Abstract
The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 Å2. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal water (R = 0.212). A reciprocal space refinement of the water and the protein coordinates has been performed. Monte Carlo calculations can be used to obtain information for crystallographically invisible parts of the unit cell and yield better coordinates for the visible part in the refinement.
Similar content being viewed by others
References
Ahlström P, Teleman O, Jönsson B, Forsén S (1987) Molecular dynamics simulation of parvalbumin in aqueous solution. J Am Chem Soc 109:1541–1551
Blake CCF, Pulford WCA, Artymiuk PJ (1983) X-ray studies of water in crystals of lysozyme. J Mol Biol 167:693–723
Bone S, Pethig R (1982) Dielectric studies of the binding of water to lysozyme. J Mol Biol 157:571–575
Careri G, Geraci M, Giansanti A, Rupley JA (1985) Protonic conductivity of hydrated lysozyme powders at megahertz frequencies. Proc Natl Acad Sci USA 82:5342–5346
Cheng X, Schoenborn BP (1990) Hydration in protein crystals. A neutron diffraction analysis of carbonmonoxy myoglobin. Acta Crystallogr B46:195–208
Clementi E, Cavallone F, Scordamaglia J (1977) Analytical potentials from ab-initio computations for the interaction between biomolecules. 1. Water with amino acids. J Am Chem Soc 99:5531–5545
Clementi E, Corongiu G, Aida M, Niesan U, Kneller G (1990) Monte Carlo and molecular dynamics simulations. In: Clementi E (ed) MOTECC-90. ESCOM, Leiden, pp 805–888
Clementi E, Corongiu G (1989) KGNMOL: A program for molecular interactions. In: Clementi E (ed) MOTECC-89. ESCOM, Leiden, pp 243–306
Corongiu G, Clementi E (1978) Intramolecular and intermolecular interactions for deriving chemical formulae and for simulate complex chemical systems. Gazz Chim Ital 108:273–280
Cruickshank DWJ (1949) The accuracy of electron-density maps in X-ray analysis with special reference to dibenzyl. Acta Crystallogr 2:65–82
Dachwitz E, Parak F, Stockhausen M (1989) On the dielectric relaxation of aqueous myoglobin solutions. Bericht. Bunsen-Ges f phys Chemie 93:1465–1458
Finney JL, Goodfellow JM, Howell PL, Vovelle F (1985) Computer simulation of aqueous biomolecular systems. J Biomol Struct Dyn 3:599–622
Frauenfelder H, Parak F, Young RD (1988) Conformational substates in proteins. Ann Rev Biophys Chem 17:451–479
Frauenfelder H, Petsko GA, Tsernoglou D (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280:558–563
Goodfellow JM (1987) Computer simulation of hydration networks around amino acids. Int J Biol Macromol 9:273–280
Van Gunsteren WF, Berendsen HJC, Hermans J, Hol WGJ, Postma JPM (1983) Computer simulation of the dynamics of hydrated protein crystals and its comparison with X-ray data. Proc Natl Acad Sci USA 80:4315–4319
Hartmann H, Steigemann W, Reuscher H, Parak F (1987) Structural disorder in proteins: A comparison of myoglobin and erythrocruorin. Eur Biophys J 14:337–348
Jeffrey GA, Saenger W (1991) Hydrogen Bonding in Biological Structures. Springer, Berlin Heidelberg New York
Kennert JH, Hendrickson WA (1980) A restrained thermal factor refinement procedure. Acta Crystallogr. A36:344–349
Kotitschke K, Kimmich R, Rommel E, Parak F (1990) NMR study of diffusion in protein hydration shells. Prog Colloid Polym Sci 83:211–213
Krupyanskii YF, Goldanskii VI, Nienhaus GU, Parak F (1990) Dynamics of protein water systems revealed by Rayleigh scattering of Mössbauer radiation (RSMR). Hyperfine Interact 53:59–73
Kuntz ID, Kauzmann W (1974) Hydration of proteins and polypeptides. Adv Protein Chem 28:239–345
Luzzati V (1952) Traitement statistique des erreurs dans la determination des structures cristalline. Acta Crystallogr 5:802–810
Mathur-De-Vré R (1979) The NMR studies of water in biological systems. Progr Biophys Mol Biol 35:103–134
Matsuoka O, Clementi E, Yoshimine M (1976) CI study of the water dimer potential surface. J Chem Phys 64:1351–1361
Metropolis N, Rosenbluth AW, Rosenbluth AH, Teller J, Teller F (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092
Otting G, Liepinsh E, Wüthrich K (1991) Protein hydration in aqueous solution. Science 254:974–980
Otting G, Wüthrich K (1989) Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. J Am Chem Soc 111:1871–1875
Phillips SEV (1980) Structure and refinement of oxymyoglobin at 1.6 Å resolution. J Mol Biol 142:1871–1875
Pissis P (1989) Dielectric studies of protein hydration. J Mol Liquids 41:271–289
Rupley JA, Careri G (1989a) Enzmye hydration and function. In: Cooper A, Houben JL, Chien LC (eds) The enzyme catalysis process. Energetics, mechanism and dynamics. Plenum Press, New York, pp 223–234
Rupley JA, Careri G (1989b) Percolation process. In: Cooper A, Houben JL, Chien LC (eds) The enzyme catalysis process. Energetics, mechanism and dynamics. Plenum Press, New York, pp 235–246
Schoenborn BP (1988) Solvent effect in protein crystals. A neutron diffraction analysis of solvent and ion density. J Mol Biol 201:741–749
Singh GP, Parak F, Hunklinger S, Dransfeld K (1981) Role of adsorbed water in the dynamics of metmyoglobin. Phys Rev Lett 47:685–688
Author information
Authors and Affiliations
Additional information
Correspondence to: F. Parak
Rights and permissions
About this article
Cite this article
Parak, F., Hartmann, H., Schmidt, M. et al. The hydration shell of myoglobin. Eur Biophys J 21, 313–320 (1992). https://doi.org/10.1007/BF00188343
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00188343