Nucleic Acids Research Advance Access originally published online on September 14, 2006
Nucleic Acids Research 2006 34(17):4846-4856; doi:10.1093/nar/gkl552
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Nucleic Acids Research, 2006, Vol. 34, No. 17 4846-4856
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
DNA bending by bHLH charge variants
1 Medical Scientist Training Program, Mayo Clinic College of Medicine Rochester, MN 55905, USA 2 Department of Chemistry and Biochemistry, University of Maryland College Park, MD 20742-2021, USA 3 Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine Rochester, MN 55905, USA
*To whom correspondence should be addressed. Tel: +1 507 284 9041; Fax: +1 507 284 2053; Email: maher{at}mayo.edu
Received June 29, 2006. Revised July 13, 2006. Accepted July 14, 2006.
We wish to understand the role of electrostatics in DNA stiffness and bending. The DNA charge collapse model suggests that mutual electrostatic repulsions between neighboring phosphates significantly contribute to DNA stiffness. According to this model, placement of fixed charges near the negatively charged DNA surface should induce bending through asymmetric reduction or enhancement of these inter-phosphate repulsive forces. We have reported previously that charged variants of the elongated basic-leucine zipper (bZIP) domain of Gcn4p bend DNA in a manner consistent with this charge collapse model. To extend this result to a more globular protein, we present an investigation of the dimeric basic-helix–loop–helix (bHLH) domain of Pho4p. The 62 amino acid bHLH domain has been modified to position charged amino acid residues near one face of the DNA double helix. As observed for bZIP charge variants, DNA bending toward appended cations (away from the protein:DNA interface) is observed. However, unlike bZIP proteins, DNA is not bent away from bHLH anionic charges. This finding can be explained by the structure of the more globular bHLH domain which, in contrast to bZIP proteins, makes extensive DNA contacts along the binding face.
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