The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity

Methods

Volumn 54, Issue 1, 2011, Pages 16-30

  Zhao, Huaying ^a   Balbo, Andrea ^b   Brown, Patrick H ^b   Schuck, Peter ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING   (United States)

Author keywords

Bayesian analysis; Effective particle theory; Gilbert Jenkins theory; Protein interactions; Sedimentation coefficient distributions; Sedimentation velocity analysis

Indexed keywords

CHYMOTRYPSIN A; SOYBEAN TRYPSIN INHIBITOR;

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; EFFECTIVE PARTICLE THEORY; ENTROPY; ISOTHERM; MATHEMATICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN INTERACTION; SEDIMENTATION RATE;

BAYES THEOREM; CHYMOTRYPSIN; ENTROPY; KINETICS; MODELS, CHEMICAL; SOYBEAN PROTEINS; TRYPSIN INHIBITORS; ULTRACENTRIFUGATION;

GLYCINE MAX;

EID: 79955638852     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2011.01.010     Document Type: Article

References (59)

1. Svedberg T., Pedersen K.O. The Ultracentrifuge 1940, Oxford University Press, London.
2. Schwert G.W. J. Biol. Chem. 1949, 179:655-664.
3. Oncley J.L., Ellenbogen E., Gitlin D., Gurt F.R.N. J. Phys. Chem. 1952, 56:85-92.
4. von Hippel P.H., Waugh D.F. J. Am. Chem. Soc. 1955, 77:4311-4319.
5. Schachman H.K. Ultracentrifugation in Biochemistry 1959, Academic Press, New York.
6. Balbo A., Minor K.H., Velikovsky C.A., Mariuzza R., Peterson C.B., Schuck P. Proc. Natl Acad. Sci. USA 2005, 102:81-86.
7. Houtman J.C., Yamaguchi H., Barda-Saad M., Braiman A., Bowden B., Appella E., Schuck P., Samelson L.E. Nat. Struct. Mol. Biol. 2006, 13:798-805.
8. Schuck P. Protein Interactions: Biophysical Approaches for the Study of Complex Reversible Systems 2007, 469-518. Springer, New York. P. Schuck (Ed.).
9. Barda-Saad M., Shirasu N., Pauker M.H., Hassan N., Perl O., Balbo A., Yamaguchi H., Houtman J.C., Appella E., Schuck P., Samelson L.E. EMBO J. 2010, 29:2315-2328.
10. Padrick S.B., Deka R.K., Chuang J.L., Wynn R.M., Chuang D.T., Norgard M.V., Rosen M.K., Brautigam C.A. Anal. Biochem. 2010, 407:89-103.
11. Tanford C., Reynolds J.A. Biochim. Biophys. Acta 1976, 457:133-170.
12. Schubert D., Schuck P. Progr. Colloid. Polym. Sci. 1991, 86:12-22.
13. Howlett G.J. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 470-483. The Royal Society of Chemistry, Cambridge, UK. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
14. le Maire M., Arnou B., Olesen C., Georgin D., Ebel C., Moller J.V. Nat. Protoc. 2008, 3:1782-1795.
15. Svitel J., Boukari H., Van Ryk D., Willson R.C., Schuck P. Biophys. J. 2007, 92:1742-1758.
16. Schuck P., Zhao H. Methods Mol. Biol. 2010, 627:15-54.
17. Steiner R.F. Arch. Biochem. Biophys. 1954, 49:400-416.
18. Schuck P. Anal. Biochem. 2003, 320:104-124.
19. Lamm O. Ark. Mat. Astr. Fys. 1929, 21B(2):1-4.
20. Fujita H. Foundations of Ultracentrifugal Analysis 1975, John Wiley & Sons, New York.
21. Schuck P. Biophys. J. 1998, 75:1503-1512.
22. Stafford W.F., Sherwood P.J. Biophys. Chem. 2004, 108:231-243.
23. Urbanke C., Witte G., Curth U. Protein-Ligand Interactions: Methods and Applications 2005, vol. 305:101-113. Humana Press, Totowa.
24. Dam J., Velikovsky C.A., Mariuzza R., Urbanke C., Schuck P. Biophys. J. 2005, 89:619-634.
25. B. Kindler, Ph.D. Thesis. University Hannover, Hannover, Germany, 1997.
26. Goad W.B., Cann J.R. Ann. NY Acad. Sci. 1969, 164:192-225.
27. Claverie J.-M., Dreux H., Cohen R. Biopolymers 1975, 14:1685-1700.
28. Gilbert G.A., Gilbert L.M. Biochem. Soc. Trans. 1980, 8:520-522.
29. Cox D.J., Dale R.S. Protein-protein interactions 1981, Wiley, New York. C. Frieden, L.W. Nichol (Eds.).
30. Schuck P. Anal. Biochem. 2010, 401:280-287.
31. Taraporewala Z.F., Schuck P., Ramig R.F., Silvestri L., Patton J.T. J. Virol. 2002, 76:7082-7093.
32. Brown P.H., Balbo A., Schuck P. Eur. Biophys. J. 2009, 38:1079-1099.
33. Zhao H., Brown P.H., Balbo A., Fernandez-Alonso Mdel C., Polishchuck N., Chaudhry C., Mayer M.L., Ghirlando R., Schuck P. Macromol. Biosci. 2010, 10:736-745.
34. Brautigam C.A. Methods 2011, 54:4-15.
35. Werner W.E., Schachman H.K. J. Mol. Biol. 1989, 206:221-230.
36. Gabrielson J.P., Arthur K.K. Methods 2011, 54:83-91.
37. Dam J., Schuck P. Methods Enzymol. 2004, 384:185-212.
38. Schuck P. Biophys. J. 2000, 78:1606-1619.
39. Brown P.H., Schuck P. Biophys. J. 2006, 90:4651-4661.
40. Schuck P. Eur. Biophys. J. 2010, 39:1261-1275.
41. Schuck P. Biophys. J. 2010, 98:2741-2751.
42. Padrick S.B., Brautigam C.A. Methods 2011, 54:39-55.
43. Gilbert G.A., Jenkins R.C. Nature 1956, 177:853-854.
44. Gilbert L.M., Gilbert G.A. Methods Enzymol 1978, 48:195-211.
45. P. Schuck, Sedimentation patterns of rapidly reversible protein interactions, Biophys. J., in press.
46. Brown P., Schuck P. Comp. Phys. Comm. 2007, 178:105-120.
47. S.E. Harding, P. Schuck, A.S. Abdelhameed, G. Adams, M.S. Kok, G.A. Morris, Methods, this issue, doi:10.1016/j.ymeth.2011.01.009.
48. Pavlov G.M., Perevyazko I.Y., Okatova O.V., Schubert U.S. Methods 2011, 54:124-135.
49. Schuck P. Biophys. J. 2010, 98:2005-2013.
50. P. Schuck, 2010. Available from: <>. http://sedfitsedphat.nibib.nih.gov/tools/Reaction%20Boundary%20Movies/Forms/AllItems.aspx.
51. Zahnley J.C. J. Biol. Chem. 1975, 250:7879-7884.
52. Brown P., Balbo A., Schuck P. Biomacromolecules 2007, 8:2011-2024.
53. Vistica J., Dam J., Balbo A., Yikilmaz E., Mariuzza R.A., Rouault T.A., Schuck P. Anal. Biochem. 2004, 326:234-256.
54. Zhi L., Mans J., Paskow M.J., Brown P.H., Schuck P., Jonjic S., Natarajan K., Margulies D.H. Biochemistry 2010, 49:2443-2453.
55. P. Schuck, in: 18th International AUC Conference, Uppsala, Sweden, 2009.
56. Brown P.H., Balbo A., Schuck P. AAPS J 2008, 10:481-493.
57. Houtman J.C., Brown P.H., Bowden B., Yamaguchi H., Appella E., Samelson L.E., Schuck P. Protein Sci. 2007, 16:30-42.
58. Brown P.H., Balbo A., Schuck P. Curr. Protoc. Immunol. 2008, (Unit 18 15, Chapter 18).
59. Balbo A., Zhao H., Brown P.H., Schuck P. J. Vis. Exp. 2009.