SUNY at Albany
June 19-23, 2001
Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator
We have carried out molecular dynamics simulation of the lambda OL1 DNA operator on the free and the protein-bound forms. Our results lead us to conclude that the binding of the repressor actually makes the N-7 atom of Gua8' more solvent-exposed, thereby enhancing its reactivity to chemical methylation. This increase in solvent accessibility surface area occurs simultaneously with the formation of hydrogen-bonds between Lys-4 of the non-consensus flexible N-terminal arm and Gua6' of the non-consensus half-site operator DNA. Calculations of protein-DNA interaction energies reveal that among the residues of the arm, Lys-4 contributes the most favorably to the interaction energies. This result is consistent with mutagenesis studies that established that lysine at position 4 is absolutely required for tight binding. We find that the non-consensus arm and the non-consensus monomer interacts less favorably with DNA than do their respective counterparts of the consensus monomer. Moreover, the six-residue flexible arm accounts for at least half the total protein-DNA interactions energy. These results are in agreement with previous experimental studies. In accord with the diffuse electron density map observed in crystallographic studies of the non-consensus flexible arm, we find that our model built for this region is more flexible and exhibit more conformations than its consensus counterpart. The simulation also reveals that DNA-bending observed near the outer edge of the operator site, is an intrinsic sequence-dependent property. By contrast, the DNA-bending features observed towards the center of the operator, are induced by the protein. On the whole, stepwise protein-induced bending is more pronounced in the consensus half-site operator. We also find that the unusually large helical twist (49 degrees) observed in the protein-bound form near the center of the operator results from the binding of the protein at a base step with some propensity for high twists.
David C. Kombo(1), Kevin J. McConnell(1), Matthew A. Young(1,2) & David L. Beveridge(1)
Department of Chemistry & Molecular Biophysics Program(1), Hall-Atwater Laboratory, Wesleyan University, Middletown, CT 06457
Laboratories of Molecular Biophysics(2), Howard Hughes Medical Institute, The Rockefeller University 1230 York Avenue New York NY 10021