Reconstruction of SAXS profiles from protein structures

Computational and Structural Biotechnology Journal

Volumn 8, Issue 11, 2013, Pages e201308006-

  Putnam, Daniel K ^a,b   Lowe, Edward W ^a,c   Meiler, Jens ^a,b,c  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c VANDERBILT UNIVERSITY   (United States)

Author keywords

AXES; CRYSOL; DALAI; Debye formula; FOXS; PHAISTOS; SASTBX; SAXSTER; Small angle X ray scattering; Spherical Harmonics

Indexed keywords

EID: 84902129110     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201308006     Document Type: Short Survey

References (38)

1. Clatter O, Kratky O (1982) Small Angle X-Ray Scattering. New York: Academic Press Inc. 515 p.
2. Koch MHJ, Vachette P, Svergun DI (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36:147-227. (Pubitemid 37493573)
3. 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)
4. Svergun DI, Koch MHJ (2003) Small-angle scattering studies of biological macromolecules in solution. Reports on Progress in Physics 66:1735-1782. (Pubitemid 37365734)
5. Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946-2953. (Pubitemid 32521666)
6. Tsuruta H, Irving TC (2008) Experimental approaches for solution X-ray scattering and fiber diffraction. Curr Opin Struct Biol 18:601-608.
7. Alber F, Forster F, Korkin D, Topf M, Sali A (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443-477.
8. Zheng W, Doniach S (2005) Fold recognition aided by constraints from small angle X-ray scattering data. Protein Eng Des Sel 18:209-219. (Pubitemid 40863425)
9. Stuhrmann HB (1970) Interpretation of small-angle scattering functions of dilute solutions and gases. A representation of the structures related to a one-particle scattering function. Acta Crystallographica Section A 26:297-306.
10. Pelikan M, Hura GL, Hammel M (2009) Structure and flexibility within proteins as identified through small angle X-ray scattering. General Physiology and Biophysics 28:174-189.
11. Schneidman-Duhovny D, Kim SJ, Sali A (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12:17.
12. Bernado P, Svergun DI (2012) Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. Mol Biosyst 8:151-167.
13. Feigin LA, Svergun DI (1987) Structure Analysis by Small-Angle X-Ray and Neutron Scattering. New York: Plenum Press.
14. Blessing RH (2006) Introduction to X-Ray Diffraction Physics. Hauptman-Woodward Medical Research Institute, pp. 55.
15. Mertens HD, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172:128-141.
16. Forster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, et al. (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol 382:1089-1106.
17. Debye P (1915) Zerstreuung von Rontgenstrahlen. Annalen der Physik 351:809-823.
18. Cromer DT, Mann JB (1967) X-ray scattering factors computed from numerical Hartree-Fock Wave Functions. Los Alamos: University of California.
19. Cromer DT, Waber JT (1965) Scattering Factors Computed from Relativistic Dirac-Slater Wave Functions. Acta Crystallographica 18:104-&.
20. Doyle PA, Turner PS (1968) Relativistic Hartree-Fock X-ray and electron scattering factors. Acta Crystallographica Section A 24:390-397.
21. Fox AG, Okeefe MA, Tabbernor MA (1989) Relativistic Hartree-Fock X-Ray and Electron Atomic Scattering Factors at High Angles. Acta Crystallographica Section A 45:786-793.
22. Brown PJR, AG.; Maslen, EN.; O'Keefe, M. A; Willis, B. T. M (2006) Intensity of diffracted intensities. In: Prince E, editor. International Tables for Crystallography: John Wiley and Sons. pp. 554-595.
23. Fraser RDB, MacRae TP, Suzuki E (1978) An Improved Method for Calculating the Contribution of Solvent to the X-ray Diffraction Pattern of Biological Molecules. Journal of Applied Crystallography 11:693-694.
24. Svergun D, Barberato C, Koch MHJ (1995) CRYSOL - A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. Journal of Applied Crystallography 28:768-773. (Pubitemid 3014671)
25. Pantos E, Bordas J (1994) Supercomputer simulation of small angle X-ray scattering, electron micrographs and X-ray diffraction patterns of macromolecular structures. Pure and Applied Chemistry 66:77-82.
26. Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T (2010) Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. BMC Bioinformatics 11:429.
27. Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38:W540-544.
28. dos Reis MA, Aparicio R, Zhang Y (2011) Improving protein template recognition by using small-angle x-ray scattering profiles. BiophysJ 101:2770-2781.
29. Edmonds AR (1960) Angular Momentum in Quantum Mechanics. Princeton, New Jersey: Princeton University Press.
30. Liu H, Morris RJ, Hexemer A, Grandison S, Zwart PH (2012) Computation of small-angle scattering profiles with three-dimensional Zernike polynomials. Acta Crystallographica Section A 68:278-285.
31. Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496:477-481.
32. Gumerov NA, Berlin K, Fushman D, Duraiswami R (2012) A hierarchical algorithm for fast Debye summation with applications to small angle scattering. J Comput Chem 33:1981-1996.
33. Grossmann JG, Abraham ZHL, Adman ET, Neu M, Eady RR, et al. (1993) X-Ray-Scattering Using Synchrotron-Radiation Shows Nitrite Reductase from Achromobacter-Xylosoxidans to Be a Trimer in Solution. Biochemistry 32:7360-7366. (Pubitemid 23232307)
34. Svergun DI, Richard S, Koch MH, Sayers Z, Kuprin S, et al. (1998) Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci U S A 95:2267-2272. (Pubitemid 28145930)
35. Rambo RP, Tainer JA (2013) Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu Rev Biophys 42:415-441.
36. Grishaev A, Guo L, Irving T, Bax A (2010) Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling. J Am Chem Soc 132:15484-15486.
37. Novotni M, Klein R. 3D Zernike Descriptors for Content Based Shape Retrieval; 2003; New York.
38. Antonov LD, Andreetta C, Habeck M. An Efficient Parallel Gpu Evaluation of Small Angle X-Ray Scattering Profiles; 2012. pp. 102-108.