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J M Goodfellow

Publications and source records attributed to J M Goodfellow.

42 records · Page 3Linked to original sources
PubMed1983

Monte Carlo studies on water in the dCpG/proflavin crystal hydrate.

The extensive water network identified in the crystallographic studies of the dCpG/Proflavin hydrate by Neidle, Berman and Shieh (Nature 288, 129, 1980) forms an ideal test case for a) assessing the accuracy of theoretical calculations on nucleic acid--water systems based on statistical thermodynamic computer simulation, and b) the possible use of computer simulation in predicting the water positions in crystal hydrates for use in the further refinement and interpretation of diffraction data. Monte Carlo studies have been carried out on water molecules in the unit cell of dCpG/proflavin, with the nucleic acid complex fixed and the condensed phase environment of the system treated by means of periodic boundary conditions. Intermolecular interactions are described by potential functions representative of quantum mechanical calculations developed by Clementi and coworkers, and widely used in recent studies of the aqueous hydration of various forms of DNA fragments. The results are analyzed in terms of hydrogen bond topology, hydrogen bond distances and energies, mean water positions, and water crystal probability density maps. Detailed comparison of calculated and experimentally observed results are given, and the sensitivity of results to choice of potential is determined by comparison with simulation results based on a set of empirical potentials.

Acridines↗
PubMed1982

Monte Carlo computer simulation of water-amino acid interactions.

The sensitivity of computer simulated solvent structures to changes in both non-bonded (Lennard-Jones) coefficients and partial atomic charges has been investigated with use of amino acid hydrate crystals in which the water structure is well defined experimentally. The polarizable electropole (p.e.) model of water has been extended to describe water-protein interactions; thus, the cooperative nature of the hydrogen bond (i.e. non-pair additive effects) is allowed for through a polarizable dipole. By means of Monte Carlo calculations, the predicted water positions were found to be very sensitive to the input parameters used to define both the non-bonded and electrostatic interactions. Root mean square deviations between simulated and X-ray structures were not always adequate to describe these differences and so more detailed comparisons were made. Non-pair additive effects were shown to lead to large changes in water dipoles, the values of which depended specifically on the system under consideration.

Amino Acids↗
PubMed1982

Cooperative effects in water-biomolecule crystal systems.

Monte Carlo computer simulation techniques have been used to model non-pair-additive (cooperative) effects in the water organization around several biomolecules. Although most models for water assume pair-additive potentials, both quantum mechanical calculations and experimental data indicate that cooperative effects are not negligible in hydrogen-bounded systems such as water. The many-body polarizable electropole (PE) model for water is used to examine the extent and the consequences of this cooperative behavior in several biomolecule hydrate crystals. Increases in the dipole moments of water molecules are predicted in all systems studied so far and can be as much as 50% more than the monomer value of 1.855 debyes. The average value of the individual dipole moments for any one system differs from that of another system and, therefore, should be considered a property of the system and not of the water molecule itself. When this previously calculated average value of the dipole moment for water molecules in a given system is used as a fixed parameter in the simulation, we find differences between this fixed calculation and the original unfixed simulation. An alternative procedure, which allows for a spread in dipole moments and is not dependent on a predetermined average value, has been developed to make simulations of large water-protein systems, including cooperative effects, computationally feasible.

Arginine↗
PubMed1980

Swelling studies of bovine corneal stroma without bounding membranes.

1. The swelling characteristics of demembranated bovine corneal stroma were studied as a function of time and of the pH and ionic strength of the bathing solution. 2. Compared with other pH values, the stroma swelled least near pH 4. 3. In the pH range 6--10, increasing the pH resulted in an increase both in the rate of swelling and in the hydration reached in a given time. 4. At pH 2 and 4, a final constant value of hydration was attained. At higher pH values no such equilibrium was attained when the hydration of the tissue was followed for at least 100 hr. 5. The swelling at high pH values was consistent with the hypothesis that the Donnan-osmotic contribution is the major component of the swelling pressure. 6. The ionic strength dependence was complex. There was a general decrease of swelling with increase in the ionic strength (mu) until around mu = 0.1. The swelling at mu = 0.15 was greater than at mu = 0.1 and mu = 0.25. 7. The results were interpreted on the assumption that the Donnan-osmotic effect is the major component of the swelling pressure.

Animals↗