SpringerLink
Log in

Modeling of the Dodecameric Subunit of Lumbricus Hemoglobin

  • Conference paper
  • First Online:
Analytical Ultracentrifugation VIII

Part of the book series: Progress in Colloid and Polymer Science ((PROGCOLLOID,volume 131))

  • 204 Accesses

Abstract

For modeling the low-resolution shape of the dodecameric subunit of Lumbricus terrestris hemoglobin, experimental small-angle X-ray scattering (SAXS) data and ab initio modeling approaches using a genetic algorithm or simulated annealing have been applied. In addition to the use of strict ab initio approaches, procedures which additionally include available structural information concerning symmetry and shape in the form of constraints or templates have been employed to improve the results. Templates for the subunit were preferably derived from SAXS-based models for the native hexagonal bilayer (HBL) complex that were biased by electron microscopic reconstructions. The obtained subunit models were carefully examined by variation of different selection and averaging methods and other checks such as surface renderings of the models. The findings were quantified by prediction of scattering profiles, I(h) and p(r), and structural and hydrodynamic parameters (V, R G, d  max, s, D). The best matching models for the subunit were also scrutinized by comparing them to a model derived from currently available crystallographic data. The following results could be obtained: (i) The obtained parameter predictions for the dodecameric subunit are satisfactory, if compared to the SAXS data (consensus model, profiles and molecular parameters) or the results from hydrodynamic studies. (ii) The comparison between solution and crystal data of the dodecameric subunit, however, unequivocally proves a different behavior of the subunit in solution and the crystalline state.

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

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Lamy JN, Green BN, Toulmond A, Wall JS, Weber RE, Vinogradov SN (1996) Chem Rev 96:3113–3124

    Article  CAS  Google Scholar 

  2. Weber RE, Vinogradov SN (2001) Physiol Rev 81:569–628

    CAS  Google Scholar 

  3. Daniel E, Lustig A, David MM, Tsfadia Y (2003) Biochim Biophys Acta 1649:1–15

    CAS  Google Scholar 

  4. Royer WE Jr, Hendrickson WA (1988) J Biol Chem 263:13762–13765

    CAS  Google Scholar 

  5. Boekema EJ, van Heel M (1989) Biochim Biophys Acta 957:370–379

    Article  Google Scholar 

  6. Vinogradov SN, Lugo SD, Mainwaring MG, Kapp OH, Crewe AV (1986) Proc Natl Acad Sci USA 83:8034–8038

    Article  CAS  Google Scholar 

  7. Vinogradov SN, Sharma PK, Qabar AN, Wall JS, Westrick JA, Simmons JH, Gill SJ (1991) J Biol Chem 266:13091–13096

    CAS  Google Scholar 

  8. Zhu H, Ownby DW, Riggs CK, Nolasco NJ, Stoops JK, Riggs AF (1996) J Biol Chem 271:30007–30021

    Article  CAS  Google Scholar 

  9. Kuchumov AR, Taveau J-C, Lamy JN, Wall JS, Weber RE, Vinogradov SN (1999) J Mol Biol 289:1361–1374

    Article  CAS  Google Scholar 

  10. Schatz M, Orlova EV, Dube P, Jäger J, van Heel M (1995) J Struct Biol 114:28–40

    Article  CAS  Google Scholar 

  11. de Haas F, Boisset N, Taveau J-C, Lambert O, Vinogradov SN, Lamy JN (1996) Biophys J 70:1973–1984

    Article  Google Scholar 

  12. de Haas F, Taveau J-C, Boisset N, Lambert O, Vinogradov SN, Lamy JN (1996) J Mol Biol 255:140–153

    Article  Google Scholar 

  13. de Haas F, Kuchumov A, Taveau J-C, Boisset N, Vinogradov SN, Lamy JN (1997) Biochemistry 36:7330–7338

    Article  Google Scholar 

  14. Taveau J-C, Boisset N, Vinogradov SN, Lamy JN (1999) J Mol Biol 289:1343–1359

    Article  CAS  Google Scholar 

  15. Mouche F, Boisset N, Penczek PA (2001) J Struct Biol 133:176–192

    Article  CAS  Google Scholar 

  16. Pilz I, Schwarz E, Vinogradov SN (1980) Int J Biol Macromol 2:279–283

    Article  CAS  Google Scholar 

  17. Krebs A (1996) Thesis, University of Graz, Austria

    Google Scholar 

  18. Krebs A, Zipper P, Vinogradov SN (1996) Biochim Biophys Acta 1297:115–118

    Article  Google Scholar 

  19. Krebs A, Lamy J, Vinogradov SN, Zipper P (1998) Biopolymers 45:289–298

    Article  CAS  Google Scholar 

  20. Krebs A, Durchschlag H, Zipper P (2004) Biophys J 87:1173–1185

    Article  CAS  Google Scholar 

  21. Royer WE Jr, Strand K, van Heel M, Hendrickson WA (2000) Proc Natl Acad Sci USA 97:7107–7111

    Article  CAS  Google Scholar 

  22. David MM, Daniel E (1974) J Mol Biol 87:89–101

    Article  CAS  Google Scholar 

  23. Kapp OH, Polidori G, Mainwaring MG, Crewe AV, Vinogradov SN (1984) J Biol Chem 259:628–639

    CAS  Google Scholar 

  24. Mainwaring MG, Lugo SD, Fingal RA, Kapp OH, Vinogradov SN (1986) J Biol Chem 261:10899–10908

    CAS  Google Scholar 

  25. Martin PD, Kuchumov AR, Green BN, Oliver RWA, Braswell EH, Wall JS, Vinogradov SN (1996) J Mol Biol 255:154–169

    Article  CAS  Google Scholar 

  26. Green BN, Bordoli RS, Hanin LG, Lallier FH, Toulmond A, Vinogradov SN (1999) J Biol Chem 274:28206–28212

    Article  CAS  Google Scholar 

  27. Sharma PK, Kuchumov AR, Chottard G, Martin PD, Wall JS, Vinogradov SN (1996) J Biol Chem 271:8754–8762

    Article  CAS  Google Scholar 

  28. Krebs A, Kuchumov AR, Sharma PK, Braswell EH, Zipper P, Weber RE, Chottard G, Vinogradov SN (1996) J Biol Chem 271:18695–18704

    Article  CAS  Google Scholar 

  29. Martin PD, Eisele KL, Doyle MA, Kuchumov AR, Walz DA, Arutyunyan EG, Vinogradov SN, Edwards BFP (1996) J Mol Biol 255:170–175

    Article  CAS  Google Scholar 

  30. Strand K, Knapp JE, Bhyravbhatla B, Royer WE Jr (2004) J Mol Biol 344:119–134

    Article  CAS  Google Scholar 

  31. Zipper P, Durchschlag H (2000) J Appl Crystallogr 33:788–792

    Article  CAS  Google Scholar 

  32. Zipper P, Durchschlag H, Krebs A (2005) In: Scott DJ, Harding SE, Rowe AJ (eds) Analytical ultra- centrifugation: techniques and methods, Royal Society of Chemistry, Cambridge UK, in press

    Google Scholar 

  33. Durchschlag H, Zipper P (2002) Prog Colloid Polym Sci 119:121–130

    Article  CAS  Google Scholar 

  34. Durchschlag H, Zipper P (1997) J Appl Crystallogr 30:1112–1124

    Article  CAS  Google Scholar 

  35. Durchschlag H, Zipper P (1999) Prog Colloid Polym Sci 113:87–105

    Article  CAS  Google Scholar 

  36. Zipper P, Krebs A, Durchschlag H (2002) Prog Colloid Polym Sci 119:141–148

    Article  CAS  Google Scholar 

  37. Zipper P, Durchschlag H (2002) Physica A 314:613–622

    Article  CAS  Google Scholar 

  38. Zipper P, Durchschlag H (2003) J Appl Crystallogr 36:509–514

    Article  CAS  Google Scholar 

  39. Zipper P, Krebs A, Durchschlag H (2004) Prog Colloid Polym Sci 127:126–135

    CAS  Google Scholar 

  40. Chacón P, Morán F, Díaz JF, Pantos E, Andreu JM (1998) Biophys J 74:2760–2775

    Article  Google Scholar 

  41. Chacón P, Díaz JF, Morán F, Andreu JM (2000) J Mol Biol 299:1289–1302

    Article  Google Scholar 

  42. Svergun DI (1999) Biophys J 76:2879–2886

    Article  CAS  Google Scholar 

  43. Svergun DI (2000) J Appl Crystallogr 33:530–534

    Article  CAS  Google Scholar 

  44. Volkov VV, Svergun DI (2003) J Appl Crystallogr 36:860–864

    Article  CAS  Google Scholar 

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

    Google Scholar 

  46. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235–242

    Article  CAS  Google Scholar 

  47. Svergun DI (1992) J Appl Crystallogr 25:495–503

    Article  Google Scholar 

  48. Kozin MB, Svergun DI (2001) J Appl Crystallogr 34:33–41

    Article  CAS  Google Scholar 

  49. Svergun DI, Petoukhov MV, Koch MHJ (2001) Biophys J 80:2946–2953

    Article  CAS  Google Scholar 

  50. Petoukhov MV, Svergun DI (2003) J Appl Crystallogr 36:540–544

    Article  CAS  Google Scholar 

  51. Vorobjev YN, Hermans J (1997) Biophys J 73:722–732

    Article  CAS  Google Scholar 

  52. Durchschlag H, Zipper P (2001) Biophys Chem 93:141–157

    Article  CAS  Google Scholar 

  53. Durchschlag H, Zipper P (2002) J Phys Condens Matter 14:2439–2452

    CAS  Google Scholar 

  54. Durchschlag H, Zipper P (2002) Prog Colloid Polym Sci 119:131–140

    Article  CAS  Google Scholar 

  55. Durchschlag H, Zipper P (2003) Eur Biophys J 32:487–502

    Article  CAS  Google Scholar 

  56. Durchschlag H, Zipper P (2004) Prog Colloid Polym Sci 127:98–112

    CAS  Google Scholar 

  57. Kuntz ID (1971) J Am Chem Soc 93:514–516

    Article  CAS  Google Scholar 

  58. Glatter O (1980) Acta Phys Austriaca 52:243–256

    Google Scholar 

  59. García de la Torre J, Navarro S, López Martínez MC, Díaz FG, López Cascales JJ (1994) Biophys J 67:530–531

    Article  Google Scholar 

  60. García de la Torre J, Huertas ML, Carrasco B (2000) Biophys J 78:719–730

    Article  Google Scholar 

  61. Zipper P, Durchschlag H (1997) Prog Colloid Polym Sci 107:58–71

    Article  CAS  Google Scholar 

  62. Zipper P, Durchschlag H (1998) Biochem Soc Trans 26:726–731

    CAS  Google Scholar 

  63. Zipper P, Durchschlag H (1999) Prog Colloid Polym Sci 113:106–113

    Article  CAS  Google Scholar 

  64. Carrasco B, García de la Torre J, Zipper P (1999) Eur Biophys J 28:510–515

    Article  CAS  Google Scholar 

  65. Sayle RA, Milner-White EJ (1995) Trends Biochem Sci 20:374–376

    Article  CAS  Google Scholar 

  66. Collaborative Computational Project, Number 4 (1994) Acta Cryst D50:760–763

    Google Scholar 

  67. Avila R, He T, Hong L, Kaufman A, Pfister H, Silva C, Sobierajski L, Wang S (1994) In: Bergeron R, Kaufman A (eds) Proceedings IEEE Visualization '94, IEEE Computer Society, Washington DC, p 31–38

    Google Scholar 

  68. Kratky O, Pilz I (1978) Q Rev Biophys 11:39–70

    Article  CAS  Google Scholar 

  69. Durchschlag H, Zipper P, Wilfing R, Purr G (1991) J Appl Crystallogr 24:822–831

    Article  Google Scholar 

  70. Durchschlag H, Zipper P, Purr G, Jaenicke R (1996) Colloid Polym Sci 274:117–137

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors are much obliged to several scientists and institutions for use of their computer programs: to D.I. Svergun for DAMMIN, the DAMAVER suite, GNOM and SUPCOMB, to P. Chacón for DALAI_GA, to Y.N. Vorobjev for SIMS, to J. García de la Torre for HYDRO, to R.A Sayle for RASMOL, to the SERC Daresbury Laboratory for the CCP4 suite, and to the Research Foundation of the State University of New York for VOLVIS, respectively. A.K. thanks the Austrian Academy of Sciences for support (APART fellowship).

Author information

Authors and Affiliations

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

    Peter Zipper

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

    Helmut Durchschlag

  3. Structural and Computational Biology Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany

    Angelika Krebs

Authors
  1. Peter Zipper
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Helmut Durchschlag
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Angelika Krebs
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Helmut Durchschlag .

Editor information

Christine Wandrey Helmut Cölfen

Rights and permissions

Reprints and permissions

About this paper

Cite this paper

Zipper, P., Durchschlag, H., Krebs, A. Modeling of the Dodecameric Subunit of Lumbricus Hemoglobin. In: Wandrey, C., Cölfen, H. (eds) Analytical Ultracentrifugation VIII. Progress in Colloid and Polymer Science, vol 131. Springer, Berlin, Heidelberg. https://doi.org/10.1007/2882_005

Download citation

Publish with us

Policies and ethics

Search

Navigation