A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: Comparison with crystallographic ordered water sites
✍ Scribed by P. S. Subramanian; S. Pitchumani; D. L. Beveridge; Helen M. Berman
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 1990
- Tongue
- English
- Weight
- 999 KB
- Volume
- 29
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. T h e simulation was subjected to proximit) analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one-and two-water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x-ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and amnioniurn salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation t o compete unfavorably with the adjacent donor site at guanine 3 2 . There is, however, a significant probability of finding a one-water G-N:)-W-G-N2 bridge indicated in the simulation. An explanation for the guanine N:i discrepancy in terms of electrostatic potentials is also offered. Tne calculated one-and two-water bridges in the rGpC hydration complex coincide in a number of cases to those $&served in the ordered water structure of the sodium rGpC crystal hydrate.