The backbone conformational entropy of protein folding: Experimental measures from atomic force microscopy

Journal of Molecular Biology

Volumn 322, Issue 3, 2002, Pages 645-652

  Thompson, James B ^a   Hansma, Helen G ^a   Hansma, Paul K ^a   Plaxco, Kevin W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Configurational entropy; Worm like chain

Indexed keywords

POLYPROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; BETA SHEET; ENERGY; ENTROPY; MEASUREMENT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; STRENGTH;

EID: 0036385794     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00801-X     Document Type: Article

References (35)

1. Kellermayer, M. S., Smith, S. B., Granzier, H. L. & Bustamante, C. (1997). Folding-unfolding transitions in single titin molecules characterized with laser tweezers. Science, 276, 112-116.
2. Reif, M., Gautel, M., Oesterhelt, F., Fernandez, J. M. & Gaub, H. E. (1997). Reversible unfolding of individual titin immunoglobulin domains by AFM. Science, 276, 1109-1112.
3. Reif, M., Gautel, M., Schemmel, A. & Gaub, H. E. (1998). The mechanical stability of immunoglobin and fibronectin III domains in the muscle protein titin measured by atomic fore microscopy. Biophys. J. 75, 3008-3014.
4. Reif, M., Pascual, J., Saraste, M. & Gaub, H. E. (1999). Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundle. J. Mol. Biol. 286, 553-561.
5. Fisher, T. E., Oberhauser, A. F., Carrion-Vazquez, M., Marszalek, P. E. & Fernandez, J. M. (1999). The study of protein mechanics with the atomic force microscope. Trends Biochem. Sci. 24, 379-384.
6. Carrion-Vazquez, M., Oberhauser, A. F., Fowler, S. B., Marszalek, P. E., Broedel, S. E., Clarke, J. & Fernandez, J. M. (1999). Mechanical and chemical unfolding of a single protein: a comparison. Proc. Natl Acad. Sci. USA, 96, 3694-3699.
7. Carrion-Vazquez, M., Marszalek, P. E., Oberhauser, A. F. & Fernandez, J. M. (1999). Atomic force microscopy captures length phenotypes in single proteins. Proc. Natl Acad. Sci. USA, 96, 11288-11292.
8. Carrion-Vazquez, M., Oberhauser, A. F., Fisher, T. E., Marszalek, P. E., Li, H. B. & Fernandez, J. M. (2000). Mechanical design of proteins-studied by single-molecule force spectroscopy and protein engineering. Prog. Biophys. Mol. Biol. 74, 63-91.
9. Li, H. B., Oberhauser, A. F., Fowler, S. B., Clarke, J. & Fernandez, J. M. (2000). Atomic force microscopy reveals the mechanical design of a modular protein. Proc. Natl Acad. Sci. USA, 97, 6527-6531.
10. Yang, G. L., Cecconi, C., Baase, W. A., Vetter, I. R., Breyer, W. A., Haack, J. A. et al. (2000). Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proc. Natl Acad. Sci. USA, 97, 139-144.
11. Oberhauser, A. F., Marszadek, P. E., Erickson, H. P. & Fernandez, J. M. (1998). The molecular elasticity of tenascin, an extracellular matrix protein. Nature, 313, 181-185.
12. Craig, D., Krammer, A., Schulten, K. & Vogel, V. (2001). Comparison of the early stages of forced unfolding for fibronectin type III modules. Proc. Natl Acad. Sci. USA, 98, 5590-5595.
13. Best, R. B., Li, B., Steward, A., Daggett, V. & Clarke, J. (2001). Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81, 2344-2356.
14. Oroudjev, E., Soares, J., Arcidiacono, S., Thompson, J. B., Fossey, S. A. & Hansma, H. G. (2002). Segmented nanofibers of spider dragline silk: atomic force microscopy and single-molecule force spectroscopy. Proc. Natl Acad. Sci. USA, 99, 6460-6465.
15. Thompson, J. B., Kindt, J. H., Drake, B., Hansma, H. G., Morse, D. E. & Hansma, P. K. (2001). Bone indentation recovery time correlates with bond reforming time. Nature, 414, 773-776.
16. Pauling, L. & Corey, R. (1951). Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc. Natl Acad. Sci. USA, 37, 729-740.
17. Schellman, J. A. (1955). The stability of hydrogen-bonded peptide structure in aqueous solution. Trav. Lab. Carlsberg Ser. Chim. 29, 230-259.
18. Nemethy, G. & Scheraga, H. A. (1965). Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers, 3, 155-184.
19. D'Aquino, J. A., Gomez, J., Hilser, V. J., Lee, K. H., Amzel, L. M. & Freire, E. (1996). The magnitude of the backbone conformational entropy change in protein folding. Proteins: Struct. Funct. Genet. 25, 143-156.
20. Wang, J. & Purisima, E. (1996). Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through a novel free energy calculation. J. Am. Chem. Soc. 118, 995-1001.
21. Yang, D. & Kay, L. E. (1996). Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J. Mol. Biol. 263, 369-382.
22. Zhang, C., Cornette, J. L. & Delisi, C. (1997). Consistency in structural energetics of protein folding and peptide recognition. Protein Sci. 6, 1057-1064.
23. Privalov, P. L. (1997). Thermodynamics of protein folding. J. Chem. Thermodynam. 29, 447-474.
24. Yang, D., Mok, Y.-K., Forman-Kay, J. D., Farrow, N. A. & Kay, L. E. (1997). Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation. J. Mol. Biol. 272, 790-804.
25. Alexandrescu, A. T., Rathgeb-Szabo, K., Rumpel, K., Jahnke, W., Schulthess, T. & Kammerer, R. A. (1998). N-15 backbone dynamics of the S-peptide from ribonuclease A in its free and S-protein bound forms: toward a site-specific analysis of entropy changes upon folding. Protein Sci. 7, 389-402.
26. Viani, M. B., Schaffer, T. E., Paloczi, G. T., Pietrasanta, L., Smith, B. L., Thompson, J. B. et al. (1999). Fast imaging and fast force spectroscopy of single biopolymers with a new atomic force microscope designed for small cantilevers. Rev. Sci. Instrum. 70, 4300-4303.
27. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217.
28. Dyson, H. J. & Wright, P. E. (1998). Equilibrium NMR studies of unfolded and partially folded proteins. Nature Struct. Biol. 5, 499-503.
29. Millett, I. S., Doniach, S. & Plaxco, K. W. (2002). Towards a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Advan. Protein Chem. In press.
30. Makarov, D. E., Hansma, P. K. & Metiu, H. (2001). Kinetic Monte Carlo simulation of titin unfolding. J. Chem. Phys. 114, 9663-9673.
31. Creamer, T. P. (2001). Conformational entropy in protein folding. In Protein Folding and Stability (Murphy, K. P., ed.), 2nd edit., pp. 117-132, Humana Press, Totowa, NJ.
32. Yang, A. S. & Honig, B. (1995). Free-energy determinants of secondary structure formation 1. Alpha-helicies. J. Mol. Biol. 252, 351-365.
33. Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. (1994). Entropic elasticity of λ-phage DNA. Science, 265, 1599-1600.
34. Bouchiat, C., Wang, M. D., Allemand, J. F., Strick, T., Block, S. M. & Croquette, V. (1999). Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76, 409-413.
35. Pauling, L. & Corey, R. B. (1951). The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl Acad. Sci. USA, 37, 251-256.