Skip to main content
SpringerLink
Log in
Book cover

Analytical Ultracentrifugation VIII pp 55–73Cite as

Ab initio and Constrained Modeling of Phosphorylase

  • Conference paper
  • First Online:

  • 203 Accesses

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

Abstract

The joint use of small-angle X-ray scattering (SAXS) and hydrodynamic data permits biologically useful reconstructions of protein structures to be determined. Low-resolution shapes of proteins can be obtained by SAXS-based modeling approaches, among them the ab initio approaches being the most recent and challenging ones. The programs DAMMIN and GASBOR have been applied to C. callunae starch phosphorylase in a case study, to test in a systematic manner the principles governing the evaluation strategies of the approaches applied. Therefore, emphasis was laid on the elaboration of modeling aspects rather than on biological details. Optimum results concerning the predictions of particle shapes and molecule properties have been obtained by utilizing tight constraints for modeling, such as symmetry and anisometry information. The use of pure ab initio conditions yields rather moderate shape and parameter predictions. Application of erroneous constraints generally leads to unrealistic particle shapes, although the parameter predictions may be satisfactory. The usage of the program DAMMIN turned out to be superior to application of the program GASBOR, whether the latter approach was used in the reciprocal- or real-space version. For hydrodynamic modeling, a modified version of the program HYDRO was adopted. By recourse to known crystallographic 3D structures for phosphorylases from other sources, SAXS profiles of anhydrous proteins can be modeled. Procedures for the addition of individual water molecules to anhydrous protein envelopes based on the atomic coordinates yield biologically relevant models for hydrated phosphorylases. This requires the usage of advanced surface calculation programs such as SIMS and of appropriate hydration algorithms such as those implemented in our programs HYDCRYST and HYDMODEL. The resulting SAXS profiles and structural and hydrodynamic parameters of the hydrated proteins can be compared with the data obtained by solution scattering.

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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Palm D, Klein HW, Schinzel R, Buehner M, Helmreich EJM (1990) Biochemistry 29:1099–1107

    Article  CAS  Google Scholar 

  2. Acharya KR, Stuart DI, Varvill KM, Johnson LN (1991) Glycogen phosphorylase b: description of the protein structure. World Scientific, Singapore

    Google Scholar 

  3. Barford D, Hu S-H, Johnson LN (1991) J Mol Biol 218:233–260

    Article  CAS  Google Scholar 

  4. Johnson LN (1992) FASEB J 6:2274–2282

    CAS  Google Scholar 

  5. Browner MF, Fletterick RJ (1992) Trends Biochem Sci 17:66–71

    Article  CAS  Google Scholar 

  6. Schinzel R, Nidetzky B (1999) FEMS Microbiol Lett 171:73–79

    CAS  Google Scholar 

  7. Yunis AA, Fischer EH, Krebs EG (1960) J Biol Chem 235:3163–3168

    Google Scholar 

  8. Yunis AA, Fischer EH, Krebs EG (1962) J Biol Chem 237:2809–2815

    CAS  Google Scholar 

  9. Wang JH, Graves DJ (1963) J Biol Chem 238:2386–2389

    CAS  Google Scholar 

  10. Seery VL, Fischer EH, Teller DC (1967) Biochemistry 6:3315–3327

    Article  CAS  Google Scholar 

  11. DeVincenzi DL, Hedrick JL (1967) Biochemistry 6:3489–3497

    Article  CAS  Google Scholar 

  12. Sevilla CL, Fischer EH (1969) Biochemistry 8:2161–2171

    Article  CAS  Google Scholar 

  13. Childress CC, Sacktor B (1970) J Biol Chem 245:2927–2936

    CAS  Google Scholar 

  14. Puchwein G, Kratky O, Gölker CF, Helmreich E (1970) Biochemistry 9:4691–4698

    Article  CAS  Google Scholar 

  15. Cohen P, Duewer T, Fischer EH (1971) Biochemistry 10:2683–2694

    Article  CAS  Google Scholar 

  16. Buc MH, Ullmann A, Goldberg M, Buc H (1971) Biochimie 53:283–289

    Article  CAS  Google Scholar 

  17. Chebotareva NA, Harding SE, Winzor DJ (2001) Eur J Biochem 268:506–513

    Article  CAS  Google Scholar 

  18. Wang Z-X, Tsuruta H, Honda Y, Tachi-iri Y, Wakabayashi K, Amemiya Y, Kihara H (1989) Biophys Chem 33:153–160

    Article  CAS  Google Scholar 

  19. Weinhäusel A, Griessler R, Krebs A, Zipper P, Haltrich D, Kulbe KD, Nidetzky B (1997) Biochem J 326:773–783

    Google Scholar 

  20. Johnson LN, Barford D (1990) J Biol Chem 265:2409–2412

    CAS  Google Scholar 

  21. O'Reilly M, Watson KA, Schinzel R, Palm D, Johnson LN (1997) Nature Struct Biol 4:405–412

    Google Scholar 

  22. Watson KA, Schinzel R, Palm D, Johnson LN (1997) EMBO J 16:1–14

    Article  CAS  Google Scholar 

  23. Watson KA, McCleverty C, Geremia S, Cottaz S, Driguez H, Johnson LN (1999) EMBO J 18:4619–4632

    Article  CAS  Google Scholar 

  24. Rath VL, Fletterick RJ (1994) Nature Struct Biol 1:681–690

    CAS  Google Scholar 

  25. Lin K, Rath VL, Dai SC, Fletterick RJ, Hwang PK (1996) Science 273:1539–1541

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  30. Walter D, Cohen FE, Doniach S (2000) J Appl Crystallogr 33:350–363

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  33. Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M (2003) Nucleic Acids Res 31:365–370

    Article  CAS  Google Scholar 

  34. 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 

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

    Article  CAS  Google Scholar 

  36. Durchschlag H (1975) Biophys Struct Mechanism 1:169–188

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  43. Heller WT, Abusamhadneh E, Finley N, Rosevear PR, Trewhella J (2002) Biochemistry 41:15654–15663

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  45. Durchschlag H, Zipper P (2005) In: Scott DJ, Harding SE, Rowe AJ (eds) Analytical ultracentrifugation: techniques and methods, Royal Society of Chemistry, Cambridge UK, in press

    Google Scholar 

  46. Connolly ML (1993) J Mol Graph 11:139–141

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  51. Zipper P, Durchschlag H (2002) Physica A 304:283–293

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

  57. 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 

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

    Article  CAS  Google Scholar 

  63. Zipper P, Durchschlag H (2005) Physica Scripta T118:228–232

    CAS  Google Scholar 

  64. Svergun DI, Koch MHJ (2002) Curr Opin Struct Biol 12:654–660

    Article  CAS  Google Scholar 

  65. Svergun DI, Koch MHJ (2003) Rep Prog Phys 66:1735–1782

    Article  CAS  Google Scholar 

  66. Koch MHJ, Vachette P, Svergun DI (2003) Q Rev Biophys 36:147–227

    Article  CAS  Google Scholar 

  67. Takahashi Y, Nishikawa Y, Fujisawa T (2003) J Appl Crystallogr 36:549-552

    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, GASBOR, the DAMAVER suite, GNOM and SUPCOMB, 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. 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

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

    Angelika Krebs

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

  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

Durchschlag, H., Zipper, P., Krebs, A. Ab initio and Constrained Modeling of Phosphorylase. 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_017

Download citation

Publish with us

Policies and ethics

Search

Navigation