Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator

We ha ve carried out molecular dynamics simulation of the lambda OL I DNA o perator on the free and the protein-bound forms. Our results lead us to con clude that the binding of the repressor actually makes the N-7 atom of Gua8 ' more solvent exposed, thereby enhancing its reactivity to chemical methy lation. This increase in solvent accessibility surface area occurs simultan eously with the formation Of hydrogen bonds between Lys-4 of the nonconsens us flexible N-terminal arm and Gua6 ' of the nonconsensus half-site operato r DNA. Calculations of protein-DNA interaction energies reveal that among t he residues of the arm, Lys-4 contributes the most favorably to the interac tion energies. This result is consistent with mutagenesis studies that esta blished that lysine at position 4 is absolutely required for tight binding. We find that the nonconsensus arm and the nonconsensus monomer interacts l ess favorably with DNA than do their respective counterparts of the consens us monomer. Moreover, the six-residue flexible ann accounts for at least ha lf the total protein-DNA interactions energy. These results are in agreemen t with previous experimental studies. In accord with the diffuse electron d ensity map observed in crystallographic studies of the nonconsensus flexibl e arm, we find that our model built for this region is more flexible and ex hibits more conformations than its consensus counterpart. The simulation al so reveals that DNA bending observed near the outer edge of the operator si te is an intrinsic sequence-dependent property,. Av contrast, the DNA-bendi ng features observed toward the center of the operator are induced by the p rotein. On the whole, stepwise protein-induced bending is more pronounced i n the consensus half-site operator. We also find that the unusually large h elical twist (49 degrees) observed in the protein-bound form near the cente r of the operator results from the binding of the protein at abase step wit h some propensity for high twists, (C) 2001 John Wiley & Sons, Inc.