Protein folding: Defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins

Protein Science

Volumn 14, Issue 3, 2005, Pages 602-616

  Maxwell, Karen L ^a   Wildes, David ^c   Zarrine Afsar, Arash ^a   De Los Rios, Miguel A ^d   Brown, Andrew G ^e   Friel, Claire T ^f   Hedberg, Linda ^g   Horng, Jia Cherng ^h   Bona, Diane ^a   Miller, Erik J ^c   Vallée Bélisle, Alexis ⁱ   Main, Ewan R G ^e   Bemporad, Francesco ^j   Qiu, Linlin ^k   Teilum, Kaare ^l   Vu, Ngoc Diep ^m   Edwards, Aled M ^a,b   Ruczinski, Ingo ⁿ   Poulsen, Flemming M ^l   Kragelund, Birthe B ^l   Michnick, Stephen W ⁱ   Chiti, Fabrizio ^j   Bai, Yawen ^m   Hagen, Stephen J ^k   Serrano, Luis ^o   Oliveberg, Mikael ^g   Raleigh, Daniel P ^h   Wittung Stafshede, Pernilla ^p   Radford, Sheena E ^f   Jackson, Sophie E ^e   Sosnick, Tobin R ^q   Marqusee, Susan ^c   Davidson, Alan R ^a   Plaxco, Kevin W ^d   more..

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f UNIVERSITY OF LEEDS   (United Kingdom)

^g UMEÅ UNIVERSITY   (Sweden)

^h STONY BROOK UNIVERSITY   (United States)

ⁱ UNIVERSITÉ DE MONTRÉAL   (Canada)

^j UNIVERSITY OF FLORENCE   (Italy)

^k Department of Protein Chemistry ^*  (United States)

^l INSTITUTE OF MOLECULAR BIOLOGY   (Armenia)

^m NATIONAL CANCER INSTITUTE   (United States)

ⁿ JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^o EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^p RICE UNIVERSITY   (United States)

^q UNIVERSITY OF CHICAGO   (United States)

more..

Author keywords

Chevron plots; Equilibrium; Kinetics; Protein folding; Two state

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOASSAY; CONSENSUS; EXPERIMENT; KINETICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS;

BIOCHEMISTRY; DATA INTERPRETATION, STATISTICAL; KINETICS; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN RENATURATION; PROTEINS;

EID: 20044363782     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041205405     Document Type: Article

References (47)

1. Capaldi, A.P., Kleanthous, C., and Radford, S.E. 2002. Im7 folding mechanism: Misfolding on a path to the native state. Nat. Struct. Biol. 9: 209-216.
2. Chiti, F., Taddei, N., van Nuland, N.A., Magherini, F., Stefani, M., Ramponi, G., and Dobson, C.M. 1998. Structural characterization of the transition state for folding of muscle acylphosphatase. J. Mol. Biol. 283: 893-903.
3. de los Rios, M. A., and Plaxco, K.W. 2005. Apparent Debye-Huckel electrostatic effects in the folding of a simple, single domain protein. Biochemistry (in press).
4. Ferguson, N., Capaldi, A.P., James, R., Kleanthous, C., and Radford, S.E. 1999. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 286: 1597-1608.
5. Friel, C.T., Capaldi, A.P., and Radford, S.E. 2003. Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: Similarities and differences in the folding of homologous proteins. J. Mol. Biol. 326: 293-305.
6. Grantcharova, V.P. and Baker, D. 1997. Folding dynamics of the src SH3 domain. Biochemistry 36: 15685-15692.
7. Hamill, S.J., Meekhof, A.E., and Clarke, J. 1998. The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Biochemistry 37: 8071-8079.
8. †. Proc. Natl. Acad. Sci. 101: 7606-7611.
9. Ivankov, D.N., Alm, E., Plaxco, K.W., Baker, D., and Finkelstein, A.V. 2003. Contact order revisited: The influence of protein size on folding rates. Protein Sci. 12: 2057-2062.
10. Jackson, S.E. 1998. How do small single-domain proteins fold? Fold. Des. 3: R81-R91.
11. Jackson, S.E. and Fersht, A.R. 1991a. Folding of chymotrypsin inhibitor-2, 1: Evidence for a two-state transition. Biochemistry 30: 10428-10435.
12. _. 1991b. Folding of chymotrypsin inhibitor-2, 2: Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition-state of folding. Biochemistry 30: 10436-10443.
13. Jones, K. and Wittung-Stafshede, P. 2003. The largest protein observed to fold by two-state kinetic mechanism does not obey contact-order correlation. J. Am. Chem. Soc. 125: 9606-9607.
14. Jones, K., Guidry, J., and Wittung-Stafshede, P. 2001. Characterization of surface antigen from Lyme disease spirochete Borrelia burgdorferi. Biochem. Biophys. Res. Commun. 289: 389-394.
15. Kamagata, K., Arai, M., and Kuwajima, K. 2004. Unification of the folding mechanisms of non-two-state and two-state proteins. J. Mol. Biol. 339: 951-965.
16. Krantz, B.A. and Sosnick, T.R. 2000. Distinguishing between two-state and three-state models for ubiquitin folding. Biochemistry 39: 11696-11701.
17. Krantz, B.A., Srivastava, A.K., Nauli, S., Baker, D., Sauer, R.T., and Sosnick, T.R. 2002. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nat. Struct. Biol. 9: 458-463.
18. Kuhlman, B., Luisi, D.L., Evans, P.A., and Raleigh, D.P. 1998. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the ribosomal protein L9. J. Mol. Biol. 284: 1661-1670.
19. Main, E.R., Fulton, K.F., and Jackson, S.E. 1999. Folding pathway of FKBP12 and characterisation of the transition state. J. Mol. Biol. 291: 429-444.
20. Makhatadze, G.I. 1999. Thermodynamics of protein interactions with urea and guanidinium hydrochloride. J. Phys. Chem. B 103: 4781-4785.
21. Maxwell, K.L. and Davidson, A.R. 1998. Mutagenesis of a buried polar interaction in an SH3 domain: Sequence conservation provides best prediction of stability effects. Biochemistry 37: 16172-16182.
22. Maxwell, K.L., Bona, D., Liu, C., Arrowshmith, C.H., and Edwards, A.M. 2003. Refolding out of guanidine hydrochloride is an effective approach for highthroughput structural studies of small proteins. Protein Sci. 12: 2073-2080.
23. Miller, E.J., Fischer, K.F., and Marqusee, S. 2002. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. 99: 10359-10363.
24. Mogensen, J.E., Ipsen, H., Holm, J., and Otzen, D.E. 2004. Elimination of a misfolded folding intermediate by a single point mutation. Biochemistry 43: 3357-3367.
25. Otzen, D.E., Kristensen, O., Proctor, M., and Oliveberg, M. 1999. Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots. Biochemistry 38: 6499-6511.
26. Pace, C.N. and Shaw, K.L. 2000. Linear extrapolation method of analyzing solvent denaturation curves. Proteins 4 (Suppl.): 1-7.
27. Plaxco, K.W., Guijarro, J.I., Morton, C.J., Pitkeathly, M., Campbell, I.D., and Dobson, C.M. 1998a. The folding kinetics and thermodynamics of the FynSH3 domain. Biochemistry 37: 2529-2537.
28. Plaxco, K.W., Simons, K.T., and Baker, D. 1998b. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
29. Plaxco, K.W., Simons, K.T., Ruczinski, I., and Baker, D. 2000. Sequence, stability, topology and length: The determinants of two-state protein folding kinetics. Biochemistry 39: 11177-11183.
30. Pozdnyakova, I. and Wittung-Stafshede, P. 2001. Copper binding before polypeptide folding speeds up formation of active holo: Pseudomonas aeruginosa azurin. Biochemistry 40: 13728-13733.
31. Pozdnyakova, I., Guidry, J., and Wittung-Stafshede, P. 2002. Studies of Pseudomonas aeruginosa azurin mutants: Cavities in β-barrel do not affect refolding speed. Biophys. J. 82: 2645-2651.
32. Qiu, L.L., Pabit, S.A., Roitberg, A.E., and Hagen, S.J. 2002. Smaller and faster: The 20-residue Trp-cage protein folds in 4 μs. J. Am. Chem. Soc. 124: 12952-12953.
33. Raschke, T.M., Kho, J., and Marqusee, S. 1999. Confirmation of the hierarchical folding of RNase H: A protein engineering study. Nat. Struct. Biol. 6: 825-831.
34. Santoro, M.M. and Bolen, D.W. 1988. Unfolding free energy changes determined by the linear extrapolation method, 1: Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants. Biochemistry 27: 8063-8068.
35. Sato, S. 2002. "Folding of ribosomal protein L9 and its isolated N- and C-terminal domains." Ph.D. thesis, Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY.
36. Sato, S. and Raleigh, D.P. 2002. pH-dependent stability and folding kinetics of a protein with an unusual α-β topology: The C-terminal domain of the ribosomal protein L9. J. Mol. Biol. 318: 571-582.
37. Sato, S., Xiang, S., and Raleigh, D.P. 2001. On the relationship between protein stability and folding kinetics: A comparative study of the N-terminal domains of RNase HI, E. coli and Bacillus stearothermophilus L9. J. Mol. Biol. 312: 569-577.
38. Scalley, M.L., Yi, Q., Gu, H.D., McCormack, A., Yates, J.R., and Baker, D. 1997. Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L. Biochemistry 36: 3373-3382.
39. Silow, M. and Oliveberg, M. 1997. Transient aggregates in protein folding are easily mistaken for folding intermediates. Proc. Natl. Acad. Sci. 94: 6084-6086.
40. Spector, S. and Raleigh, D.P. 1999. Submillisecond folding of the peripheral subunit-binding domain. J. Mol. Biol. 293: 763-768.
41. Taddei, N., Stefani, M., Magherini, F., Chiti, F., Modesti, A., Raugei, G., and Ramponi, O. 1996. Looking for residues involved in the muscle acylphosphatase catalytic mechanism and structural stabilization: Role of Asn 41: Thr 42 and Thr 46. Biochemistry 35: 7077-7083.
42. Thomsen, J.K., Kragelund, B.B., Teilum, K., Knudsen, J., and Poulsen, F.M. 2002. Transient intermediary states with high and low folding probabilities in the apparent two-state folding equilibrium of ACBP at low pH. J. Mol. Biol. 318: 805-814.
43. Vallée-Bélisle, A., Turcotte, J.-F., and Michnick, S.W. 2004. raf RBD and ubiquitin proteins share similar folds, folding rates and mechanisms despite having unrelated amino acid sequences. Biochemistry 43: 8447-8458.
44. Viguera, A.R., Wilmanns, M., and Serrano, L. 1996. Different folding transition states could result in the some native structure. Nat. Struct. Biol. 3: 874-880.
45. Villegas, V., Martinez, J.C., Aviles, F.X., and Serrano, L. 1998. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283: 1027-1036.
46. Went, H.M., Benitez-Cardoza, C.B., and Jackson, S.E. 2004. Is there an intermediate populated on the folding pathway of ubiquitin? FEBS Lett. 567: 333-338.
47. Zitzewitz, J.A., Bilsel, O., Luo, J.B., Jones, B.E., and Matthews, C.R. 1995. Probing the folding mechanisms of a leucine-zipper peptide by stopped-flow circular-dichroism spectroscopy. Biochemistry 34: 12812-12819.