Bending and adaptability to proteins of the cAMP DNA-responsive element: Molecular dynamics contrasted with NMR

DNA bending is assumed to play a crucial role during recognition of the cAM P-responsive element (CRE) by transcription factors, However, diverging res ults have been obtained for the bending direction of the unbound double hel ix. The refined NMR structures present a bend directed toward the minor gro ove, while biochemical methods conclude that there is a bend toward the maj or groove. The present 10-ns molecular dynamics (MD) simulation of d(GAGATG ACGTCATCTC)(2), which contains the octamer CRE in its center, was carried o ut with AMBER in explicit water and counterions. It shows that CRE is a fle xible segment, although it is bent slightly toward the major groove (7 degr ees-8 degrees) on the average. The MD structure agrees with both the bioche mical results and unrefined NMR data. The divergence with the NMR refined s tructures suggests an improper electrostatic parameterization in the refine ment software. The malleability of the central CpG is certainly the major c ontribution to the curving of the whole CRE segment in both the unbound and bound states. Comparison with the crystal structure of CRE bound to GCN4 s hows that the deformation induced by the protein is concentrated mainly on the CpG step, rendering the bound structure of CRE closer to the structure of the 12-0 tetradecanoylphorbol-beta-acetate-responsive element.