Weak operator binding enhances simulated lac repressor-mediated DNA looping

Authors

  • Andrew V. Colasanti,

    1. Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
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  • Michael A. Grosner,

    1. Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
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  • Pamela J. Perez,

    1. Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
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  • Nicolas Clauvelin,

    1. Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
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  • Xiang-Jun Lu,

    1. Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
    Current affiliation:
    1. Department of Biological Sciences, Columbia University, New York, NY
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  • Wilma K. Olson

    Corresponding author
    • Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: Wilma Olson; e-mail: wilma.olson@rutgers.edu

ABSTRACT

The 50th anniversary of Biopolymers coincides closely with the like celebration of the discovery of the Escherichia coli (lac) lactose operon, a classic genetic system long used to illustrate the influence of biomolecular structure on function. The looping of DNA induced by the binding of the Lac repressor protein to sequentially distant operator sites on DNA continues to serve as a paradigm for understanding long-range genomic communication. Advances in analyses of DNA structures and in incorporation of proteins in computer simulations of DNA looping allow us to address long-standing questions about the role of protein-mediated DNA loop formation in transcriptional control. Here we report insights gained from studies of the sequence-dependent contributions of the natural lac operators to Lac repressor-mediated DNA looping. Novel superposition of the ensembles of protein-bound operator structures derived from NMR measurements reveals variations in DNA folding missed in conventional structural alignments. The changes in folding affect the predicted ease with which the repressor induces loop formation and the ways that DNA closes between the protein headpieces. The peeling of the auxiliary operators away from the repressor enhances the formation of loops with the 92-bp wildtype spacing and hints of a structural reason behind their weak binding. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1070–1081, 2013.

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