O. Tapia et I. Velazquez, MOLECULAR-DYNAMICS SIMULATIONS OF DNA WITH PROTEINS CONSISTENT GROMOSFORCE-FIELD AND THE ROLE OF COUNTERIONS SYMMETRY, Journal of the American Chemical Society, 119(25), 1997, pp. 5934-5938
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.