Skip to main content
SpringerLink
Log in

Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data

  • Article
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

    We’re sorry, something doesn't seem to be working properly.

    Please try refreshing the page. If that doesn't work, please contact support so we can address the problem.

Abstract

The implications of protein-water interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution. Starting from the atomic coordinates, by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably (Debye modeling, program HYDRO). By advanced modeling techniques the hydration can be taken into account appropriately: by some kind of rescaling procedures, by modeling a water shell, by iterative comparisons to experimental scattering curves (ab initio modeling) or by special hydration algorithms. In the latter case, the surface topography of proteins is visualized in terms of dot surface points, and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope. Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules. Among the tuning parameters, the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial. The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from X-ray crystallography, and the capability to predict hydration, structural and hydrodynamic parameters (hydrated volume, radius of gyration, translational diffusion and sedimentation coefficients) was compared with the findings generated by the water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.
Fig. 7.

Similar content being viewed by others

Abbreviations

AA:

amino acid

CS:

citrate synthase

EM:

electron microscopy

GA:

genetic algorithm

IM:

initial model

MB:

multibody

MS:

malate synthase

OE:

oblate ellipsoid of revolution

PDB:

Protein Data Bank

PE:

prolate ellipsoid of revolution

RdM:

reduced model

SAXS:

small-angle X-ray scattering

WB:

whole body

References

  • Allison SA, Tran VT (1995) Modeling the electrophoresis of rigid polyions: application to lysozyme. Biophys J 68:2261-2270

    CAS  PubMed  Google Scholar 

  • Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45-48

    CAS  PubMed  Google Scholar 

  • Barel AO, Prieels JP, Maes E, Looze Y, Léonis J (1972) Comparative physicochemical studies of human α-lactalbumin and human lysozyme. Biochim Biophys Acta 257:288-296

    Article  CAS  PubMed  Google Scholar 

  • Beavil AJ, Young RJ, Sutton BJ, Perkins SJ (1995) Bent domain structure of recombinant human IgE-Fc in solution by X-ray and neutron scattering in conjunction with an automated curve fitting procedure. Biochemistry 34:14449-14461

    CAS  PubMed  Google Scholar 

  • Behlke J (2001) Protein oligomerization requires correct folding of the protomers. Nova Acta Leopoldina Suppl 16:93-95

    CAS  Google Scholar 

  • Berman HM, Westbrook Z, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242

    PubMed  Google Scholar 

  • Blake CCF, Pulford WCA, Artymiuk PJ (1983) X-ray studies of water in crystals of lysozyme. J Mol Biol 167:693-723

    CAS  PubMed  Google Scholar 

  • Bon C, Lehmann MS, Wilkinson C (1999) Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme. Acta Crystallogr Sect D 55:978-987

    Article  CAS  Google Scholar 

  • Brooks CL III, Karplus M (1989) Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. J Mol Biol 208:159-181

    CAS  PubMed  Google Scholar 

  • Brunne RM, Liepinsh E, Otting G, Wüthrich K, van Gunsteren WF (1993) Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol 231:1040-1048

    Article  CAS  PubMed  Google Scholar 

  • Byron O (1997) Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data. Biophys J 72:408-415

    CAS  PubMed  Google Scholar 

  • Byron O (2000) Hydrodynamic bead modeling of biological macromolecules. Methods Enzymol 321:278-304

    CAS  PubMed  Google Scholar 

  • Byron O, Gilbert RJC (2000) Neutron scattering: good news for biotechnology. Curr Opin Biotechnol 11:72-80

    Article  CAS  PubMed  Google Scholar 

  • Carrasco B, García de la Torre J (1999) Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures. Biophys J 75:3044-3057

    Google Scholar 

  • Carrasco B, García de la Torre J, Zipper P (1999) Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres. Eur Biophys J 28:510-515

    Google Scholar 

  • Carugo O, Bordo D (1999) How many water molecules can be detected by protein crystallography? Acta Crystallogr Sect D 55:479-483

    Article  Google Scholar 

  • Chacón P, Morán F, Díaz JF, Pantos E, Andreu JM (1998) Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J 74:2760-2775

    PubMed  Google Scholar 

  • Chacón P, Díaz JF, Morán F, Andreu JM (2000) Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J Mol Biol 299:1289-1302

    PubMed  Google Scholar 

  • Chaplin M (2002) Water structure and behavior. http://www.sbu.ac.uk/water/

  • Colvin JR (1952) The size and shape of lysozyme. Can J Chem 30:831-834

    CAS  Google Scholar 

  • Connolly ML (1993) The molecular surface package. J Mol Graph 11:139-141

    CAS  Google Scholar 

  • Creighton TE (1993) Proteins: structures and molecular properties, 2nd edn. Freeman, New York

  • Denisov VP, Halle B (1996) Protein hydration dynamics in aqueous solution. Faraday Discuss Chem Soc 103:227-244

    CAS  Google Scholar 

  • Diamond R (1974) Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol 82:371-391

    CAS  PubMed  Google Scholar 

  • Dubin SB, Lunacek JH, Benedek GB (1967) Observation of the spectrum of light scattered by solutions of biological macromolecules. Proc Natl Acad Sci USA 57:1164-1171

    CAS  PubMed  Google Scholar 

  • Dubin SB, Clark NA, Benedek GB (1971) Measurement of the rotational diffusion coefficient of lysozyme by depolarized light scattering: configuration of lysozyme in solution. J Chem Phys 54:5158-5164

    CAS  Google Scholar 

  • Dubin SB, Feher G, Benedek GB (1973) Study of the chemical denaturation of lysozyme by optical mixing spectroscopy. Biochemistry 12:714-720

    CAS  PubMed  Google Scholar 

  • Ducruix A, Guilloteau JP, Riès-Kautt M, Tardieu A (1996) Protein interactions as seen by solution X-ray scattering prior to crystallogenesis. J Crystal Growth 168:28-39

    Article  CAS  Google Scholar 

  • Durchschlag H (1975) X-ray small-angle studies of the pyruvate dehydrogenase core complex from Escherichia coli K-12. II. Subunit structure of the core complex. Biophys Struct Mechanism 1:169-188

    CAS  Google Scholar 

  • Durchschlag H (1986) Specific volumes of biological macromolecules and some other molecules of biological interest: In: Hinz H-J (ed) Thermodynamic data for biochemistry and biotechnology. Springer, Berlin Heidelberg New York, pp 45-128

  • Durchschlag H (2003) Partial specific volumes and other volumetric properties of proteins and substances related to protein chemistry, In: Hinz H-J (ed) Landolt-Börnstein new series, VII/2A. Springer, Berlin Heidelberg New York (in press)

  • Durchschlag H, Zipper P (1997a) Prediction of hydrodynamic parameters of biopolymers from small-angle scattering data. J Appl Crystallogr 30:1112-1124

    Article  CAS  Google Scholar 

  • Durchschlag H, Zipper P (1997b) Calculation of hydrodynamic parameters of biopolymers from scattering data using whole-body approaches. Prog Colloid Polym Sci 107:43-57

    CAS  Google Scholar 

  • Durchschlag H, Zipper P (1997c) Calculation of partial specific volumes and other volumetric properties of small molecules and polymers. J Appl Crystallogr 30:803-807

    Article  CAS  Google Scholar 

  • Durchschlag H, Zipper P (1999) Calculation of structural parameters from hydrodynamic data. Prog Colloid Polym Sci 113:87-105

    CAS  Google Scholar 

  • Durchschlag H, Zipper P (2001) Comparative investigations of biopolymer hydration by physicochemical and modeling techniques. Biophys Chem 93:141-157

    Article  CAS  PubMed  Google Scholar 

  • Durchschlag H, Zipper P (2002a) Modelling of protein hydration. J Phys Condens Matter 14:2439-2452

    Article  CAS  Google Scholar 

  • Durchschlag H, Zipper P (2002b) Correlations between crystallographic, small-angle scattering and hydrodynamic data of biopolymers. Prog Colloid Polym Sci 119:121-130

    CAS  Google Scholar 

  • Durchschlag H, Zipper P (2002c) Modeling of protein hydration with respect to X-ray scattering and hydrodynamics. Prog Colloid Polym Sci 119:131-140

    CAS  Google Scholar 

  • Durchschlag H, Bogner F, Wilhelm D, Jaenicke R, Zipper P, Mayer F (1978) The subunit structure of malate synthase from baker's yeast. Hoppe-Seyler's Z Physiol Chem 359:1077

    Google Scholar 

  • Durchschlag H, Biedermann G, Eggerer H (1981) Large-scale purification and some properties of malate synthase from baker's yeast. Eur J Biochem 114:255-262

    CAS  PubMed  Google Scholar 

  • Durchschlag H, Zipper P, Wilfing R, Purr G (1991) Detection of small conformational changes of proteins by small-angle scattering. J Appl Crystallogr 24:822-831

    Article  Google Scholar 

  • Durchschlag H, Zipper P, Purr G, Jaenicke R (1996) Comparative studies of structural properties and conformational changes of proteins by analytical ultracentrifugation and other techniques. Colloid Polym Sci 274:117-137

    CAS  Google Scholar 

  • Durchschlag H, Hefferle T, Zipper P (2003) Comparative investigations of the effects of X- and UV-irradiation on lysozyme in the absence or presence of additives. Radiat Phys Chem (in press)

  • Ebel C, Eisenberg H, Ghirlando R (2000) Probing protein-sugar interactions. Biophys J 78:385-393

    CAS  PubMed  Google Scholar 

  • Eberstein W, Georgalis Y, Saenger W (1994) Molecular interactions in crystallizing lysozyme solutions studied by photon correlation spectroscopy. J Crystal Growth 143:71-78

    Article  CAS  Google Scholar 

  • Finney JL (1996) Overview lecture: hydration processes in biological and macromolecular systems. Faraday Discuss Chem Soc 103:1-18

    CAS  Google Scholar 

  • Foord R, Jakeman E, Oliver CJ, Pike ER, Blagrove RJ, Wood E, Peacocke AR (1970) Determination of diffusion coefficients of haemocyanin at low concentration by intensity fluctuation spectroscopy of scattered laser light. Nature 227:242-245

    CAS  PubMed  Google Scholar 

  • Fraser RDB, MacRae TP, Suzuki E (1978) An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. J Appl Crystallogr 11:693-694

    Article  CAS  Google Scholar 

  • García de la Torre J (1989) Hydrodynamic properties of macromolecular assemblies. In: Harding SE, Rowe AJ (eds) Dynamic properties of biomolecular assemblies. Royal Society of Chemistry, Cambridge, pp 3-31

  • García de la Torre J (2001) Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins. Biophys Chem 93:159-170

    Article  PubMed  Google Scholar 

  • García de la Torre J, Bloomfield VA (1981) Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q Rev Biophys 14:81-139

    Google Scholar 

  • García de la Torre J, Carrasco B (1998) Intrinsic viscosity and rotational diffusion of bead models for rigid macromolecules and bioparticles. Eur Biophys J 27:549-557

    Article  Google Scholar 

  • García de la Torre J, Navarro S, López Martínez MC, Díaz FG, López Cascales JJ (1994) HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophys J 67:530-531

    PubMed  Google Scholar 

  • García de la Torre J, Carrasco B, Harding SE (1997) SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles. Eur Biophys J 25:361-372

    PubMed  Google Scholar 

  • García de la Torre J, Huertas ML, Carrasco B (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78:719-730

    PubMed  Google Scholar 

  • García de la Torre J, Llorca O, Carrascosa JL, Valpuesta JM (2001) HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images. Eur Biophys J 30:457-462

    Article  PubMed  Google Scholar 

  • Gerstein M, Chothia C (1996) Packing at the protein-water interface. Proc Natl Acad Sci USA 93:10167-10172

    CAS  PubMed  Google Scholar 

  • Gerstein M, Tsai J, Levitt M (1995) The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol 249:955-966

    Article  CAS  PubMed  Google Scholar 

  • Glatter O, Kratky O (eds) (1982) Small angle X-ray scattering. Academic Press, London

  • Gmachowski L (2001) Intrinsic viscosity of bead models for macromolecules and bioparticles. Eur Biophys J 30:453-456

    Article  CAS  PubMed  Google Scholar 

  • Gregory RB (ed) (1995) Protein-solvent interactions. Dekker, New York

  • Grigsby JJ, Blanch HW, Prausnitz JM (2000) Diffusivities of lysozyme in aqueous MgCl2 solutions from dynamic light-scattering data: effect of protein and salt concentrations. J Phys Chem B 104:3645-3650

    Article  CAS  Google Scholar 

  • Harding SE (1989) Modelling the gross conformation of assemblies using hydrodynamics: the whole body approach. In: Harding SE, Rowe AJ (eds) Dynamic properties of biomolecular assemblies. Royal Society of Chemistry, Cambridge, pp 32-56

  • Harding SE (1995) On the hydrodynamic analysis of macromolecular conformation. Biophys Chem 55:69-93

    Article  CAS  Google Scholar 

  • Harding SE (1997) The intrinsic viscosity of biological macromolecules. Progress in measurement, interpretation and application to structure in dilute solution. Prog Biophys Mol Biol 68:207-262

    CAS  PubMed  Google Scholar 

  • Harding SE (2001a) The hydration problem in solution biophysics: an introduction. Biophys Chem 93:87-91

    Article  CAS  PubMed  Google Scholar 

  • Harding SE (ed) (2001b) Special issue: the hydration problem in solution biophysics. Biophys Chem 93:87-246

    Article  CAS  PubMed  Google Scholar 

  • Henchman RH, McCammon JA (2002) Extracting hydration sites around proteins from explicit water simulations. J Comput Chem 23:861-869

    Article  CAS  PubMed  Google Scholar 

  • Hopfinger AJ (1977) Intermolecular interactions and biomolecular organization. Wiley, New York

  • Kakalis LT, Kumosinski TF (1992) The dynamics of water in protein solutions: the field dispersion of deuterium NMR longitudinal relaxation. Biophys Chem 43:39-49

    Article  CAS  Google Scholar 

  • Kodandapani R, Suresh CG, Vijayan M (1990) Crystal structure of low humidity tetragonal lysozyme at 2.1-Å resolution. Variability in hydration shell and its structural consequences. J Biol Chem 265:16126-16131

    CAS  PubMed  Google Scholar 

  • Krigbaum WR, Kügler FR (1970) Molecular conformation of egg-white lysozyme and bovine α-lactalbumin in solution. Biochemistry 9:1216-1223

    CAS  PubMed  Google Scholar 

  • Kuhn LA, Siani MA, Pique ME, Fisher CL, Getzoff ED, Tainer JA (1992) The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J Mol Biol 228:13-22

    CAS  PubMed  Google Scholar 

  • Kumosinski TF, Pessen H (1982) Estimation of sedimentation coefficients of globular proteins: an application of small-angle X-ray scattering. Arch Biochem Biophys 219:89-100

    CAS  PubMed  Google Scholar 

  • Kuntz ID (1971) Hydration of macromolecules. III. Hydration of polypeptides. J Am Chem Soc 93:514-516

    CAS  Google Scholar 

  • Kuntz ID Jr, Kauzmann W (1974) Hydration of proteins and polypeptides. Adv Protein Chem 28:239-345

    CAS  PubMed  Google Scholar 

  • Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55:379-400

    CAS  PubMed  Google Scholar 

  • Lee JC, Timasheff SN (1974) Partial specific volumes and interactions with solvent components of proteins in guanidine hydrochloride. Biochemistry 13:257-265

    CAS  PubMed  Google Scholar 

  • Levitt M, Park PH (1993) Water: now you see it, now you don't. Structure 1:223-226

    CAS  PubMed  Google Scholar 

  • Luzzati V, Witz J, Nicolaieff A (1961) Détermination de la masse et des dimensions des protéines en solution par la diffusion centrale des rayons X mesurée à l'échelle absolue: exemple du lysozyme. J Mol Biol 3:367-378

    CAS  Google Scholar 

  • Merzel F, Smith JC (2002) SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallogr Sect D 58:242-249

    Article  Google Scholar 

  • Mikol V, Hirsch E, Giegé R (1990) Diagnostic of precipitant for biomacromolecule crystallization by quasi-elastic light-scattering. J Mol Biol 213:187-195

    CAS  PubMed  Google Scholar 

  • Müller JJ (1983) Calculation of scattering curves for macromolecules in solution and comparison with results of methods using effective atomic scattering factors. J Appl Crystallogr 16:74-82

    Article  Google Scholar 

  • Müller JJ (1991) Prediction of the rotational diffusion behavior of biopolymers on the basis of their solution or crystal structure. Biopolymers 31:149-160

    PubMed  Google Scholar 

  • Müller JJ, Schrauber H (1992) The inertia-equivalent ellipsoid: a link between atomic structure and low-resolution models of small globular proteins determined by small-angle X-ray scattering. J Appl Crystallogr 25:181-191

    Article  Google Scholar 

  • Murphy LR, Matubayasi N, Payne VA, Levy RM (1998) Protein hydration and unfolding: insights from experimental partial specific volumes and unfolded protein models. Fold Des 3:105-118

    CAS  PubMed  Google Scholar 

  • Nicoli DF, Benedek GB (1976) Study of thermal denaturation of lysozyme and other globular proteins by light-scattering spectroscopy. Biopolymers 15:2421-2437

    CAS  PubMed  Google Scholar 

  • Niimura N, Minezaki Y, Nonaka T, Castagna J-C, Cipriani F, Høghøj P, Lehmann MS, Wilkinson C (1997) Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Biol 4:909-914

    CAS  PubMed  Google Scholar 

  • Otting G, Liepinsh E (1995) Protein hydration viewed by high-resolution NMR spectroscopy: implications for magnetic resonance image contrast. Acc Chem Res 28:171-177

    CAS  Google Scholar 

  • Otting G, Liepinsh E, Wüthrich K (1991) Protein hydration in aqueous solution. Science 254:974-980

    CAS  PubMed  Google Scholar 

  • Pal SK, Peon J, Zewail AH (2002) Biological water at the protein interface: dynamical solvation probed directly with femtosecond resolution. Proc Natl Acad Sci USA 99:1763-1768

    Article  CAS  PubMed  Google Scholar 

  • Perkins SJ (1986) Protein volumes and hydration effects: the calculation of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences. Eur J Biochem 157:169-180

    CAS  PubMed  Google Scholar 

  • Perkins SJ (2001) X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modelling fits. Biophys Chem 93:129-139

    Article  CAS  PubMed  Google Scholar 

  • Perkins SJ, Ashton AW, Boehm MK, Chamberlain D (1998) Molecular structures from low angle X-ray and neutron scattering studies. Int J Biol Macromol 22:1-16

    Article  CAS  PubMed  Google Scholar 

  • Pessen H, Kumosinski TF (1985) Measurements of protein hydration by various techniques. Methods Enzymol 117:219-255

    CAS  PubMed  Google Scholar 

  • Pessen H, Kumosinski TF, Timasheff SN (1971) The use of small-angle X-ray scattering to determine protein conformation. J Agric Food Chem 19:698-702

    CAS  PubMed  Google Scholar 

  • Rashin AA, Iofin M, Honig B (1986) Internal cavities and buried waters in globular proteins. Biochemistry 25:3619-3625

    CAS  PubMed  Google Scholar 

  • Remington S, Wiegand G, Huber R (1982) Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 Å resolution. J Mol Biol 158:111-152

    CAS  PubMed  Google Scholar 

  • Rowe AJ (2001) Probing hydration and the stability of protein solutions: a colloid science approach. Biophys Chem 93:93-101

    Article  CAS  PubMed  Google Scholar 

  • Rupley JA, Careri G (1991) Protein hydration and function. Adv Protein Chem 41:37-172

    CAS  PubMed  Google Scholar 

  • Sayle RA, Milner-White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 20:374-376

    CAS  PubMed  Google Scholar 

  • Schoenborn BP, Garcia A, Knott R (1995) Hydration in protein crystallography. Prog Biophys Mol Biol 64:105-119

    Article  CAS  PubMed  Google Scholar 

  • Singh M, Brooks GC, Srere P (1970) Subunit structure and chemical characteristics of pig heart citrate synthase. J Biol Chem 245:4636-4640

    CAS  PubMed  Google Scholar 

  • Smith JC, Merzel F, Verma CS, Fischer S (2002) Protein hydration water: Structure and thermodynamics. J Mol Liquids 101:27-33

    Article  CAS  Google Scholar 

  • Smith PE, van Gunsteren WF (1994) Translational and rotational diffusion of proteins. J Mol Biol 236:629-636

    Article  CAS  PubMed  Google Scholar 

  • Sophianopoulos AJ, Rhodes CK, Holcomb DN, Van Holde KE (1962) Physical studies of lysozyme. I. Characterization. J Biol Chem 237:1107-1112

    CAS  Google Scholar 

  • Spotorno B, Piccinini L, Tassara G, Ruggiero C, Nardini M, Molina F, Rocco M (1997) BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins. Eur Biophys J 25:373-384; erratum 26:417

    Article  Google Scholar 

  • Squire PG, Himmel ME (1979) Hydrodynamics and protein hydration. Arch Biochem Biophys 196:165-177

    CAS  PubMed  Google Scholar 

  • Stuhrmann HB, Fuess H (1976) A neutron small-angle scattering study of hen egg-white lysozyme. Acta Crystallogr Sect A 32:67-74

    Article  Google Scholar 

  • Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495-503

    Article  Google Scholar 

  • Svergun DI (1994) Solution scattering from biopolymers: advanced contrast-variation data analysis. Acta Crystallogr Sect A 50:391-402

    Article  Google Scholar 

  • Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879-2886

    CAS  PubMed  Google Scholar 

  • Svergun DI (2000) Advanced solution scattering data analysis methods and their applications. J Appl Crystallogr 33:530-534

    Article  CAS  Google Scholar 

  • Svergun D, Barberato C, Koch MHJ (1995) CRYSOL: a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768-773

    Article  CAS  Google Scholar 

  • Svergun DI, Richard S, Koch MHJ, Sayers Z, Kuprin S, Zaccai G (1998) Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci USA 95:2267-2272

    CAS  PubMed  Google Scholar 

  • Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946-2953

    CAS  PubMed  Google Scholar 

  • Teeter MM (1991) Water-protein interactions: theory and experiment. Annu Rev Biophys Biophys Chem 20:577-600

    Google Scholar 

  • Thanki N, Thornton JM, Goodfellow JM (1988) Distributions of water around amino acid residues in proteins. J Mol Biol 202:637-657

    CAS  PubMed  Google Scholar 

  • Van Holde KE, Johnson WC, Ho PS (1998) Principles of physical biochemistry. Prentice Hall, Upper Saddle River, NJ

  • Vorobjev YN, Hermans J (1997) SIMS: computation of a smooth invariant molecular surface. Biophys J 73:722-732

    CAS  PubMed  Google Scholar 

  • Walther D, Cohen FE, Doniach S (2000) Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. J Appl Crystallogr 33:350-363

    CAS  Google Scholar 

  • Westhof E (ed) (1993) Water and biological macromolecules. Macmillan, London

  • Winzor DJ, Carrington LE, Harding SE (2001) Analysis of the thermodynamic non-ideality in terms of protein solvation. Biophys Chem 93:231-240

    Article  CAS  PubMed  Google Scholar 

  • Wu J-Y, Yang JT (1970) Physicochemical characterization of citrate synthase and its subunits. J Biol Chem 245:212-218

    CAS  PubMed  Google Scholar 

  • Wüthrich K, Otting G, Liepinsh E (1992) Protein hydration in aqueous solution. Faraday Discuss Chem Soc 93:35-45

    Google Scholar 

  • Wüthrich K, Billeter M, Güntert P, Luginbühl P, Riek R, Wider G (1996) NMR studies of the hydration of biological macromolecules. Faraday Discuss Chem Soc 103:245-253

    Google Scholar 

  • Zhang X-J, Matthews BW (1994) Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Protein Sci 3:1031-1039

    CAS  PubMed  Google Scholar 

  • Zhou H-X (1995) Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys J 69:2298-2303

    CAS  PubMed  Google Scholar 

  • Zhou H-X (2001) A unified picture of protein hydration: prediction of hydrodynamic properties from known structures. Biophys Chem 93:171-179

    Article  CAS  PubMed  Google Scholar 

  • Zipper P, Durchschlag H (1978) Small-angle X-ray scattering on malate synthase from baker's yeast. The native substrate-free enzyme and enzyme-substrate complexes. Eur J Biochem 87:85-99

    CAS  PubMed  Google Scholar 

  • Zipper P, Durchschlag H (1997) Calculation of hydrodynamic parameters of proteins from crystallographic data using multibody approaches. Prog Colloid Polym Sci 107:58-71

    CAS  Google Scholar 

  • Zipper P, Durchschlag H (1998) Recent advances in the calculation of hydrodynamic parameters from crystallographic data by multibody approaches. Biochem Soc Trans 26:726-731

    CAS  PubMed  Google Scholar 

  • Zipper P, Durchschlag H (1999) Prediction of hydrodynamic parameters from 3D structures. Prog Colloid Polym Sci 113:106-113

    CAS  Google Scholar 

  • Zipper P, Durchschlag H (2000) Prediction of hydrodynamic and small-angle scattering parameters from crystal and electron microscopic structures. J Appl Crystallogr 33:788-792

    Article  CAS  Google Scholar 

  • Zipper P, Durchschlag H (2002a) Prediction of structural and hydrodynamic parameters of hydrated proteins by computer modeling based on the results from high-resolution techniques. Physica A 304:283-293

    Article  CAS  Google Scholar 

  • Zipper P, Durchschlag H (2002b) Modeling of complex protein structures. Physica A 314:613-622

    Article  CAS  Google Scholar 

  • Zipper P, Durchschlag H (2003) Modeling of protein solution structures. J Appl Crystallogr (in press)

  • Zipper P, Krebs A, Durchschlag H (2002) Prediction of hydrodynamic parameters of Lumbricus terrestris hemoglobin from small-angle X-ray and electron microscopic structures. Prog Colloid Polym Sci 119:141-148

    Google Scholar 

Download references

Acknowledgements

The authors are much obliged to several scientists for making available some of the computer programs used in this study: Y.N. Vorobjev (SIMS), D.I. Svergun (GNOM, CRYSOL, GASBOR), J. García de la Torre (HYDRO) and R.A. Sayle (RASMOL).

Author information

Authors and Affiliations

  1. Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93040 , Regensburg, Germany

    Helmut Durchschlag

  2. Physical Chemistry, Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 , Graz, Austria

    Peter Zipper

Authors
  1. Helmut Durchschlag
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter Zipper
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Helmut Durchschlag.

Additional information

Presented at the Conference for Advances in Analytical Ultracentrifugation and Hydrodynamics, 8-11 June 2002, Grenoble, France

Rights and permissions

Reprints and permissions

About this article

Cite this article

Durchschlag, H., Zipper, P. Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data. Eur Biophys J 32, 487–502 (2003). https://doi.org/10.1007/s00249-003-0293-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-003-0293-z

Keywords

Search

Navigation