Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin

Biophysical Journal

Volumn 87, Issue 2, 2004, Pages 1173-1185

  Krebs, Angelika ^a   Durchschlag, Helmut ^b   Zipper, Peter ^c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF REGENSBURG   (Germany)

^c UNIVERSITY OF GRAZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROCRUORIN; GLOBIN; HEMOGLOBIN; UNCLASSIFIED DRUG;

ANNELID WORM; ARTICLE; ELECTRON MICROSCOPY; EUDISTYLIA VANCOUVERII; HYDRODYNAMICS; MACROBDELLA DECORA; NONHUMAN; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

ANNELIDA; EUDISTYLIA; EUDISTYLIA VANCOUVERI; EUDISTYLIA VANCOUVERII; INVERTEBRATA; MACROBDELLA; MACROBDELLA DECORA;

EID: 4143146265     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.037929     Document Type: Article

References (51)

1. Boekema, E. J., and M. van Heel. 1989. Molecular shape of Lumbricus terrestris erythrocruorin studied by electron microscopy and image analysis. Biochim. Biophys. Acta. 957:370-379.
2. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Cryst. D50:760-763.
3. David, M. M., and E. Daniel. 1974. Subunit structure of earthworm erythrocruorin. J. Mol. Biol. 87:89-101.
4. de Haas, F., N. Boisset, J.-C. Taveau, O. Lambert, S. N. Vinogradov, and J. N. Lamy. 1996a. Three-dimensional reconstruction of Macrobdella decora (Leech) hemoglobin by cryoelectron microscopy. Biophys. J. 70:1973-1984.
5. de Haas, F., A. Kuchumov, J.-C. Taveau, N. Boisset, S. N. Vinogradov, and J. N. Lamy. 1997. Three-dimensional reconstruction of native and reassembled Lumbricus terrestris extracellular hemoglobin. Localization of the monomeric globin chains. Biochemistry. 36:7330-7338.
6. de Haas, F., J.-C. Taveau, N. Boisset, O. Lambert, S. N. Vinogradov, and J. N. Lamy. 1996b. Three-dimensional reconstruction of the chlorocruorin of the polychaete annelid Eudistylia vancouverii. J. Mol. Biol. 255: 140-153.
7. García de la Torre, J., M. L. Huertas, and B. Carrasco. 2000. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J. 78:719-730.
8. García de la Torre, J., S. Navarro, M. C. López Martínez, F. G. Díaz, and J. J. López Cascales. 1994. HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophys. J. 67:530-531.
9. Glatter, O. 1977. A new method for the evaluation of small-angle scattering data. J. Appl. Crystallogr. 10:415-421.
10. Glatter, O. 1980. Computation of distance distribution functions and scattering functions of models for small angle scattering experiments. Acta Phys. Austriaca. 52:243-256.
11. Glatter, O., and O. Kratky, editors. 1982. Small Angle X-ray Scattering. Academic Press, London, UK.
12. Gros, G. 1978. Concentration dependence of the self-diffusion of human and Lumbricus terrestris hemoglobin. Biophys. J. 22:453-468.
13. Jouan, L., J.-C. Taveau, S. Marco, F. H. Lallier, and J. N. Lamy. 2001. Occurrence of two architectural types of hexagonal bilayer hemoglobin in annelids: comparison of 3D reconstruction volumes of Arenicola marina and Lumbricus terrestris hemoglobins. J. Mol. Biol. 305:757-771.
14. Kapp, O. H., A. N. Qabar, M. C. Bonner, M. S. Stern, D. A. Walz, M. Schmuck, I. Pilz, J. S. Wall, and S. N. Vinogradov. 1990. Quaternary structure of the giant extracellular hemoglobin of the leech Macrobdella decora. J. Mol. Biol. 213:141-158.
15. Krebs, A. 1996. Röntgenkleinwinkelstreuung an extrazellulären Sauerstofftransportproteinen und an einer Phosphorylase. PhD thesis. University of Graz, Austria.
16. Krebs, A., J. Lamy, S. N. Vinogradov, and P. Zipper. 1998. Lumbricus terrestris hemoglobin: a comparison of small-angle X-ray scattering and cryoelectron microscopy data. Biopolymers. 45:289-298.
17. Krebs, A., P. Zipper, and S. N. Vinogradov. 1996. Lack of size and shape alteration of oxygenated and deoxygenated Lumbricus terrestris hemoglobin? Biochim. Biophys. Acta. 1297:115-118.
18. Lamy, J. N., B. N. Green, A. Toulmond, J. S. Wall, R. E. Weber, and S. N. Vinogradov. 1996. Giant hexagonal bilayer hemoglobins. Chem. Rev. 96:3113-3124.
19. Martin, P. D., K. L. Eisele, M. A. Doyle, A. R. Kuchumov, D. A. Walz, E. G. Arutyunyan, S. N. Vinogradov, and B. F. P. Edwards. 1996a. Molecular symmetry of the dodecamer subunit of Lumbricus terrestris hemoglobin. J. Mol. Biol. 255:170-175.
20. Martin, P. D., A. R. Kuchumov, B. N. Green, R. W. A. Oliver, E. H. Braswell, J. S. Wall, and S. N. Vinogradov. 1996b. Mass spectrometric composition and molecular mass of Lumbricus terrestris hemoglobin: a refined model of its quaternary structure. J. Mol. Biol. 255:154-169.
21. Mouche, F., N. Boisset, and P. A. Penczek. 2001. Lumbricus terrestris hemoglobin - the architecture of linker chains and structural variation of the central toroid. J. Struct. Biol. 133:176-192.
22. Ohtsuki, M., and A. V. Crewe. 1983. Evidence for a central substructure in a Lumbricus terrestris hemoglobin obtained with STEM low-dose and digital processing techniques. J. Ultrastruct. Res. 83:312-318.
23. Ownby, D. W., H. Zhu, K. Schneider, R. C. Beavis, B. T. Chait, and A. F. Riggs. 1993. The extracellular hemoglobin of the earthworm, Lumbricus terrestris. Determination of subunit stoichiometry. J. Biol. Chem. 268:13539-13547.
24. Pilz, I., E. Schwarz, and S. N. Vinogradov. 1980. Small-angle X-ray studies of Lumbricus terrestris haemoglobin. Int. J. Biol. Macromol. 2:279-283.
25. Qabar, A. N., M. S. Stern, D. A. Walz, J.-T. Chiu, R. Timkovich, J. S. Wall, O. H. Kapp, and S. N. Vinogradov. 1991. Hierarchy of globin complexes. The quaternary structure of the extracellular chlorocruorin of Eudistylia vancouverii. J. Mol. Biol. 222:1109-1129.
26. Rossi Fanelli, M. R., E. Chiancone, P. Vecchini, and E. Antonini. 1970. Studies on erythrocruorin. I. Physicochemical properties of earthworm erythrocruorin. Arch. Biochem. Biophys. 141:278-283.
27. Royer, W. E., Jr., and W. A. Hendrickson. 1988. Molecular symmetry of Lumbricus erythrocruorin. J. Biol. Chem. 263:13762-13765.
28. Royer, W. E., Jr., K. Strand, M. van Heel, and W. A. Hendrickson. 2000. Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids. Proc. Natl. Acad. Sci. USA. 97:7107-7111.
29. Sayle, R. A., and E. J. Milner-White. 1995. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20:374-376.
30. Schatz, M., E. V. Orlova, P. Dube, J. Jäger, and M. van Heel. 1995. Structure of Lumbricus terrestris hemoglobin at 30 Å resolution determined using angular reconstitution. J. Struct. Biol. 114:28-40.
31. Schmuck, M. 1989. Röntgenkleinwinkeluntersuchungen an extrazellulären Annelid-hämoglobinen und einer Cellobiohydrolase. PhD thesis. University of Graz, Austria.
32. Semenyuk, A. V., and D. I. Svergun. 1991. GNOM - a program package for small-angle scattering data processing. J. Appl. Crystallogr. 24:537-540.
33. Shlom, J. M., and S. N. Vinogradov. 1973. A study of the subunit structure of the extracellular hemoglobin of Lumbricus terrestris. J. Biol. Chem. 248:7904-7912.
34. Svedberg, T. 1937. The ultra-centrifuge and the study of high-molecular compounds. Nature. 139:1051-1062.
35. Svedberg, T., and I.-B. Eriksson. 1933. The molecular weight of erythrocruorin. J. Am. Chem. Soc. 55:2834-2841.
36. Svergun, D. I. 1999. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76:2879-2886.
37. Svergun, D. I. 2000. Advanced solution scattering data analysis methods and their applications. J. Appl. Crystallogr. 33:530-534.
38. Taveau, J.-C., N. Boisset, S. N. Vinogradov, and J. N. Lamy. 1999. Three-dimensional reconstruction of Lumbricus terrestris hemoglobin at 22 Å resolution: intramolecular localization of the globin and linker chains. J. Mol. Biol. 289:1343-1359.
39. Terwilliger, R. C., R. L. Garlick, N. B. Terwilliger, and D. P. Blair. 1975. Molecular weight of Eudistylia vancouveri chlorocruorin and its subunits. Biochim. Biophys. Acta. 400:302-309.
40. Vinogradov, S. N., O. H. Kapp, and M. Ohtsuki. 1982. The extracellular haemoglobins and chorocruorins of annelids. In Electron Microscopy of Proteins, Vol. 3. J. R. Harris, editor. Academic Press, London, UK. 135-164.
41. Vinogradov, S. N., S. D. Lugo, M. G. Mainwaring, O. H. Kapp, and A. V. Crewe. 1986. Bracelet protein: a quaternary structure proposed for the giant extracellular hemoglobin of Lumbricus terrestris. Proc. Natl. Acad. Sci. USA. 83:8034-8038.
42. Vinogradov, S. N., and P. K. Sharma. 1994. Preparation and characterization of invertebrate globin complexes. Methods Enzymol. 231:112-124.
43. Vinogradov, S. N., P. K. Sharma, A. N. Qabar, J. S. Wall, J. A. Westrick, J. H. Simmons, and S. J. Gill. 1991. A dodecamer of globin chains is the principal functional subunit of the extracellular hemoglobin of Lumbricus terrestris. J. Biol. Chem. 266:13091-13096.
44. Volkov, V. V., and D. I. Svergun. 2003. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36:860-864.
45. Weber, R. E., H. Malte, E. H. Braswell, R. W. A. Oliver, B. N. Green, P. K. Sharma, A. Kuchumov, and S. N. Vinogradov. 1995. Mass spectrometric composition, molecular mass and oxygen binding of Macrobdella decora hemoglobin and its tetramer and monomer subunits. J. Mol. Biol. 251:703-720.
46. Weber, R. E., and S. N. Vinogradov. 2001. Nonvertebrate hemoglobins: functions and molecular adaptations. Physiol. Rev. 81:569-628.
47. Zhu, H., D. W. Ownby, C. K. Riggs, N. J. Nolasco, J. K. Stoops, and A. F. Riggs. 1996. Assembly of the gigantic hemoglobin of the earthworm Lumbricus terrestris. J. Biol. Chem. 271:30007-30021.
48. Zipper, P., and H. Durchschlag. 2000. Prediction of hydrodynamic and small-angle scattering parameters from crystal and electron microscopic structures. J. Appl. Crystallogr. 33:788-792.
49. Zipper, P., and H. Durchschlag. 2003. Modeling of protein solution structures. J. Appl. Crystallogr. 36:509-514.
50. Zipper, P., A. Krebs, and H. Durchschlag. 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.
51. Zipper, P., A. Krebs, and H. Durchschlag. 2004. Comparative modeling of giant annelid hemoglobins. Prog. Colloid Polym. Sci. In press.