A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering

European Biophysics Journal

Volumn 41, Issue 1, 2012, Pages 1-11

  Gabel, Frank ^a  

^a CEA GRENOBLE   (France)

Author keywords

Modeling; Nuclear magnetic resonance; Protein complex; Residual dipolar couplings; Small angle neutron scattering; Small angle X ray scattering

Indexed keywords

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN DATABASE; PROTEIN SUBUNIT; PROTEIN TERTIARY STRUCTURE; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; PROTEINS; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 84857363292     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-011-0751-y     Document Type: Article

References (49)

1. Back JW, de Jong L, Muijsers AO, de Koster CG (2003) Chemical cross-linking and mass spectrometry for protein structural modeling. J Mol Biol 331:303-313 (Pubitemid 36904016)
2. Battiste JL, Wagner G (2000) Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. Biochemistry 39:5355-5365 (Pubitemid 30257075)
3. Bax A (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12:1-16 (Pubitemid 36020129)
4. Bernadó P, Blackledge M (2010) Structural biology: proteins in dynamic equilibrium. Nature 468:1046-1048
5. Blackledge M (2005) Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings. Prog Nucl Magn Reson Spectrosc 46:23-46
6. Capel MS, Engelman DM, Freeborn BR, Kjeldgaard M, Langer JA, Ramakrishnan V, Schindler DG, Schneider DK, Schoenborn BP, Sillers IY, Yabuki S, Moore BP (1987) A complete mapping of the proteins in the small ribosomal subunit of Escherischia coli. Science 238:1403-1406 (Pubitemid 18015960)
7. Chantalat L, Skoufias DA, Kleman JP, Jung B, Dideberg O, Margolis RL (2000) Crystal structure of human survivin reveals a bow tieshaped dimer with two unusual alpha-helical extensions. Mol Cell 6:183-189
8. Debye P (1915) Zerstreuung von Roentgenstrahlen. Ann Physik 28:809-823
9. Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731-1737 (Pubitemid 36232568)
10. Engelman DM, Moore PB (1972) A new method for the determination of biological quaternary structure by neutron scattering. Proc Natl Acad Sci USA 69:1997-1999
11. Gabel F, Simon B, Sattler M (2006) A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints. Eur Biophys J 35:313-327 (Pubitemid 43357586)
12. Gabel F, Simon B, Nilges M, Petoukhov M, Svergun D, Sattler M (2008) A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints. J Biomol NMR 41:199-208
13. Garcia KC, Degano M, Stanfield RL, Brunmark A, Jackson MR, Peterson PA, Teyton L, Wilson IA (1996) An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science 274:209-219 (Pubitemid 26353190)
14. Glatter O (1979) The interpretation of real-space information from small-angle scattering experiments. J Appl Crystallogr 12:166-175
15. Glatter O, Kratky O (1982) Small angle X-ray scattering. Academic Press, London
16. Goldstein H (1977) Classical mechanics. Addison-Wesley, Reading
17. Grishaev A, Wu J, Trewhella J, Bax A (2005) Refinement of multidomain protein structures by combination of solution smallangle X-ray scattering and NMR data. J Am Chem Soc 127:16621-16628 (Pubitemid 41740413)
18. Heller WT (2010) Small-angle neutron scattering and contrast variation: a powerful combination for studying biological structures. Acta Crystallogr Sect D Biol Crystallogr 66: 1213-1217
19. Hoppe W (1973) The label triangulation method and mixed isomorphous replacement principle. J Mol Biol 78:581-585
20. Hoppe W, May R, Stoeckel P, Lorenz S, Erdmann VA, Wittmann HG, Crespi HL, Katz JJ, Ibel K (1975) Neutron scattering measurements with the label triangulation method on the 50S subunit of E. Coli ribosomes. In: Schoenborn BP (ed) Neutron scattering for the analysis of biological structures, vol 27. Brookhaven National Laboratory, Brookhaven, pp IV38-IV48
21. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z (2008) Proteinprotein docking benchmark version 3.0. Proteins 73:705-709 (Pubitemid 352788651)
22. Jacques DA, Trewhella J (2010) Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls. Protein Sci 19:642-657
23. Jacrot B (1976) The study of biological structures by neurtron scattering from solution. Rep Prog Phys 39:911-953
24. Konarev PV, Petoukhov MV, Svergun DI (2001) MASSHA-a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data. J Appl Crystallogr 34:527-532 (Pubitemid 32852302)
25. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51-55 (Pubitemid 26152976)
26. Kratky O (1972) Recent advances and applications of diffuse X-ray small-angle scattering on biopolymers in dilute solutions. Q Rev Biophys 5:481-537
27. Kratky O, Worthmann W (1946) Ueber die Bestimmabrkeit der Konfiguration geloester organischer Molekule durch interferometrische Vermessung von Roentgenstrahlen. Monatsh Chem 76:263-281
28. Kumaraswamy VS, Lindley PF, Slingsby C, Glover ID (1996) An eye lens protein-water structure: 1.2 A resolution structure of gammaB-crystallin at 150 K. Acta Crystallogr Sect D 52: 611-622
29. Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36:307-327 (Pubitemid 46998121)
30. Macheboeuf P, Piuzzi M, Finet S, Bontems F, Pérez J, Dessen A, Vachette P (2011) Solution X-ray scattering study of a fulllength class A penicillin-binding protein. Biochem Biophys Res Commun 405:107-111
31. Madl T, Gabel F, Sattler M (2011) NMR and small-angle scatteringbased structural analysis of protein complexes in solution. J Struct Biol 173:472-482
32. Mareuil F, Sizun C, Perez J, Schoenauer M, Lallemand J-Y, Bontems F (2007) A simple genetic algorithm for the optimization of multidomain protein homology models driven by NMR residual dipolar coupling and small angle X-ray scattering data. Eur Biophys J 37:95-104 (Pubitemid 350159853)
33. Marino M, Zou P, Svergun D, Garcia P, Edlich C, Simon B, Wilmanns M, Muhle-Goll C, Mayans O (2006) The Ig doublet Z1Z2: a model system for the hybrid analysis of conformational dynamics in Ig tandems from Tintin. Structure 14:1437-1447 (Pubitemid 44331621)
34. Mattinen M-L, Paakkonen K, Ikonen T, Craven J, Drakenberg T, Serimaa R, Waltho J, Annila A (2002) Quaternary structure built from subunits combining NMR and small-angle X-Ray scattering data. Biophys J 83:1177-1183 (Pubitemid 34803648)
35. Moore PB, Engelman DM (1977) Model calculations of protein pair interference functions. J Mol Biol 112:228-234 (Pubitemid 8111038)
36. Nöllmann M, He J, Byron O, Stark WM (2004) Solution structure of the Tn3 resolvase-crossover site synaptic complex. Mol Cell 16:127-137 (Pubitemid 39330158)
37. Petoukhov MV, Svergun DI (2007) Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr Opin Struct Biol 17:562-571 (Pubitemid 350041656)
38. Pons C, D'Abramo M, Svergun DI, Orozco M, Bernadó P, Fernández-Recio J (2010) Structural characterization of protein-protein complexes by integrating computational docking with smallangle scattering data. J Mol Biol 403:217-230
39. Putnam CD, Hammel M, Hura GL, Tainer JA (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40:191-285 (Pubitemid 350261954)
40. Sattler M, Liang H, Nettesheim D, Meadows RP, Harlan JE, Eberstadt M, Yoon HS, Shuker SB, Chang BS, Minn AJ, Thompson CB, Fesik SW (1997) Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science 275: 983-986 (Pubitemid 27087715)
41. Schwieters CD, Suh JY, Grishaev A, Ghirlando R, Takayama Y, Clore GM (2010) Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering. J Am Chem Soc 132:13026-13045
42. Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879-2886 (Pubitemid 29269438)
43. Svergun DI, Barberato C, Koch MHJ (1995) CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768-773 (Pubitemid 3014671)
44. Takayama Y, Schwieters CD, Grishaev A, Ghirlando R, Clore GM (2011) Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site mutant of the 128 kDa enzyme I dimer. J Am Chem Soc 133:424-427
45. Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111-1114 (Pubitemid 27517889)
46. Wang J, Zuo X, Yu P, Byeon IJ, Jung J, Wang X, Dyba M, Seifert S, Schwieters CD, Qin J, Gronenborn AM, Wang YX (2009a) Determination of multicomponent protein structures in solution using global orientation and shape restraints. J Am Chem Soc 131:10507-10515
47. Wang J, Zuo X, Yu P, Xu H, Starich MR, Tiede DM, Shapiro BA, Schwieters CD, Wang YX (2009b) A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol 393: 717-734
48. Yuzawa S, Ogura K, Horiuchi M, Suzuki NN, Fujioka Y, Kataoka M, Sumimoto H, Inagaki F (2004) Solution structure of the tandem Src homology 3 domains of pH47phox in an autoinhibited form. J Biol Chem 28:29752-29760 (Pubitemid 38915858)
49. Zuiderweg ERP (2002) Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry 41:1-7 (Pubitemid 34049375)