Dept. of Biological Sciences, Univ. of Pittsburgh, Pittsburgh PA 15260, USA
Molecular Dynamics simulations on DNA and on DNA-EcoRI and DNA-EcoRV complexes suggest that the DNA within these complexes is significantly more ordered than free DNA. Similarly, both the protein and the DNA are more ordered in the specific (cognate) DNA-EcoRV complex than they are in the noncognate DNA-protein complex, consistent with recently proposed analogies between protein folding and sequence specific DNA-protein recognition. Analysis of the trajectories shows the net entropy gain upon specific binding to be the result of opposing contributions: Solvent release, which increases entropy vs. configurational terms (as measured by the magnitude of the atomic fluctuations), and collective terms from tight coupling between the motions of the protein and the DNA.
Several simulational protocols were explored; the most successful utilized full periodic conditions, TIP3P water and the particle mesh Ewald sum (PME) to treat the long range interactions to 500 pS. This trajectory showed significantly improved fidelity to the observed X-ray structures and B-factors. The Ewald method effectively eliminates the usual "cut-off" of long range interactions and allowed us to evaluate the full effect of the electrostatic forces; not surprisingly, long- range electrostatic interactions are significant components of DNA- protein interactions.
The utility of the Ewald method is illustrated by a simulation of the dodecamer duplex d(CGCGAATTCGCG) which showed remarkable agreement with the Dickerson X-ray structure. Within the Eco RI site itself, the rms deviation between the average theoretical and observed structures was 1.1Å. The width of the minor groove fluctuated between a wide and narrow configuration with the latter corresponding closely to the X-ray structure. The simulation also suggested a strong sequence dependent signature on the minor groove width in both wide and narrow conformers. Hydration shells in both the major and minor grooves were observed. The "spine of hydration" in the minor groove was clear. In the major groove the first hydration shell appears to be a ribbon like structure that reproduces the principle features of observed X-ray structures; subtle variations of this hydration pattern suggest sequence dependencies. Sequence dependent features were also examined for helical and other geometric parameters. The successful reproduction of many experimentally observed fine structural features shows that the Ewald summation significantly improves the fidelity of the calculations.