Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface.
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.
Senear
Donald F
DF
Department of Molecular Biology and Biochemistry, College of Medicine, University of California, Irvine, CA 92697, USA. dfsenear@uci.edu
Tretyachenko-Ladokhina
Vira
V
Opel
Michael L
ML
Aeling
Kimberly A
KA
Hatfield
G Wesley
GW
Franklin
Laurie M
LM
Darlington
Reuben C
RC
Alexander Ross
J B
JB
D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay; D029968:Escherichia coli Proteins / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D006874:Hydrostatic Pressure; D034982:Integration Host Factors / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012965:Sodium Chloride / Q000737:chemistry
D029968:Escherichia coli Proteins; D034982:Integration Host Factors; C440502:integration host factor, E coli; D012965:Sodium Chloride; D004247:DNA