Binary and ternary aggregation within tethered protein constructs

Biophysical Journal

Volumn 90, Issue 8, 2006, Pages 2930-2937

  Wei, Yuan Yang ^a   Gruebele, Martin ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; MONOMER;

ARTICLE; CONCENTRATION (PARAMETERS); DIMERIZATION; ENERGY; FLOW KINETICS; KINETICS; MATHEMATICAL MODEL; MOLECULAR MODEL; MOLECULAR SIZE; PROTEIN AGGREGATION; PROTEIN FOLDING; PROTEIN STABILITY; QUANTITATIVE ANALYSIS; SEDIMENTATION; THERMODYNAMICS;

EID: 33646181198     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.075846     Document Type: Article

References (26)

1. Chen, S., F. A. Ferrone, and R. Wetzel. 2002. Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation. Proc. Natl. Acad. Sci. USA. 99:11884-11889.
2. Dobson, C. M. 2003. Protein folding and misfolding. Nature. 426:884-890.
3. Ferrone, F. 1999. Analysis of protein aggregation kinetics. Methods Enzymol. 309:256-274.
4. Come, J. H., P. E. Fraser, and P. T. Lansbury. 1993. A kinetic model for amyloid formation in the prion diseases: importance of seeding. Proc. Natl. Acad. Sci. USA. 90:5959-5963.
5. Silow, M., and M. Oliveberg. 1997. Transient aggregates in protein folding are easily mistaken for folding intermediates. Proc. Natl. Acad. Sci. USA. 94:6084-6086.
6. Jacob, M., T. Schindler, J. Balbach, and F. X. Schmid. 1997. Diffusion control in an elementary protein folding reaction. Proc. Natl. Acad. Sci. USA. 94:5622-5627.
7. Yang, W. Y., and M. Gruebele. 2003. Folding at the speed limit. Nature. 423:193-197.
8. Lu, J., and K. B. Hall. 1997. Thermal unfolding of the N-terminal RNA binding domain of the human U1A protein studied by differential scanning calorimetry. Biophys. Chem. 64:111-119.
9. Silow, M., Y. Tan, A. R. Fersht, and M. Oliveberg. 1999. Formation of short-lived protein aggregates directly from the coil in two-state folding. Biochemistry. 38:13006-13012.
10. Otzen, D. E., S. Miron, M. Akke, and M. Oliveberg. 2004. Transient aggregation and stable dimerization induced by introducing an Alzheimer sequence into a water-soluble protein. Biochemistry. 43:12964-12978.
11. Levy, Y., P. G. Wolynes, and J. N. Onuchic. 2004. Protein topology determines binding mechanism. Proc. Natl. Acad. Sci. USA. 101:511-516.
12. Nolan, S. J., J. C. Shiels, J. B. Tuite, K. L. Cecere, and A. M. Baranger. 1999. Recognition of an essential adenine at a protein-RNA interface: comparison of the contributions of hydrogen bonds and a stacking interaction. J. Am. Chem. Soc. 121:8951-8952.
13. Oliveberg, M. 1998. Alternative explanations for "multistate" kinetics in protein folding: transient aggregation and changing transition-state ensembles. Acc. Chem. Res. 31:765-772.
14. Krieger, F., B. Fierz, O. Bieri, M. Drewello, and T. Kiefhaber. 2003. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J. Mol. Biol. 332:265-274.
15. Kubelka, J., J. Hofrichter, and W. A. Eaton. 2004. The protein folding 'speed limit'. Curr. Opin. Struct. Biol. 14:76-88.
16. Chang, I. J., J. C. Lee, J. R. Winkler, and H. B. Gray. 2003. The protein- folding speed limit: intrachain diffusion times set by electron-transfer rates in denatured Ru(NH3)(5)(His-33)-Zn-cytochrome c. Proc. Natl. Acad. Sci. USA. 100:3838-3840.
17. Camacho, C. J., and D. Thirumalai. 1995. From minimal models to real proteins: time scales for folding kinetics. J. de Physique I. 5:1457-1467.
18. Szabo, A., K. Schulten, and Z. Schulten. 1980. The first passage time approach to diffusion controlled reactions. J. Chem. Phys. 72:4350-4357.
19. Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743-747.
20. Xu, X., and D. M. Leitner. 2003. Anomalous diffusion of vibrational energy in proteins. J. Chem. Phys. 119:12673-12679.
21. Muñoz, V., E. R. Henry, J. Hofrichter, and W. A. Eaton. 1998. A statistical mechanical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. USA. 95:5872-5879.
22. Yang, W., E. Larios, and M. Gruebele. 2003. On the extended β-conformational propensity of polypeptides at high temperature. J. Am. Chem. Soc. 125:16220-16227.
23. Tanford, C. 1970. Protein denaturation. Adv. Protein Chem. 24:1-95.
24. Levy, Y., S. S. Cho, T. Shen, J. N. Onuchic, and P. G. Wolynes. 2005. Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc. Natl. Acad. Sci. USA. 102:2373-2378.
25. Dima, R. I., and D. Thirumalai. 2002. Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci. 11:1036-1049.
26. Gsponer, J., U. Haberthuer, and A. Caflisch. 2003. The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc. Natl. Acad. Sci. USA. 100:5154-5159.