Calculation of hydrodynamic parameters of biopolymers from scattering data using whole-body approaches

  • H. Durchschlag
  • P. Zipper
Part of the Progress in Colloid & Polymer Science book series (PROGCOLLOID, volume 107)


A calculation procedure is presented which relates solution scattering and hydrodynamic parameters. Biopolymers are modeled by whole-body approaches, approximating their overall shape by spheres or prolate/oblate ellipsoids of revolution. Molar masses, partial specific volumes, radii of gyration, volumes and surface-to-volume ratios are used for predicting sedimentation and diffusion coefficients and intrinsic viscosities of a variety of biopolymers, in addition to the derivation of several further parameters such as frictional coefficients, Simha factors, Stokes and viscosity radii. The establishment of a comprehensive set of structural and hydrodynamic data including several correlations allows the examination of observed and predicted parameters. In this context also the validity of some empirical relations was tested. A variety of roughly globular biopolymers (simple and conjugated proteins, ribonucleic acids) of different molar mass and shape have been examined. The comparisons comprise both the native states of the biopolymers under analysis and structural alterations in response to changes in environment or state of ligation. Far-reaching conformity between experimental values and anticipated parameters was achieved. Detailed error propagation calculations allow a close scrutiny of the accuracy of the parameters to be predicted.

Key words

Biopolymers analytical ultracentrifugation viscometry scattering parameter predictions modeling whole-body approaches 




analytical ultracentrifugation


small-angle scattering


small-angle X-ray scattering



oblate ellipsoid


prolate ellipsoid




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  1. 1.
    Harding SE (1989) In: Harding SE, Rowe AJ (eds) Dynamic Properties of Biomolecular Assemblies. Royal Society of Chemistry, Cambridge UK, p 32Google Scholar
  2. 2.
    Pessen H, Kumosinski, TF (1993) In: Baianu IC, Pessen H, Kumosinski TF (eds) Physical Chemistry of Food Processes, Vol 2: Advanced Techniques, Structures, and Applications. Van Nostrand Reinhold, New York, p 274Google Scholar
  3. 3.
    García de la Torre J, Navarro S, Lopez Martinez MC, Diaz FG, Lopez Cascalez JJ (1994) Biophys J 67:530PubMedGoogle Scholar
  4. 4.
    Durchschlag H, Zipper P (1997) J Appl Cryst, in pressGoogle Scholar
  5. 5.
    Zipper P, Durchschlag H (1997) Progr Coll Polym Sci 107:58 71Google Scholar
  6. 6.
    Kumosinski TF, Pessen H (1982) Arch Biochem Biophys 219:89PubMedCrossRefGoogle Scholar
  7. 7.
    Kumosinski TF, Pessen H (1985) Meth Enzymol 117:154PubMedGoogle Scholar
  8. 8.
    Müller JJ, Damaschun H, Damaschun G, Gast K, Plietz P, Zirwer D (1984) Studia Biophysica 102:171Google Scholar
  9. 9.
    Durchschlag H, Zipper P, Purr G, Jaenicke R (1996) Colloid Polym Sci 274:117CrossRefGoogle Scholar
  10. 10.
    Durchschlag H, Zipper P (1996) J Mol Struct 383:223CrossRefGoogle Scholar
  11. 11.
    Durchschlag H, Zipper P (1997) J Appl Cryst, in pressGoogle Scholar
  12. 12.
    Glatter O, Kratky O (eds) (1982) Small Angle X-ray Scattering, Academic Press, LondonGoogle Scholar
  13. 13.
    Durchschlag H (1993) In: Baianu IC, Pessen H, Kumosinski TF (eds) Physical Chemistry of Food Processes, Vol 2: Advanced Techniques, Structures, and Applications. Van Nostrand Reinhold, New York, p 18Google Scholar
  14. 14.
    Mittelbach P, Porod G (1965) Kolloid Z 202:40CrossRefGoogle Scholar
  15. 15.
    Scheraga HA (1955) J Chem Phys 23:1526CrossRefGoogle Scholar
  16. 16.
    le Maire M, Viel A, Møller, JV (1989) Anal Biochem 177:50PubMedCrossRefGoogle Scholar
  17. 17.
    Durchschlag H, Zipper P, Wilfing R, Purr G (1991) J Appl Cryst 24:822CrossRefGoogle Scholar
  18. 18.
    Potschka M (1988) J Chromatogr 441:239CrossRefGoogle Scholar
  19. 19.
    Tyn MT, Gusek TW (1990) Biotechnol Bioeng 35:327CrossRefPubMedGoogle Scholar
  20. 20.
    Teller DC (1976) Nature (London) 260:729CrossRefGoogle Scholar
  21. 21.
    Dayhoff MO (ed) (1972) Atlas of Protein Sequence and Structure, Vol 5; (1973) Suppl 1; (1976) Suppl 2; (1978) Suppl 3. Natl Biomed Res Found, Washington, DCGoogle Scholar
  22. 22.
    Durchschlag H (1986) In: Hinz H-J (ed) Thermodynamic Data for Biochemistry and Biotechnology. Springer, Berlin p 45Google Scholar
  23. 23.
    Durchschlag H (1996) In: Hinz H-J (ed) Landolt-Börnstein New Series VII. Springer, Berlin, submittedGoogle Scholar
  24. 24.
    Pessen H, Kumosinski TF, Timasheff SN (1971) J Agric Food Chem 19:698PubMedCrossRefGoogle Scholar
  25. 25.
    Yphantis DA (1959) J Phys Chem 63:1742CrossRefGoogle Scholar
  26. 26.
    Creeth JM (1958) J Phys Chem 62:66CrossRefGoogle Scholar
  27. 27.
    Buzzell JG, Tanford C (1956) J Phys Chem 60:1204CrossRefGoogle Scholar
  28. 28.
    Kronman MJ, Andreotti RE (1964) Biochemistry 3:1145PubMedCrossRefGoogle Scholar
  29. 29.
    Polson A (1939) Kolloid Z 88:51CrossRefGoogle Scholar
  30. 30.
    Lee JC, Timasheff SN (1974) Biochemistry 13:257PubMedCrossRefGoogle Scholar
  31. 31.
    Sophianopoulos AJ, Rhodes CK, Holcomb DN, Van Holde KE (1962) J Biol Chem 237:1107PubMedGoogle Scholar
  32. 32.
    Krigbaum WR, Godwin RW (1968) Biochemistry 7:3126PubMedCrossRefGoogle Scholar
  33. 33.
    Schwert GW, Kaufman S (1951) J Biol Chem 190:807PubMedGoogle Scholar
  34. 34.
    Müller JJ, Damaschun G, Wilhelm P, Welfle H, Pilz I (1982) Int J Biol Macromol 4:289CrossRefGoogle Scholar
  35. 35.
    Müller JJ, Zirwer D, Damaschun G, Welfle H, Gast P, Plietz P (1983) Studia Biophysica 96:103Google Scholar
  36. 36.
    Wilcox PE, Kraut J, Wade RD, Neurath H (1957) Biochim Biophys Acta 24:72PubMedCrossRefGoogle Scholar
  37. 37.
    Schwert GW (1951) J Biol Chem 190:790Google Scholar
  38. 38.
    Kumosinski TF, Pessen H, Farrell HM Jr (1982) Arch Biochem Biophys 214:714PubMedCrossRefGoogle Scholar
  39. 39.
    Rajagopalan TG, Moore S, Stein WH (1966) J Biol Chem 241:4940PubMedGoogle Scholar
  40. 40.
    McMeekin TL, Wilensky M, Groves ML (1962) Biochem Biophys Res Commun 7:151CrossRefGoogle Scholar
  41. 41.
    Vazina AA, Lednev VV, Lemagikhin BK (1966) Biochimija (Moscow) 31:720Google Scholar
  42. 42.
    Edelhoch H (1957) J Am Chem Soc 79:6100CrossRefGoogle Scholar
  43. 43.
    Witz J, Timasheff SN, Luzzati V (1964) J Am Chem Soc 86:168CrossRefGoogle Scholar
  44. 44.
    Kumosinski TF, Timasheff SN (1966) J Am Chem Soc 88:5635CrossRefGoogle Scholar
  45. 45.
    Cecil R, Ogston AG (1949) Biochem J 44:33Google Scholar
  46. 46.
    Müller JJ, Zalkova TN, Zirwer D, Misselwitz R, Gast K, Serdyuk IN, Welfle H, Damaschun G (1986) Eur Biophys J 13:301PubMedCrossRefGoogle Scholar
  47. 47.
    Luzzati V, Witz J, Nicolaieff A (1961) J Mol Biol 3:379PubMedCrossRefGoogle Scholar
  48. 48.
    Peters T Jr (1985) Adv Prot Chem 37:161CrossRefGoogle Scholar
  49. 49.
    Damaschun H, Zalenskaya IA, Damaschun G, Vorob'ev VI, Misselwitz R, Zirwer D (1983) Studia Biophysica 97:105Google Scholar
  50. 50.
    Damaschun G, Damaschun H, Dembo AT, Kayushina RL, Kröber R, Moshkov KA, Müller JJ, Neifakh SA, Rolbin JA, Shavlovsky MM, Zirwer D (1978) Studia Biophysica 71:53Google Scholar
  51. 51.
    Plietz P, Damaschun G, Zirwer D, Gast K, Schlesier B (1983) Int J Biol Macromol 5:356CrossRefGoogle Scholar
  52. 52.
    Lane AN, Kirschner K (1983) Eur J Biochem 129:675PubMedCrossRefGoogle Scholar
  53. 53.
    Wilhelm P, Pilz I, Lane AN, Kirschner K (1982) Eur J Biochem 129:51PubMedCrossRefGoogle Scholar
  54. 54.
    Pesce A, Fondy TP, Stolzenbach F, Castillo F, Kaplan NO (1967) J Biol Chem 242:2151PubMedGoogle Scholar
  55. 55.
    Jaenicke R, Gregori E, Laepple M (1979) Biophys Struct Mechanism 6:57CrossRefGoogle Scholar
  56. 56.
    Müller K, Kratky O, Röschlau P, Hess B (1972) Hoppe-Seyler's Z Physiol Chem 353:803PubMedGoogle Scholar
  57. 57.
    Bischofberger H, Hess B, Röschlau P (1971) Hoppe-Seyler's Z Physiol Chem 352:1139PubMedGoogle Scholar
  58. 58.
    Malmon AG (1957) Biochim Biophys Acta 26:233PubMedCrossRefGoogle Scholar
  59. 59.
    Sumner JB, Gralén N (1938) J Biol Chem 125:33Google Scholar
  60. 60.
    Pilz I, Ullrich J (1973) Eur J Biochem 34:256PubMedCrossRefGoogle Scholar
  61. 61.
    Müller JJ, Damaschun G, Hübner G (1979) Acta biol med germ 38:1PubMedGoogle Scholar
  62. 62.
    Ullrich J, Kempfle M (1969) FEBS Letters 4:273PubMedCrossRefGoogle Scholar
  63. 63.
    Plietz P, Damaschun G, Zirwer D, Gast K, Schwenke KD, Prakash V (1986) J Biol Chem 261:12686PubMedGoogle Scholar
  64. 64.
    Plietz P, Damaschun G, Müller JJ, Schwenke K-D (1983) Eur J Biochem 130:315PubMedCrossRefGoogle Scholar
  65. 65.
    Schwenke KD, Schultz M, Linow K-J, Gast K, Zirwer D (1980) Int J Peptide Protein Res 16:12CrossRefGoogle Scholar
  66. 66.
    Plietz P, Zirwer D, Schlesier B, Gast K, Damaschun G (1984) Biochim Biophys Acta 784:140PubMedGoogle Scholar
  67. 67.
    Damaschun G, Damaschun H, Hanson H, Müller JJ, Pürschel H-V (1973) Studia Biophysica 35:59Google Scholar
  68. 68.
    Plietz P, Damaschun H, Zirwer D, Gast K, Schwenke KD, Paehtz W, Damaschun G (1978) FEBS Letters 91:227PubMedCrossRefGoogle Scholar
  69. 69.
    Reisler E, Pouyet J, Eisenberg H (1970) Biochemistry 9:3095PubMedCrossRefGoogle Scholar
  70. 70.
    Pilz I, Sund H (1971) Eur J Biochem 20:561PubMedCrossRefGoogle Scholar
  71. 71.
    Müller JJ, Kayushina RL (1987) Studia Biophysica 120:15Google Scholar
  72. 72.
    Zipper P, Kratky O, Herrmann R, Hohn T (1971) Eur J Biochem 18:1PubMedCrossRefGoogle Scholar
  73. 73.
    Gesteland RF, Boedtker H (1964) J Mol Biol 8:496PubMedGoogle Scholar
  74. 74.
    Jacrot B, Chauvin C, Witz J (1977) Nature (London) 266:417CrossRefGoogle Scholar
  75. 75.
    Anderegg JW (1967) In: Brumberger H (ed) Small-Angle X-ray Scattering. Gordon & Breach, New York, p 243Google Scholar
  76. 76.
    Bockstahler LE, Kaesberg P (1962) Biophys J 2:1PubMedGoogle Scholar
  77. 77.
    Markham R (1951) Faraday Soc Discuss 11:221CrossRefGoogle Scholar
  78. 78.
    Harding SE, Johnson P (1985) Biochem J 231:549PubMedGoogle Scholar
  79. 79.
    Hadidi AF, Fraenkel-Conrat H (1974) In: King RC (ed) Handbook of Genetics, Vol 2. Plenum Press, New York, p 381Google Scholar
  80. 80.
    Anderegg JW, Geil PH, Beeman WW, Kaesberg P (1961) Biophys J 1:657PubMedGoogle Scholar
  81. 81.
    Chauvin C, Witz J, Jacrot B (1978) J Mol Biol 124:641PubMedCrossRefGoogle Scholar
  82. 82.
    Tanford C (1961) Physical Chemistry of Macromolecules. Wiley, New YorkGoogle Scholar
  83. 83.
    Jacrot B, Pfeiffer P, Witz J (1976) Phil Trans R Soc Lond B 276:109CrossRefGoogle Scholar
  84. 84.
    Krüse J, Krüse KM, Witz J, Chauvin C, Jacrot B, Tardieu A (1982) J Mol Biol 162:393PubMedCrossRefGoogle Scholar

Copyright information

© Dr. Dietrich Steinkopff Verlag GmbH & Co. KG 1997

Authors and Affiliations

  • H. Durchschlag
    • 1
  • P. Zipper
    • 2
  1. 1.Institute of Biophysics and Physical BiochemistryUniversity of RegensburgRegensburgGermany
  2. 2.Institute of Physical ChemistryUniversity of GrazGrazAustria

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