Nucleic Acids Research Advance Access originally published online on February 25, 2007
Nucleic Acids Research 2007 35(6):1761-1772; doi:10.1093/nar/gkl1122
Nucleic Acids Research, 2007, Vol. 35, No. 6 1761-1772
© 2007 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 |
Pressure dissociation of integration host factor–DNA complexes reveals flexibility-dependent structural variation at the protein–DNA interface
1Department of Molecular Biology and Biochemistry, 2Department of Microbiology and Molecular Genetics, College of Medicine, 3Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and 4Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
*To whom correspondence should be addressed: Tel: (949) 824-8014; Fax: (949) 824-8551; Email: dfsenear{at}uci.edu
Correspondence may also be addressed to J.B. Alexander Ross. Tel: (406) 243-6026; Fax: (406) 243-4227; Email: sandy.ross{at}umontana.edu
Received October 17, 2006. Revised December 9, 2006. Accepted December 10, 2006.
E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236–39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences with differing flexibility have interactions with IHF that compensate for unfavorable deformation energy. Time-resolved Förster resonance energy transfer (FRET) shows that global topologies are indistinguishable for three complexes with oligonucleotides of different flexibility. However, pressure perturbation shows that the volume change upon binding is smaller with increasing flexibility. We interpret these results in the context of Record and coworker's model for IHF binding (J. Mol. Biol. 310, 379–401, 2001). We propose that the volume changes reflect differences in hydration that arise from structural variation at IHF–DNA interfaces while the resulting energetic compensation maintains the same net binding energy.
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