Probing the average local structure of biomolecules using small-angle scattering and scaling laws

Biophysical Journal

Volumn 106, Issue 11, 2014, Pages 2474-2482

  Watson, Max C ^a   Curtis, Joseph E ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; INTRINSICALLY DISORDERED PROTEIN;

CHEMISTRY; PROCEDURES; PROTEIN CONFORMATION; PROTEIN FOLDING; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

BACTERIAL PROTEINS; INTRINSICALLY DISORDERED PROTEINS; PROTEIN CONFORMATION; PROTEIN FOLDING; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 84901999651     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.03.050     Document Type: Article

References (39)

1. M. Doi Introduction to Polymer Physics 1996 Oxford University Press London, UK
2. J.E. Kohn, and I.S. Millett K.W. Plaxco Random-coil behavior and the dimensions of chemically unfolded proteins Proc. Natl. Acad. Sci. USA 101 2004 12491 12496 (Pubitemid 39122051)
3. H. Hofmann, and A. Soranno B. Schuler Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy Proc. Natl. Acad. Sci. USA 109 2012 16155 16160
4. I.S. Millett, S. Doniach, and K.W. Plaxco Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins Adv. Protein Chem. 62 2002 241 262 (Pubitemid 35204872)
5. T. Dewey Protein structure and polymer collapse J. Phys. Chem. 98 1993 2250
6. R.P. Rambo, and J.A. Tainer Accurate assessment of mass, models and resolution by small-angle scattering Nature 496 2013 477 481
7. D. Svergun, G. Taylor, and L. Feigin Structure Analysis by Small-Angle X-Ray and Neutron Scattering 1987 Plenum Press New York
8. H.D. Mertens, and D.I. Svergun Structural characterization of proteins and complexes using small-angle x-ray solution scattering J. Struct. Biol. 172 2010 128 141
9. A.V. Semenyuk, and D.I. Svergun GNOM - a program package for small-angle scattering data processing J. Appl. Cryst. 24 1991 537 540
10. O. Glatter A new method for the evaluation of small-angle scattering data J. Appl. Cryst. 10 1977 415 421
11. D. Svergun, and M. Koch Small-angle scattering studies of biological macromolecules in solution Rep. Prog. Phys. 66 2003 1735
12. H.M. Berman, and J. Westbrook P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242 (Pubitemid 30047768)
13. R.P. Joosten, and T.A. te Beek G. Vriend A series of PDB-related databases for everyday needs Nucleic Acids Res. 39 Database issue 2011 D411 D419
14. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
15. D. Schneidman-Duhovny, M. Hammel, and A. Sali FOXS: a web server for rapid computation and fitting of SAXS profiles Nucleic Acids Res. 38 Web Server issue 2010 W540 W544
16. C. Yang, and M.J. van der Woerd K. Luger Biophysical analysis and small-angle x-ray scattering-derived structures of MeCP2-nucleosome complexes Nucleic Acids Res. 39 2011 4122 4135
17. G.C. Bressan, and J.C. Silva J. Kobarg Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein J. Proteome Res. 7 2008 4465 4474
18. T. Konno, and N. Tanaka M. Maki A circular dichroism study of preferential hydration and alcohol effects on a denatured protein, pig calpastatin domain I Biochim. Biophys. Acta 1342 1997 73 82 (Pubitemid 27464831)
19. A.D. Gazi, and M. Bastaki M. Kokkinidis Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems J. Biol. Chem. 283 2008 34062 34068
20. H. Boze, and T. Marlin B. Cabane Proline-rich salivary proteins have extended conformations Biophys. J. 99 2010 656 665
21. Z. Lens, and F. Dewitte A. Verger Solution structure of the N-terminal transactivation domain of ERM modified by SUMO-1 Biochem. Biophys. Res. Commun. 399 2010 104 110
22. M.R. Alborghetti, and A.S. Furlan J. Kobarg Human FEZ1 protein forms a disulfide bond mediated dimer: implications for cargo transport J. Proteome Res. 9 2010 4595 4603
23. M. Wells, and H. Tidow A.R. Fersht Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain Proc. Natl. Acad. Sci. USA 105 2008 5762 5767 (Pubitemid 351758446)
24. K. Moncoq, and I. Broutin D. Durand SAXS study of the PIR domain from the Grb14 molecular adaptor: a natively unfolded protein with a transient structure primer? Biophys. J. 87 2004 4056 4064 (Pubitemid 39602909)
25. 0-binding region of the vesicular stomatitis virus phosphoprotein is globally disordered but contains transient α-helices Protein Sci. 20 2011 542 556
26. D. Eliezer Biophysical characterization of intrinsically disordered proteins Curr. Opin. Struct. Biol. 19 2009 23 30
27. P. Bernadó, and D.I. Svergun Structural analysis of intrinsically disordered proteins by small-angle x-ray scattering Mol. Biosyst. 8 2012 151 167
28. A. Garcia-Pino, and S. Balasubramanian R. Loris Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity Cell 142 2010 101 111
29. N.J. Clark, and H. Zhang J.E. Curtis Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints J. Phys. Chem. B 117 2013 14029 14038
30. phox behaves in solution as a multidomain protein with semi-flexible linkers J. Struct. Biol. 169 2010 45 53
31. D. Schneidman-Duhovny, S.J. Kim, and A. Sali Integrative structural modeling with small angle x-ray scattering profiles BMC Struct. Biol. 12 2012 17
32. W. Press, and B. Flannery W. Vetterling Numerical Recipes 1990 Cambridge University Press London, UK
33. J. Tsai, and R. Taylor M. Gerstein The packing density in proteins: standard radii and volumes J. Mol. Biol. 290 1999 253 266 (Pubitemid 29308589)
34. P. Bernadó, and M. Blackledge A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering Biophys. J. 97 2009 2839 2845
35. V. Receveur-Brechot, and D. Durand How random are intrinsically disordered proteins? A small angle scattering perspective Curr. Protein Pept. Sci. 13 2012 55 75
36. R.P. Rambo, and J.A. Tainer Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law Biopolymers 95 2011 559 571
37. P. Bernadó, and E. Mylonas D.I. Svergun Structural characterization of flexible proteins using small-angle x-ray scattering J. Am. Chem. Soc. 129 2007 5656 5664 (Pubitemid 46697655)
38. G.L. Hura, and A.L. Menon J.A. Tainer Robust, high-throughput solution structural analyses by small angle x-ray scattering (SAXS) Nat. Methods 6 2009 606 612
39. B. Hammouda SANS from homogeneous polymer mixtures: a unified overview Polymer Characteristics 1993 Springer New York 87 133