Determination of protein complex stoichiometry through multisignal sedimentation velocity experiments

Analytical Biochemistry

Volumn 407, Issue 1, 2010, Pages 89-103

  Padrick, Shae B ^a   Deka, Ranjit K ^b   Chuang, Jacinta L ^a   Wynn, R Max ^a,b   Chuang, David T ^a,b   Norgard, Michael V ^b   Rosen, Michael K ^a,b   Brautigam, C A ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

Analytical ultracentrifugation; Arp2 3 complex; Human lactoferrin; Pyruvate dehydrogenase complex; Sedimentation velocity

Indexed keywords

CENTRIFUGATION; MACROMOLECULES; PROTEINS; SEDIMENTATION; VELOCITY;

ANALYTICAL ULTRACENTRIFUGATION; ARP2/3 COMPLEX; HUMAN LACTOFERRIN; PYRUVATE DEHYDROGENASE COMPLEX; SEDIMENTATION VELOCITIES;

STOICHIOMETRY;

BINDING PROTEIN; CORTACTIN; DIHYDROLIPOAMIDE DEHYDROGENASE; LACTOFERRIN; PROTEIN; SUGAR; WISKOTT ALDRICH SYNDROME PROTEIN;

ACTIN FILAMENT; ARTICLE; CALCULATION; HOST PATHOGEN INTERACTION; HUMAN; METABOLISM; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DETERMINATION; PROTEIN PROTEIN INTERACTION; SEDIMENTATION RATE; SPECTROSCOPY; STOICHIOMETRY; TREPONEMA PALLIDUM;

EID: 77956884570     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2010.07.017     Document Type: Article

References (43)

1. Balbo A., Minor K.H., Velikovsky C.A., Mariuzza R.A., Peterson C.B., Schuck P. Studying multiprotein complexes by multisignal sedimentation velocity analytical ultracentrifugation. Proc. Natl. Acad. Sci. USA 2005, 102:81-86.
2. Brown P.H., Schuck P. Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys. J. 2006, 90:4651-4661.
3. Dam J., Schuck P. Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory. Biophys. J. 2005, 89:651-666.
4. Dam J., Velikovsky C.A., Mariuzza R.A., Urbanke C., Schuck P. Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s). Biophys. J. 2005, 89:619-634.
5. Howlett G.J., Minton A.P., Rivas G. Analytical ultracentrifugation for the study of protein association and assembly. Curr. Opin. Chem. Biol. 2006, 10:430-436.
6. Schuck P. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal. Biochem. 2003, 320:104-124.
7. Gilbert G.A., Jenkins R.C.L. Boundary problems in the sedimentation and electrophoresis of complex systems in rapid reversible equilibrium. Nature 1956, 177:853-854.
8. Deka R.K., Brautigam C.A., Tomson F.L., Lumpkins S.B., Tomchick D.R., Machius M., Norgard M.V. Crystal structure of the Tp34 (TP0971) lipoprotein of Treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin. J. Biol. Chem. 2007, 282:5944-5958.
9. Padrick S.B., Cheng H.-C., Ismail A.M., Panchal S.C., Doolittle L.K., Kim S., Skehan B.M., Umetani J., Brautigam C.A., Leong J.M., Rosen M.K. Hierarchical regulation of WASP/WAVE proteins. Mol. Cell 2008, 32:426-438.
10. Brautigam C.A., Wynn R.M., Chuang J.L., Chuang D.T. Subunit and catalytic component stoichiometries of an in vitro reconstituted human pyruvate dehydrogenase complex. J. Biol. Chem. 2009, 284:13086-13098.
11. Brautigam C.A., Wynn R.M., Chuang J.L., Machius M., Tomchick D.R., Chuang D.T. Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex. Structure 2006, 14:611-621.
12. Ciszak E.M., Makal A., Hong Y.S., Vettaikkorumakankauv A.K., Korotchkina L.G., Patel M.S. How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex. J. Biol. Chem. 2006, 281:648-655.
13. Schuck P. Size distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 2000, 78:1606-1619.
14. Schuck P., Perugini M.A., Gonzales N.R., Howlett G.J., Schubert D. Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophys. J. 2002, 82:1096-1111.
15. +/NADH binding and the structural basis of disease-causing mutations. J. Mol. Biol. 2005, 350:543-552.
16. Jabeen T., Sharma S., Singh N., Bhushan A., Singh T.P. Structure of the zinc-saturated C-terminal lobe of bovine lactoferrin at 2.0Å resolution. Acta Crystallogr. D 2005, 61:1107-1115.
17. Cole J.L., Lary J.W., Moody T.P., Laue T.M. Analytical ultracentrifugation: sedimentation velocity and sedimentation equilibrium. In Vitro Techniques 2008, vol. 1:143-179. Academic Press, San Diego. J.J. Correia, H.W.I. Detrich (Eds.).
18. Pace C.N., Vajdos F., Fee L., Grimsley G., Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 1995, 4:2411-2423.
19. Schuck P., Demeler B. Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys. J. 1999, 76:2288-2296.
20. Laue T.M., Shah B.D., Ridgeway R.M., Pelletier S.L. Computer-aided interpretation of analytical sedimentation data for proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 90-125. Royal Society of Chemistry, Cambridge, UK. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
21. P.H. Brown, A. Balbo, P. Schuck, Characterizing protein-protein interactions by sedimentation velocity analytical ultracentrifugation, Curr. Protoc. Immunol. (2008) unit 18.15.
22. Schuck P. Diffusion of the reaction boundary of rapidly interacting macromolecules in sedimentation velocity. Biophys. J. 2010, 98:2741-2751.
23. Smolle M., Lindsay J.G. Molecular architecture of the pyruvate dehydrogenase complex: bridging the gap. Biochem. Soc. Trans. 2006, 34:815-818.
24. Smolle M., Prior A.E., Brown A.E., Cooper A., Byron O., Lindsay J.G. A new level of architectural complexity in the human pyruvate dehydrogenase complex. J. Biol. Chem. 2006, 281:19772-19780.
25. 4+. J. Am. Chem. Soc. 1994, 116:7889-7890.
26. Teuwissen B., Masson P.L., Osinski P., Heremans J.F. Metal-combining properties of human lactoferrin. Eur. J. Biochem. 1972, 31:239-245.
27. Beltzner C.C., Pollard T.D. Identification of functionally important residues of Arp2/3 complex by analysis of homology models from diverse species. J. Mol. Biol. 2004, 336:551-565.
28. Boczkowska M., Rebowski G., Petoukhov M.V., Hayes D.B., Svergun D.I., Dominguez R. X-ray scattering study of activated Arp2/3 complex with bound actin-WCA. Structure 2008, 16:695-704.
29. Kreishman-Dietrick M., Goley E.D., Burdine L., Denison C., Egile C., Li R., Murali N., Kodadek T.J., Welch M.D., Rosen M.K. NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein. Biochemistry 2005, 44:15247-15256.
30. Marchand J.B., Kaiser D.A., Pollard T.D., Higgs H.N. Interaction of WASP/Scar proteins with actin and vertebrate Arp2/3 complex. Nat. Cell Biol. 2001, 3:76-82.
31. Weaver A.M., Heuser J.E., Karginov A.V., Lee W.L., Parsons J.T., Cooper J.A. Interaction of cortactin and N-WASP with Arp2/3 complex. Curr. Biol. 2002, 12:1270-1278.
32. Pierce M.M., Raman C.S., Nall B.T. Isothermal titration calorimetry of protein-protein interactions. Methods 1999, 19:213-221.
33. 2+-ATPase as an example. Nat. Protoc. 2008, 3:1782-1795.
34. ++-ATPase and ExbB. J. Biol. Phys. 2007, 33:399-419.
35. Bailey M.F., Davidson B.E., Minton A.P., Sawyer W.H., Howlett G.J. The effect of self-association on the interaction of the Escherichia coli regulatory protein TyrR with DNA. J. Mol. Biol. 1996, 263:671-684.
36. Burgess B.R., Schuck P., Garboczi D.N. Dissection of merozoite surface protein 3, a representative of a family of Plasmodium falciparum surface proteins, reveals an oligomeric and highly elongated molecule. J. Biol. Chem. 2005, 280:37236-37245.
37. Minton A.P. Alternative strategies for the characterization of associations in multicomponent solutions via measurement of sedimentation equilibrium. Prog. Colloid Polym. Sci. 1997, 107:11-19.
38. Ucci J.W., Cole J.L. Global analysis of non-specific protein-nucleic interactions by sedimentation equilibrium. Biophys. Chem. 2004, 108:127-140.
39. Yikilmaz E., Rouault T.A., Schuck P. Self-association and ligand induced conformational changes of iron regulatory proteins 1 and 2. Biochemistry 2005, 44:8470-8478.
40. Houtman J.C.D., Yamaguchi H., Barda-Saad M., Braiman A., Bowden B., Appella E., Schuck P., Samelson L.E. Oligomerization of signaling complexes by the multipoint binding of GRB2 to both LAT and SOS1. Nat. Struct. Mol. Biol. 2006, 13:798-805.
41. Jensen J.K., Dolmer K., Schar C., Gettins P.G.W. Receptor-associated protein (RAP) has two high-affinity binding sites for the low-density lipoprotein receptor-related protein (LRP): consequences for the chaperone functions of RAP. Biochem. J. 2009, 421:273-282.
42. Minor K.H., Schar C.R., Blouse G.E., Shore J.D., Lawrence D.A., Schuck P., Peterson C.B. A mechanism for assembly of complexes of vitronectin and plasminogen activator inhibitor-1 from sedimentation velocity analysis. J. Biol. Chem. 2005, 280:28711-28720.
43. Barda-Saad M., Shirasu N., Pauker M.H., Hasan N., Perl O., Balbo A., Yamaguchi H., Houtman J.C.D., Appella E., Schuck P., Samelson L.E. Cooperative interactions at the SLP-76 complex are critical for actin polymerization. EMBO J. 2010, 29:2315-2328.