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Axis Curvature and Ligand Induced Bending in the CAP-DNA Oligomers

Department of Chemistry and Molecular Biophysics Program, Hall-Atwater Laboratories, Wesleyan University, Middletown, Connecticut 06459

Correspondence: Address reprint requests and inquiries to D. L. Beveridge, E-mail: dbeveridge{at}wesleyan.edu.

The origin of DNA axis curvature in complexes of the catabolite activator protein with DNA is studied using multiple molecular dynamics (MD) simulations of the free and protein-bound forms of the DNA. The results are compared to available solution and crystal structure data. The MD simulations reproduce the experimentally observed bend in DNA and indicate that 40% of the bending observed in the complex is intrinsic to the DNA sequence, whereas 60% is induced on protein binding. The MD provides a model for the dynamical structure of the DNA free in solution and for ligand-induced bending.

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