Skip to main content
Biophysical Journal logoLink to Biophysical Journal
. 2002 Sep;83(3):1578–1588. doi: 10.1016/S0006-3495(02)73927-1

A model for water motion in crystals of lysozyme based on an incoherent quasielastic neutron-scattering study.

C Bon 1, A J Dianoux 1, M Ferrand 1, M S Lehmann 1
PMCID: PMC1302255  PMID: 12202382

Abstract

This paper reports an incoherent quasielastic neutron scattering study of the single particle, diffusive motions of water molecules surrounding a globular protein, the hen egg-white lysozyme. For the first time such an analysis has been done on protein crystals. It can thus be directly related and compared with a recent structural study of the same sample. The measurement temperature ranged from 100 to 300 K, but focus was on the room temperature analysis. The very good agreement between the structural and dynamical studies suggested a model for the dynamics of water in triclinic crystals of lysozyme in the time range approximately 330 ps and at 300 K. Herein, the dynamics of all water molecules is affected by the presence of the protein, and the water molecules can be divided into two populations. The first mainly corresponds to the first hydration shell, in which water molecules reorient themselves fivefold to 10-fold slower than in bulk solvent, and diffuse by jumps from hydration site to hydration site. The long-range diffusion coefficient is five to sixfold less than for bulk solvent. The second group corresponds to water molecules further away from the surface of the protein, in a second incomplete hydration layer, confined between hydrated macromolecules. Within the time scale probed they undergo a translational diffusion with a self-diffusion coefficient reduced approximately 50-fold compared with bulk solvent. As protein crystals have a highly crowded arrangement close to the packing of macromolecules in cells, our conclusion can be discussed with respect to solvent behavior in intracellular media: as the mobility is highest next to the surface, it suggests that under some crowding conditions, a two-dimensional motion for the transport of metabolites can be dominant.

Full Text

The Full Text of this article is available as a PDF (154.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Badger J., Caspar D. L. Water structure in cubic insulin crystals. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):622–626. doi: 10.1073/pnas.88.2.622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bon C., Lehmann M. S., Wilkinson C. Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme. Acta Crystallogr D Biol Crystallogr. 1999 May;55(Pt 5):978–987. doi: 10.1107/s0907444998018514. [DOI] [PubMed] [Google Scholar]
  3. Bone S., Pethig R. Dielectric studies of protein hydration and hydration-induced flexibility. J Mol Biol. 1985 Jan 20;181(2):323–326. doi: 10.1016/0022-2836(85)90096-8. [DOI] [PubMed] [Google Scholar]
  4. Burling F. T., Weis W. I., Flaherty K. M., Brünger A. T. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science. 1996 Jan 5;271(5245):72–77. doi: 10.1126/science.271.5245.72. [DOI] [PubMed] [Google Scholar]
  5. Cameron I. L., Kanal K. M., Keener C. R., Fullerton G. D. A mechanistic view of the non-ideal osmotic and motional behavior of intracellular water. Cell Biol Int. 1997 Feb;21(2):99–113. doi: 10.1006/cbir.1996.0123. [DOI] [PubMed] [Google Scholar]
  6. Careri G. Cooperative charge fluctuations by migrating protons in globular proteins. Prog Biophys Mol Biol. 1998;70(3):223–249. doi: 10.1016/s0079-6107(98)00030-3. [DOI] [PubMed] [Google Scholar]
  7. Chung E., Henriques D., Renzoni D., Zvelebil M., Bradshaw J. M., Waksman G., Robinson C. V., Ladbury J. E. Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides. Structure. 1998 Sep 15;6(9):1141–1151. doi: 10.1016/s0969-2126(98)00115-4. [DOI] [PubMed] [Google Scholar]
  8. Cooper A. Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics. Biophys Chem. 2000 May 31;85(1):25–39. doi: 10.1016/s0301-4622(00)00136-8. [DOI] [PubMed] [Google Scholar]
  9. Denisov V. P., Halle B. Hydrogen exchange and protein hydration: the deuteron spin relaxation dispersions of bovine pancreatic trypsin inhibitor and ubiquitin. J Mol Biol. 1995 Feb 3;245(5):698–709. doi: 10.1006/jmbi.1994.0056. [DOI] [PubMed] [Google Scholar]
  10. Doster W., Cusack S., Petry W. Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature. 1989 Feb 23;337(6209):754–756. doi: 10.1038/337754a0. [DOI] [PubMed] [Google Scholar]
  11. Ehtezazi T., Govender T., Stolnik S. Hydrogen bonding and electrostatic interaction contributions to the interaction of a cationic drug with polyaspartic acid. Pharm Res. 2000 Jul;17(7):871–878. doi: 10.1023/a:1007520628237. [DOI] [PubMed] [Google Scholar]
  12. Ferrand M., Dianoux A. J., Petry W., Zaccaï G. Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9668–9672. doi: 10.1073/pnas.90.20.9668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fitter J., Lechner R. E., Buldt G., Dencher N. A. Internal molecular motions of bacteriorhodopsin: hydration-induced flexibility studied by quasielastic incoherent neutron scattering using oriented purple membranes. Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7600–7605. doi: 10.1073/pnas.93.15.7600. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fitter J., Lechner R. E., Dencher N. A. Picosecond molecular motions in bacteriorhodopsin from neutron scattering. Biophys J. 1997 Oct;73(4):2126–2137. doi: 10.1016/S0006-3495(97)78243-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gabriel B., Teissié J. Proton long-range migration along protein monolayers and its consequences on membrane coupling. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14521–14525. doi: 10.1073/pnas.93.25.14521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Habash J., Raftery J., Nuttall R., Price H. J., Wilkinson C., Kalb A. J., Helliwell J. R. Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography. Acta Crystallogr D Biol Crystallogr. 2000 May;56(Pt 5):541–550. doi: 10.1107/s0907444900002353. [DOI] [PubMed] [Google Scholar]
  17. Hodges M. W., Cafiso D. S., Polnaszek C. F., Lester C. C., Bryant R. G. Water translational motion at the bilayer interface: an NMR relaxation dispersion measurement. Biophys J. 1997 Nov;73(5):2575–2579. doi: 10.1016/S0006-3495(97)78286-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jaenicke R. Stability and stabilization of globular proteins in solution. J Biotechnol. 2000 May 26;79(3):193–203. doi: 10.1016/s0168-1656(00)00236-4. [DOI] [PubMed] [Google Scholar]
  19. Lounnas V., Pettitt B. M. Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin. Proteins. 1994 Feb;18(2):148–160. doi: 10.1002/prot.340180207. [DOI] [PubMed] [Google Scholar]
  20. Makarov V. A., Feig M., Andrews B. K., Pettitt B. M. Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys J. 1998 Jul;75(1):150–158. doi: 10.1016/S0006-3495(98)77502-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mason S. A., Bentley G. A., McIntyre G. J. Deuterium exchange in lysozyme at 1.4-A resolution. Basic Life Sci. 1984;27:323–334. doi: 10.1007/978-1-4899-0375-4_19. [DOI] [PubMed] [Google Scholar]
  22. McDowell R. S., Kossiakoff A. A. A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin. J Mol Biol. 1995 Jul 21;250(4):553–570. doi: 10.1006/jmbi.1995.0397. [DOI] [PubMed] [Google Scholar]
  23. Nagendra H. G., Sukumar N., Vijayan M. Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration. Proteins. 1998 Aug 1;32(2):229–240. doi: 10.1002/(sici)1097-0134(19980801)32:2<229::aid-prot9>3.0.co;2-f. [DOI] [PubMed] [Google Scholar]
  24. Niimura N., Minezaki Y., Nonaka T., Castagna J. C., Cipriani F., Høghøj P., Lehmann M. S., Wilkinson C. Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Biol. 1997 Nov;4(11):909–914. doi: 10.1038/nsb1197-909. [DOI] [PubMed] [Google Scholar]
  25. Otting G., Liepinsh E., Wüthrich K. Protein hydration in aqueous solution. Science. 1991 Nov 15;254(5034):974–980. doi: 10.1126/science.1948083. [DOI] [PubMed] [Google Scholar]
  26. Ovádi J., Srere P. A. Channel your energies. Trends Biochem Sci. 1992 Nov;17(11):445–447. doi: 10.1016/0968-0004(92)90485-r. [DOI] [PubMed] [Google Scholar]
  27. Pocker Y. Water in enzyme reactions: biophysical aspects of hydration-dehydration processes. Cell Mol Life Sci. 2000 Jul;57(7):1008–1017. doi: 10.1007/PL00000741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Podjarny A. D., Howard E. I., Urzhumtsev A., Grigera J. R. A multicopy modeling of the water distribution in macromolecular crystals. Proteins. 1997 Jul;28(3):303–312. [PubMed] [Google Scholar]
  29. Pérez J., Zanotti J. M., Durand D. Evolution of the internal dynamics of two globular proteins from dry powder to solution. Biophys J. 1999 Jul;77(1):454–469. doi: 10.1016/S0006-3495(99)76903-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Royant A., Edman K., Ursby T., Pebay-Peyroula E., Landau E. M., Neutze R. Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin. Nature. 2000 Aug 10;406(6796):645–648. doi: 10.1038/35020599. [DOI] [PubMed] [Google Scholar]
  31. Rupley J. A., Careri G. Protein hydration and function. Adv Protein Chem. 1991;41:37–172. doi: 10.1016/s0065-3233(08)60197-7. [DOI] [PubMed] [Google Scholar]
  32. Saenger W. Structure and dynamics of water surrounding biomolecules. Annu Rev Biophys Biophys Chem. 1987;16:93–114. doi: 10.1146/annurev.bb.16.060187.000521. [DOI] [PubMed] [Google Scholar]
  33. Shu F., Ramakrishnan V., Schoenborn B. P. Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin. Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3872–3877. doi: 10.1073/pnas.060024697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Smith J., Kuczera K., Karplus M. Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1601–1605. doi: 10.1073/pnas.87.4.1601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Steinhoff H. J., Kramm B., Hess G., Owerdieck C., Redhardt A. Rotational and translational water diffusion in the hemoglobin hydration shell: dielectric and proton nuclear relaxation measurements. Biophys J. 1993 Oct;65(4):1486–1495. doi: 10.1016/S0006-3495(93)81217-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Svergun D. I., Richard S., Koch M. H., Sayers Z., Kuprin S., Zaccai G. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2267–2272. doi: 10.1073/pnas.95.5.2267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Teeter M. M., Roe S. M., Heo N. H. Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K. J Mol Biol. 1993 Mar 5;230(1):292–311. doi: 10.1006/jmbi.1993.1143. [DOI] [PubMed] [Google Scholar]
  38. Teixeira J, Bellissent-Funel M, Chen SH, Dianoux AJ. Experimental determination of the nature of diffusive motions of water molecules at low temperatures. Phys Rev A Gen Phys. 1985 Mar;31(3):1913–1917. doi: 10.1103/physreva.31.1913. [DOI] [PubMed] [Google Scholar]
  39. Trantham E. C., Rorschach H. E., Clegg J. S., Hazlewood C. F., Nicklow R. M., Wakabayashi N. Diffusive properties of water in Artemia cysts as determined from quasi-elastic neutron scattering spectra. Biophys J. 1984 May;45(5):927–938. doi: 10.1016/S0006-3495(84)84239-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Walsh M. A., Schneider T. R., Sieker L. C., Dauter Z., Lamzin V. S., Wilson K. S. Refinement of triclinic hen egg-white lysozyme at atomic resolution. Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):522–546. doi: 10.1107/s0907444997013656. [DOI] [PubMed] [Google Scholar]
  41. Wlodawer A., Savage H., Dodson G. Structure of insulin: results of joint neutron and X-ray refinement. Acta Crystallogr B. 1989 Feb 1;45(Pt 1):99–107. doi: 10.1107/s0108768188011012. [DOI] [PubMed] [Google Scholar]
  42. Zanotti J. M., Bellissent-Funel M. C., Parello J. Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin. Biophys J. 1999 May;76(5):2390–2411. doi: 10.1016/S0006-3495(99)77395-9. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES