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Bullied no more: when and how DNA shoves proteins around

Published online by Cambridge University Press:  31 July 2012

Jonathan M. Fogg ,
Graham L. Randall ,
B. Montgomery Pettitt ,
De Witt L. Sumners ,
Sarah A. Harris  and
Lynn Zechiedrich
Jonathan M. Fogg
Affiliation:
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA
Graham L. Randall
Affiliation:
Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
B. Montgomery Pettitt
Affiliation:
Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
De Witt L. Sumners
Affiliation:
Department of Mathematics, Florida State University, Tallahassee, FL 32306-4510, USA
Sarah A. Harris
Affiliation:
School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
Lynn Zechiedrich*
Affiliation:
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA
*
†Author for correspondence: Lynn Zechiedrich, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA. Tel.: 1 (713) 798-5126; Fax: 1 (713) 798-7375; Email: [email protected]
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Abstract

The predominant protein-centric perspective in protein–DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 45 , Issue 3 , August 2012 , pp. 257 - 299
Copyright
Copyright © Cambridge University Press 2012

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