Abstract
Both the ordered and disordered solvent networks of vitamin B12 coenzyme crystal hydrate have been generated by Monte Carlo simulation techniques. Several different potential functions have been use to model both water-water and water-solute (i.e., water-coenzyme) interactions. The results have been analysed in terms of the structural properties of the water networks, such as mean water oxygen and hydrogen positions, coordination of each water molecule, and maxima of probability density maps in all four asymmetric units of this crystal.
The following results were found: (I) Within each asymmetric unit only one hydrogen bonding network was predicted although there were several hydrogen atom positions for any one solvent molecule (defined as maxima in probability density). (II) Reasonable agreement was obtained between predicted and experimental positions in the ordered solvent region, independent of the potential function used. (III) The positions of the calculated probability density maxima for the disordered channel region were different in different asymmetric units; this led to different simulated hydrogen bond networks which were not always consistent with the experimentally determined alternative (lower occupancy) sites.
The results suggest that it is advisable to simulate more than one asymmetric unit if one wishes to look at disorder in the solvent regions. Probability density maps were qualitatively very useful for picturing these disordered regions. However, there were no significant differences between quantitative results predicted using either average atomic positions or maxima of the probability density distributions.
Problems in quantifying agreement between experimental and predicted disordered solvent networks are discussed. The potential which included hydrogen atoms explicitly (EMPWI) seemed to give the best overall agreement, mainly because it was successful in predicting the unusually short hydrogen bonds which are found in this crystal.
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References
Barnes P, Finney JL, Nicholas JD, Quinn JE (1979) Cooperative effects in simulated water. Nature 282:459–464
Beveridge DL, Mezei M, Mehrotra PK, Marchese F, Ravi-Shanker G, Vasu T, Swaminathan S (1983) Monte Carlo computer simulation studies of the equilibrium properties and structure of liquid water. In: Haile JM, Mansoori GA (eds) Molecular based study and prediction of fluid properties. Adv Chem American Chemical Society. New York, pp 297–351
Finney JL, Goodfellow JM (1983) Cooperative effects in aqueous biomolecular systems and processes. In: Clementi E, Sarma RA (eds) Structure and dynamics: Nucleic acids and proteins. Adenine Press, New York, pp 81–93
Finney JL, Goodfellow JM, Howell PL, Vovelle F (1985) Computer simulation of aqueous biomolecular systems. J Biomol Struct Dynamics (in press)
Gellatly BJ, Quinn JE, Barnes P, Finney JL (1983) Two, three and four body interactions in model water interactions. Mol Phys 59:949–970
Goodfellow JM, Finney JL, Barnes P (1982) Monte Carlo computer simulation of water-amino acid interactions. Proc R Soc (London) B214:213–228
Goodfellow JM (1984) Solvent interactions in nucleic acid crystal hydrates. J Theor Biol 107:261–274
Hagler AT, Moult JM (1978) Computer simulation of the solvent structure around biological macromolecules. Nature 272:222–226
Hagler AT, Moult, JM, Osguthorpe DJ (1980) Monte Carlo simulation of the solvent structure in crystals of a hydrated cyclic peptide. Biopolymers 19:395–418
Jorgensen WL (1982) Revised TIPS for simulations of liquid water and aqueous solutions. J Chem Phys 77:4156–4163
Lenhert PG (1968) The structure of vitamin B12 VII. The X-ray analysis of the vitamin B12 coenzyme. Proc R Soc (London) A303:45–84
Lifson SØ, Hagler AT, Dauber P (1979) Consistent force field studies of intermolecular forces in hydrogen-bonded crystals I. Carboxylic acids, amides and the C=O...H-hydrogen bonds. J Am Chem Soc 101:5111–5121
Madison V, Osguthorpe DJ, Dauber P, Hagler AT (1983) Monte Carlo simulations of peptide solvation. Biopolymers 22:27–31
Metropolis M, Metropolis AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092
Momany FA, Carruthers LM, McGuire RF, Scheraga HA (1974) Intermolecular potentials from crystal data III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines and amides. J Phys Chem 78:1595–1620
Savage HFJ (1983) A study of the disordered water structure in crystals of vitamin B12 coenzyme. Ph D Thesis. University of London
Stillinger FA, Rahman A (1974) Improved simulation of liquid water by molecular dynamics. J Chem Phys 60:1545–1557
Vovelle F, Geneste M, Ptak M, Maigret B (1981) Empirical models of hydration of small peptides. In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht, pp 299–315
Wood DW (1979) In: Franks F (ed) Water, vol 6. Plenum Press, New York
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Vovelle, F., Goodfellow, J.M., Savage, H.F.J. et al. Solvent structure in vitamin B12 coenzyme crystals. Eur Biophys J 11, 225–237 (1985). https://doi.org/10.1007/BF00261999
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DOI: https://doi.org/10.1007/BF00261999