DNA-STRUCTURE AND FLUCTUATIONS SENSED FROM A 1.1NS MOLECULAR-DYNAMICSTRAJECTORY OF A FULLY CHARGED ZIF268-DNA COMPLEX IN WATER

Molecular dynamics simulations of the zinc finger domain of protein Zi f268, in a complex with a high affinity DNA sequence, yields a globall y stable system with small yet significant readjustments with persiste nce time of the order of 1.1 ns. The results confirm the quality of th e standard GROMOS87 force field with a corrected solvent-to-solute int eraction that does not affect the water-water SPC interactions nor the intra-molecular cohesive forces. Specificity determinants are discuss ed. The simulations of DNA alone, with the same force field, showed th e important role played by the solvent and the symmetry of the counter ion distribution. (Tapia & Velazquez, J. Am. Chem. Soc., 119, 5934, 19 97) In the present work, this feature was retained when appropriate. T he results for root mean square deviations and temperature B-factors i llustrate the reliability of this approach. The structure of DNA is he ld by its interactions with the zinc finger protein. This behavior is not much affected by the slow whithering away of finger-1 from DNA. Th e factors contributing to the molecular stability found in GROMOS' pot ential energy function appear to be sufficient to yield stable fluctua tion patterns when surrounding medium effects are properly included.