Hydration forces between parallel DNA double helices: computer simulations.

M R Reddy; M Berkowitz

doi:10.1073/pnas.86.9.3165

Home/Archive/PubMed

PubMed · 2717614

Hydration forces between parallel DNA double helices: computer simulations.

M R Reddy·M Berkowitz

View original source ↗Export metadata ↓

Abstract

We have performed two molecular dynamics computer simulations of two 10-base-pair segments of DNA molecules immersed in water. The goal of these simulations is to study the structural and dynamical properties of water between the DNA molecules. We have observed water ordering next to DNA surfaces. Existence of such ordering was proposed earlier by Marcelja and Radic [Marcelja, S. & Radic, N. (1976) Chem. Phys. Lett. 42, 129-130] to explain strong hydration forces between macromolecular surfaces.

Explore related subjects

Chemical Phenomena Chemistry, Physical Computer Simulation DNA Macromolecular Substances Polydeoxyribonucleotides Sodium Water Journal Article Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

M R Reddy, M Berkowitz. 1989. Hydration forces between parallel DNA double helices: computer simulations.. https://doi.org/10.1073/pnas.86.9.3165

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed1992

Partitioning of tryptophan side-chain analogs between water and cyclohexane.

We have measured the partitioning of the tryptophan side-chain analogs 3-methylindole and N-methylindole between water and cyclohexane over the temperature range 8-55 degrees C to investigate the relative contribution of the imine-NH- to the free energy of transfer. We take advantage of the fact that the indole imine nitrogen is blocked by a methyl group in N-methylindole. Unlike previous studies, we take into account the water present in the cyclohexane phase. Free energies of partitioning were calculated using mole-fraction, volume-fraction, and Flory-Huggins-corrected volume-fraction partition coefficients [De Young, L. R., & Dill, K. A. (1990) J. Phys. Chem. 94, 801-809; Sharp, K. A., Nicholls, A., Friedman, R., & Honig, B. (1991) Biochemistry 30, 9686-9697]. These approaches account for configurational entropy changes in different ways and thus lead to different values for the calculated free energies of transfer. There is a 2-3-fold difference in the free energies calculated from our measurements, using the different units. Independent of units, the partitioning of both compounds involves identical entropy changes. However, 3-methylindole has an additional unfavorable enthalpic contribution to partitioning into cyclohexane of +1.6 kcal/mol (independent of units) which is presumably the cost of removing the indole -NH- group from water and transferring it to cyclohexane. In cyclohexane, 3-methylindole forms hydrogen bonds with water that cause water to copartition into cyclohexane with the solute. A method is described which allows the partitioning process to be examined independent of subsequent interactions with water in the solvent.

Chemical Phenomena↗

PubMed1992

The conformational behaviour of phosphatidylinositol in model membranes: 2H-NMR studies.

Dimyristoylphosphatidylinositol (DMPI) has been synthesized with the appropriate natural stereochemistry and labelled with deuterium at specific sites in the D-myo-inositol headgroup. 2H-NMR spectroscopy of DMPI in its lamellar phase at a molar ratio of water-to-lipid RW/L of 129 and at 70 degrees C reveals quadrupolar splittings delta v of 3.83 and 2.17 kHz, respectively, for the five axially oriented C-D bonds and the single equatorially oriented C-D bond of the D-myo-inositol headgroup. Between RW/L ratios of 129 and 210 and between 30 degrees C and 80 degrees C the value of the ratio of these splittings delta nu ax/delta nu eq varies significantly (between 1.17 and 4.38). If it is assumed that, at a particular temperature, there is a single preferred orientation of the inositol headgroup, and that motion of the DPMI molecule establishes axial symmetry with respect to the bilayer normal then the ratio of these quadrupolar splittings can be used to impose constraints on that orientation. For example, the data are inconsistent with a situation in which the inositol ring lies parallel to the membrane surface and are difficult to reconcile with an arrangement where the inositol ring lies perpendicular to the surface. Computational modelling identifies four possible 'tilted' orientations, all of which are consistent with the data, and two of these allow good intramolecular hydrogen bonds to be formed. In one there is hydrogen bonding between the inositol C2-OH and the phosphate pro-R oxygen. This is close to the conformation previously identified as being dominant in DMSO solution (Bushby, R.J., Byard, S.J., Hansbro, P.M. and Reid, D.G. (1990) Biochim. Biophys. Acta 1044, 231-236).

Chemical Phenomena↗

PubMed1992

Structure of 2,3-naphthalenedicarboxylic acid.

C12H8O4, M(r) = 216.20, monoclinic, C2/c, a = 5.087 (2), b = 19.222 (3), c = 9.552 (2) A, beta = 93.81 (3) degrees, V = 932.0 (5) A3, Z = 4, Dx = 1.54 g cm-3, lambda = 0.71073 A, mu = 1.09 cm-1, F(000) = 488, T = 295 K, R = 0.037 for 687 unique reflections having I > 3 sigma (I). In the structure reported here, a twofold axis lies in the plane of the molecule and bisects the three central ring bonds. The average C--C bond distance in the naphthalene core is 1.401 (27) A and the average interior angle 120.0 (14) degrees. The average deviation of the C atoms comprising the naphthalene rings from the best least-squares plane describing the rings is 0.021 (8) A. The plane of the single unique carboxylic acid group makes a dihedral angle of 33.1 (1) degrees with the least-squares plane of the naphthalene core. The carboxylic acid group, in which the observed O--H distance is 1.00 (3) A, forms a cyclic-dimer hydrogen bond across a center of inversion with the H...O(acceptor) distance 1.68 (3) A, the O...O-(acceptor) distance 2.676 (2) A and the O--H...O-(acceptor) angle 174 (3) degrees. The C--O bond lengths indicate no disorder in the carboxylic acid dimers. The molecules are arranged in stacks with the naphthalene cores parallel to the (102) plane and with the hydrogen bonds of the acid groups linking adjacent stacks. This structure of 2,3-naphthalenedicarboxylic acid is essentially the same as that of o-phthalic acid, but with the b cell edge correspondingly larger to accommodate the additional aromatic ring.

Chemical Phenomena↗