–Chemistry
  • Lac Operon–Genetics
  • Lac Repressors–Metabolism
  • Models, Molecular–Chemistry
  • Monte Carlo Method–Metabolism
  • Nucleic Acid Conformation–Metabolism
  • Protein Conformation–Metabolism
  • DNA, Bacterial
  • Lac Repressors
ispartof: PloS one, 2013, Vol.8(2), p.e56548
description: The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo , enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.
language: eng
source:
identifier: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0056548
fulltext: fulltext
issn:
  • 19326203
  • 1932-6203
url: Link


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titleInterplay of protein and DNA structure revealed in simulations of the lac operon.
creatorCzapla, Luke ; Grosner, Michael A ; Swigon, David ; Olson, Wilma K
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identifierE-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0056548
subjectDNA, Bacterial–Chemistry ; Lac Operon–Genetics ; Lac Repressors–Metabolism ; Models, Molecular–Chemistry ; Monte Carlo Method–Metabolism ; Nucleic Acid Conformation–Metabolism ; Protein Conformation–Metabolism ; DNA, Bacterial ; Lac Repressors
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descriptionThe E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo , enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.
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