Characterization of Protein Fold by Wide-Angle X-ray Solution Scattering

Journal of Molecular Biology

Volumn 383, Issue 3, 2008, Pages 731-744

  Makowski, Lee ^a   Rodi, Diane J ^a   Mandava, Suneeta ^a   Devarapalli, Satish ^a   Fischetti, Robert F ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

protein fold; secondary structure; tertiary structure; WAXS

Indexed keywords

ALPHA HELIX; ARTICLE; BETA SHEET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 52949104024     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.08.038     Document Type: Article

References (23)

1. Fischetti R.F., Rodi D.J., Mirza A., Kondrashkina E., Irving T., and Makowski L. Wide angle x-ray scattering of proteins: effect of beam exposure on protein integrity. J. Synchrotron Res. 10 (2003) 398-404
2. Fischetti R.F., Rodi D.J., Gore D.B., and Makowski L. Wide angle x-ray solution scattering as a probe of ligand-induced conformational changes in proteins. Chem. Biol. 11 (2004) 1431-1443
3. Hirai M., Iwase H., Hayakawa T., Miura K., and Inoue K. Structural hierarchy of several proteins observed by wide-angle solution scattering. J. Synchotron Radiat. 9 (2002) 202-205
4. Hirai M., Koizumi M., Hayakawa T., Takahashi H., Abe S., Hirai H., et al. Hierarchical map of protein unfolding and refolding at thermal equilibrium revealed by wide-angle x-ray scattering. Biochemistry 43 (2004) 9036-9049
5. Tiede D.M., Zhang R., and Seifert S. Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C. Biochemistry 28 (2002) 6605-6614
6. Zagrovic B., and Pande V.S. Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles. J. Am. Chem. Soc. 128 (2006) 11742-11743
7. Holm L., and Sander C. Dictionary of recurrent domains in protein structures. Proteins: Struct., Funct., Genet. 33 (1998) 88-96
8. Hou J., Sims G.E., Zhang C., and Kim S.H. A global representation of the protein fold space. Proc. Natl Acad. Sci. USA 100 (2003) 2386-2390
9. Hou J., Jun S.R., Zhang C., and Kim S.H. Global mapping of the protein structure space and application in structure-based inference of protein function. Proc. Natl Acad. Sci. USA 102 (2005) 5641-5642
10. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database fo the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
11. Svergun D., Barberato C., and Koch M.H.J. CRYSOL-a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28 (1995) 768-773
12. Fraser R.D.B., MacRae T.P., and Suzuki E. An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. J. Appl. Crystallogr. 11 (1978) 693-694
13. Lees J.G., Miles A.J., Wien F., and Wallace B.A. A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 22 (2007) 1955-1962
14. Guinier A. X-ray Diffraction in Crystals, Imperfect Crystals and Amorphous Bodies (1994), Dover Publications, Mineola, NY 49
15. Luzzati V., and Tardieu A. Recent developments in solution x-ray scattering. Annu. Rev. Biophys. Bioeng. 9 (1980) 1-29
16. Shannon, C. (1948). A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423; 623-656.
17. Makowski L. The use of continuous diffraction data as a phase constraint: I. One-dimensional theory. J. Appl. Crystallogr. 14 (1981) 160-168
18. Makowski L. The use of continuous diffraction data as a phase constraint: II. Application to fiber diffraction data. J. Appl. Crystallogr. 15 (1982) 546-557
19. Makowski L. An estimate of the total number of independent structural parameters measurable in a fiber diffraction pattern. Acta Crystallogr. A 47 (1991) 562-567
20. Lebart L., Morineau A., and Warwick K.M. Multivariate Descriptive Statistical Analysis (1984), Wiley, New York
21. Wallace B.A. Synchrotron radiation circular-dichroism spectroscopy as a tool for investigating protein structures. J. Synchrotron Res. 7 (2000) 289-295
22. Makowski L., Rodi D.J., Mandava S., Minh D., Gore D., and Fischetti R.F. Molecular crowding inhibits intramolecular breathing motions in proteins. J. Mol. Biol. 375 (2008) 529-546
23. Press W.H., Teukolsky S.A., Vetterling W.T., and Flannery B.P. Numerical recipes in FORTRAN: The art of scientific computing (1993), Cambridge University Press, New York