Small-angle X-ray and neutron scattering as a tool for structural systems biology

Biological Chemistry

Volumn 391, Issue 7, 2010, Pages 737-743

  Svergun, Dmitri I ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

ab initio methods; flexible macromolecules; hierarchical systems; macromolecular structure; rigid body modelling; solution scattering

Indexed keywords

CONFORMATIONAL TRANSITION; MOLECULAR SIZE; NEUTRON SCATTERING; PH; PRIORITY JOURNAL; SALINITY; SHORT SURVEY; SYSTEMS BIOLOGY; TEMPERATURE; X RAY;

MACROMOLECULAR SUBSTANCES; MOLECULAR STRUCTURE; NEUTRON DIFFRACTION; SCATTERING, SMALL ANGLE; SYSTEMS BIOLOGY;

EID: 77954580347     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2010.093     Document Type: Short Survey

References (51)

1. Aleshin, A.E., Gramatikova, S., Hura, G.L., Bobkov, A., Strongin, A.Y., Stec, B., Tainer, J.A., Liddington, R.C., and Smith, J.W. (2009). Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case. Structure 17, 1465-1475.
2. Aloy, P. and Russell, R.B. (2006). Structural systems biology: modeling protein interactions. Nat. Rev. Mol. Cell Biol. 7, 188-197.
3. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L., et al. (2009). Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73-76.
4. Baldock, C., Siegler, V., Bax, D.V., Cain, S.A., Mellody, K.T., Marson, A., Haston, J.L., Berry, R., Wang, M.C., Grossmann, J.G., et al. (2006). Nanostructure of fibrillin-1 reveals compact conformation of EGF arrays and mechanism for extensibility. Proc. Natl. Acad. Sci. USA 103, 11922-11927.
5. Bernado, P., Blanchard, L., Timmins, P., Marion, D., Ruigrok, R.W., and Blackledge, M. (2005). A structural model for unfolded proteins from residual dipolar couplings and small-angle X-ray scattering. Proc. Natl. Acad. Sci. USA 102, 17002-17007.
6. Bernado, P., Mylonas, E., Petoukhov, M.V., Blackledge, M., and Svergun, D.I. (2007). Structural characterization of flexible proteins using small-angle X-ray scattering. J. Am. Chem. Soc. 129, 5656-5664. (Pubitemid 46697655)
7. Bertini, I., Calderone, V., Fragai, M., Jaiswal, R., Luchinat, C., Melikian, M., Mylonas, E., and Svergun, D.I. (2008). Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12. J. Am. Chem. Soc. 130, 7011-7021.
8. Blobel, J., Bernado, P., Svergun, D.I., Tauler, R., and Pons, M. (2009). Low-resolution structures of transient protein-protein complexes using small-angle X-ray scattering. J. Am. Chem. Soc. 131, 4378-4386.
9. Chacon, P., Moran, F., Diaz, J.F., Pantos, E., and Andreu, J.M. (1998). Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys. J. 74, 2760-2775.
10. Diepholz, M., Venzke, D., Prinz, S., Batisse, C., Florchinger, B., Rossle, M., Svergun, D.I., Bottcher, B., and Fethiere, J. (2008). A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly. Structure 16, 1789-1798.
11. Feigin, L.A. and Svergun, D.I. (1987). Structure Analysis by Smallangle X-ray and Neutron Scattering (New York, USA: Plenum Press).
12. Franke, D. and Svergun, D.I. (2009). Dammif, a program for rapid Ab Initio shape determination in small angle scattering. J. Appl. Cryst. 42, 342-346.
13. Funari, S.S., Rapp, G., Perbandt, M., Dierks, K., Vallazza, M., Betzel, C., Erdmann, V.A., and Svergun, D.I. (2000). Structure of free thermus flavus 5 S rRNA at1.3 nm resolution from synchrotron X-ray solution scattering. J. Biol. Chem. 275, 31283-31288.
14. Hura, G.L., Menon, A.L., Hammel, M., Rambo, R.P., Poole, F.L. 2nd, Tsutakawa, S.E., Jenney, F.E. Jr., Classen, S., Frankel, K.A., Hopkins, R.C., et al. (2009). Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods 6, 606-612.
15. Koch, M.H., Vachette, P., and Svergun, D.I. (2003). Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys. 36, 147-227.
16. Konarev, P.V., Petoukhov, M.V., Volkov, V.V., and Svergun, D.I. (2006). ATSAS 2.1, a program package for small-angle scattering data analysis. J. Appl. Crystallogr. 39, 277-286.
17. Levitt, M. (2007). Growth of novel protein structural data. Proc. Natl. Acad. Sci. USA 104, 3183-3188.
18. Mylonas, E., Hascher, A., Bernado, P., Blackledge, M., Mandelkow, E., and Svergun, D.I. (2008). Domain conformation of tau protein studied by solution small-angle X-ray scattering. Biochemistry 47, 10345-10353.
19. Nicastro, G., Habeck, M., Masino, L., Svergun, D.I., and Pastore, A. (2006). Structure validation of the Josephin domain of ataxin- 3: conclusive evidence for an open conformation. J. Biomol. NMR 36, 267-277.
20. Niemann, H.H., Petoukhov, M.V., Hartlein, M., Moulin, M., Gherardi, E., Timmins, P., Heinz, D.W., and Svergun, D.I. (2008). X-ray and neutron small-angle scattering analysis of the complex formed by the Met receptor and the Listeria monocytogenes invasion protein InlB. J. Mol. Biol. 377, 489-500.
21. Oliveira, C.L., Behrens, M.A., Pedersen, J.S., Erlacher, K., and Otzen, D. (2009). A SAXS study of glucagon fibrillation. J. Mol. Biol. 387, 147-161.
22. Pedersen, M., Lo Leggio, L., Grossmann, J.G., Larsen, S., and Hammer, K. (2008). Identification of quaternary structure and functional domains of the CI repressor from bacteriophage TP901-1. J. Mol. Biol. 376, 983-996.
23. Perez, J., Vachette, P., Russo, D., Desmadril, M., and Durand, D. (2001). Heat-induced unfolding of Neocarzinostatin, a small allb protein investigated by small-angle X-ray scattering. J. Mol. Biol. 308, 721-743.
24. Petoukhov, M.V. and Svergun, D.I. (2005). Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237-1250.
25. Petoukhov, M.V. and Svergun, D.I. (2006). Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. Eur. Biophys. J. 35, 567-576.
26. Petoukhov, M.V. and Svergun, D.I. (2007). Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr. Opin. Struct. Biol. 17, 562-571.
27. Petoukhov, M.V., Monie, T.P., Allain, F.H., Matthews, S., Curry, S., and Svergun, D.I. (2006). Conformation of polypyrimidine tract binding protein in solution. Structure 14, 1021-1027.
28. Petoukhov, M.V., Konarev, P.V., Kikhney, A.G., and Svergun, D.I. (2007). ATSAS 2.1 - towards automated and web-supported small-angle scattering data analysis. J. Appl. Cryst. 40, s223-s228.
29. Pinotsis, N., Lange, S., Perriard, J.C., Svergun, D.I., and Wilmanns, M. (2008). Molecular basis of the C-terminal tail-to-tail assembly of the sarcomeric filament protein myomesin. EMBO J. 27, 253-264.
30. Putnam, C.D., Hammel, M., Hura, G.L., and Tainer, J.A. (2007). Xray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 40, 191-285.
31. Round, A.R., Franke, D., Moritz, S., Huchler, R., Fritsche, M., Malthan, D., Klaering, R., Svergun, D.I., and Roessle, M. (2008). Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J. App l. Cryst. 41, 913-917.
32. Snoep, J.L., Bruggeman, F., Olivier, B.G., and Westerhoff, H.V. (2006). Towards building the silicon cell: a modular approach. Biosystems 83, 207-216.
33. Svergun, D.I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879-2886.
34. Svergun, D.I. and Koch, M.H.J. (2003). Small angle scattering studies of biological macromolecules in solution. Rep. Progr. Phys. 66, 1735-1782.
35. Svergun, D.I. and Nierhaus, K.H. (2000). A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome. J. Biol. Chem. 275, 14432-14439.
36. Svergun, D.I., Barberato, C., and Koch, M.H.J. (1995). CRYSOL - a program to evaluate X-ray solution scatterin of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768-773.
37. Svergun, D.I., Barberato, C., Koch, M.H., Fetler, L., and Vachette, P. (1997). Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins 27, 110-117.
38. Svergun, D.I., Richard, S., Koch, M.H.J., Sayers, Z., Kuprin, S., and Zaccai, G. (1998). Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc. Natl. Acad. Sci. USA 95, 2267-2272.
39. Svergun, D.I., Petoukhov, M.V., Koch, M.H.J., and Koenig, S. (2000). Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J. Biol. Chem. 275, 297-302.
40. Svergun, D.I., Petoukhov, M.V., and Koch, M.H.J. (2001). Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80, 2946-2953.
41. Tabarani, G., Thepaut, M., Stroebel, D., Ebel, C., Vives, C., Vachette, P., Durand, D., and Fieschi, F. (2009). DC-SIGN neck domain is a pH-sensor controlling oligomerization: SAXS and hydrodynamic studies of extracellular domain. J. Biol. Chem. 284, 21229-21240.
42. Tidow, H., Melero, R., Mylonas, E., Freund, S.M., Grossmann, J.G., Carazo, J.M., Svergun, D.I., Valle, M., and Fersht, A.R. (2007). From the cover: quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proc. Natl. Acad. Sci. USA 104, 12324-12329.
43. Tjioea, E. and Heller, W.T. (2007). ORNL-SAS: software for calculation of small-angle scattering intensities of proteins and protein complexes. J. Appl. Cryst. 40, 782-785.
44. Toft, K.N., Vestergaard, B., Nielsen, S.S., Snakenborg, D., Jeppesen, M.G., Jacobsen, J.K., Arleth, L., and Kutter, J.P. (2008). Highthroughput small angle X-ray scattering from proteins in solution using a microfluidic front-end. Anal. Chem. 80, 3648-3654.
45. Tsuruta, H. and Irving, T.C. (2008). Experimental approaches for solution X-ray scattering and fiber diffraction. Curr. Opin. Struct. Biol. 18, 601-608.
46. Varga, A., Flachner, B., Konarev, P., Graczer, E., Szabo, J., Svergun, D., Zavodszky, P., and Vas, M. (2006). Substrate-induced double sided H-bond network as a means of domain closure in 3-phosphoglycerate kinase. FEBS Lett. 580, 2698-2706.
47. Vestergaard, B., Groenning, M., Roessle, M., Kastrup, J.S., van de Weert, M., Flink, J.M., Frokjaer, S., Gajhede, M., and Svergun, D.I. (2007). A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils. PLoS Biol. 5, e134.
48. Volkov, V.V. and Svergun, D.I. (2003). Uniqueness of ab initio shape determination in small angle scattering. J. Appl. Crystallogr. 36, 860-864.
49. Whitten, A.E. and Trewhella, J. (2009). Small-angle scattering and neutron contrast variation for studying bio-molecular complexes. Methods Mol. Biol. 544, 307-323.
50. Whitten, A.E., Jeffries, C.M., Harris, S.P., and Trewhella, J. (2008). Cardiac myosin-binding protein C decorates F-actin: implications for cardiac function. Proc. Natl. Acad. Sci. USA 105, 18360-18365.
51. Yang, S., Park, S., Makowski, L., and Roux, B. (2009). A rapid coarse residue-based computational method for X-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys. J. 96, 4449-4463.