Molecular Dynamics Simulation of a Zif268-DNA Complex in Water. Spatial Patterns and Fluctuations Sensed from a Nanosecond Trajectory

In this paper, with the help of a nanosecond-long molecular dynamics trajectory, we show that a fully charged protein-DNA system (Zif268-DNA) in a water environment can be simulated with a general force field (GROMOS) if solvation and counterion effects are appropriately represented. A model exhibiting ionic atmosphere effects on mobile counterions (Tapia, O.; Velazquez, I. J. Am. Chem. Soc. 1997, 119, 5934-5938) was implemented. The root-mean-square deviations (rmsds) with respect to X-ray structure for the full complex, the protein, and the 12-base pair consensus sequence were 2.0, 1.95, and 1.35 Angstrom, respectively, while the counterions displayed an rmsd from the initially equilibrated position of 1.2 Angstrom. The mean-square fluctuation with respect to the average structure correlated with temperature factors for the protein and DNA; the agreement in trend is good. The results show that GROMOS87 force field with an appropriate representation of colon (ion atmosphere) effects on the counterions, and corrections for hydrophobicity default in the water to solute C-12(Ow,Ow)(1/2) parameter, previously used for proteins (Daura X.; Oliva, B.; Querol, E.; Aviles, F. X.; Tapia, O. Proteins 1996, 25, 89-103), are sufficient to obtain a fairly realistic simulation of this protein-DNA complex.