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 A, respectively, while the counterions displayed an rmsd from the initially equilibrated position of 1.2 A. 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 coion (ion atmosphere) effects on the counterions, and corrections...