MOLECULAR-DYNAMICS SIMULATIONS OF DNA WITH PROTEINS CONSISTENT GROMOSFORCE-FIELD AND THE ROLE OF COUNTERIONS SYMMETRY

Model solvent effects, related to DNA stability in water, are explored with molecular dynamics (MD) simulations: (i) hydrophobicity and (ii) salt modulated electrostatic effects. The 2.6 Angstrom resolution X-r ay coordinates of the DNA oligomer from Zif268 are used to seed the MD simulations. The molecular model contains fully charged and geometric ally unrestricted 10 base-pairs DNA in a 2640 water molecules bath wit h 18 Na-ions at 298 K. (i) The hydrophobicity correction affects the w ater-oxygen repulsive (root C12(Ow,Ow)) parameter that transforms the ''hydrophilic'' united carbon atom in the old GROMOS-87 force field in to an hydrophobic one. The root mean square (rms) deviations stay belo w 2.8 Angstrom, and the 600 ps-averaged and regularized structure elic its the positive effect of this correction on the structure. (ii) The electrostatic effects are probed by constructing a distribution of cou nterions placed in between phosphate groups at the end of a collective equilibration; salt (co-ion) effects are modeled by imposing a weak h armonic constraint (0.58 kcal mol(-1) Angstrom(-2)) to the equilibrate d set of counterions. A 1 ns trajectory shows rms deviations from X-ra y below 1.7 Angstrom for all atoms at 600 ps and below 2.3 Angstrom in the time span up to 1 ns; counterions fluctuations are large enough t o allow for DNA bending and conformational changes. The quality of thi s simulation can be appreciated from different averaged and regularize d structures. The structural results are comparable to those obtained with state-of-the-art force fields using Ewald summation technique for an oligonucleotide of similar size.