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 t rajectory, 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 represen ted. 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 pai r consensus sequence were 2.0, 1.95, and 1.35 Angstrom, respectively, while the counterions displayed an rmsd from the initially equilibrate d position of 1.2 Angstrom. The mean-square fluctuation with respect t o the average structure correlated with temperature factors for the pr otein and DNA; the agreement in trend is good. The results show that G ROMOS87 force field with an appropriate representation of colon (ion a tmosphere) effects on the counterions, and corrections for hydrophobic ity default in the water to solute C-12(Ow,Ow)(1/2) parameter, previou sly used for proteins (Daura X.; Oliva, B.; Querol, E.; Aviles, F. X.; Tapia, O. Proteins 1996, 25, 89-103), are sufficient to obtain a fair ly realistic simulation of this protein-DNA complex.