A new view of protein folding kinetics replaces the idea of ‘folding pathways’ with the broader notions of energy landscapes and folding funnels. New experiments are needed to explore them.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Baldwin, R.L. Matching speed and stability. Nature 369, 183–184 (1994).
Baldwin, R.L. The nature of protein folding pathways: The classical versus the new view. J. Biomolec. NMR 5, 103–109 (1995).
Anfinsen, C.B., Haber, E., Sela, M. & White, F.H. Jr. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. USA 47, 1309–1314 (1961).
Anfinsen, C.B. Principles that govern the folding of protein chains. Science 181, 223–230 (1973).
Levinthal, C. Are there pathways for protein folding? J. Chim. Phys. 65, 44–45 (1968).
Levinthal, C. in Mossbauer Spectroscopy in Biological Systems. Proceedings of a meeting held at Allerton house, Monticello, Illinois. (eds P. Debrunner, J. Tsibris, & E. Munck) 22–24 (University of Illinois Press, Urbana, Illinois, 1969).
Wetlaufer, D.B. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc. Natl. Acad. Sci. USA 70, 697–701 (1973).
Dill, K.A. Theory for the folding and stability of globular proteins. Biochemistry 24, 1501–1509 (1985).
Zwanzig, R., Szabo, A. & Bagchi, B. Levinthal's paradox. Proc. Natl. Acad. Sci. USA 89, 20–22 (1992).
Ikai, A. & Tanford, C. Kinetic evidence for incorrectly folded intermediate states in the refolding of denatured proteins. Nature 230, 100–102 (1971).
Tsong, T.Y., Baldwin, R.L. & Elson, E.L. The sequential unfolding of ribonucleases A: Detection of a fast initial phase in the kinetics of unfolding. Proc. Natl. Acad. Sci. USA 68, 2712–2715 (1971).
Creighton, T.E. Conformational restrictions on the pathway of folding and unfolding of the pancreatic trypsin inhibitor. J. Mol. Biol. 113, 275–293 (1977).
Creighton, T.E. Experimental studies of protein folding and unfolding. Prog. Biophys. Mol. Biol. 33, 231–297 (1978).
Weissman, J.S. & Kim, P.S. Reexamination of the folding of BPTI: Predominance of native intermediates. Science 253, 1386–1393 (1991).
Weissman, J.S. & Kim, P.S. Kinetic role of nonnative species in the folding of bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 89, 9900–9904 (1992).
Brandts, J.F., Halvorson, H.R. & Brennan, M. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14, 4953–4963 (1975).
Hagerman, P.J. Kinetic analysis of the reversible folding reactions of small proteins: Application to the folding of lysozyme and cytochrome c. Biopolymers 16, 731–747 (1977).
Schmid, F.X. & Baldwin, R.L. Acid catalysis of the formation of the slow-folding species of RNase A: Evidence that the reaction is proline isomerization. Proc. Natl. Acad. Sci. USA 75, 4764–4768 (1978).
Kim, P.S. & Baldwin, R.L. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Ann. Rev. Biochem. 51, 459–489 (1982).
Kim, P.S. & Baldwin, R.L. Intermediates in the folding reactions of small proteins. Annu. Rev. Biochem. 59, 631–660 (1990).
Mann, C.J., Shao, X. & Matthews, C.R. Characterization of the slow folding reactions of trp aporepressor from Escherichia coli by mutational analysis of prolines and catalysis by a peptidyl-prolyl isomerase. Biochemistry 34, 14573–14580 (1995)
Englander, S.W. & Poulsen, A. Hydrogen-tritium exchange of the random chain polypeptide. Biopolymers 7, 329–393 (1969).
Woodward, C.K. & Rosenberg, A. Studies of hydrogen exchange in proteins. VI. Urea effects on RNase hydrogen exchange kinetics leading to a general model for hydrogen exchange from folded proteins. J. Biol. Chem. 246, 4114–4121 (1971).
Englander, S.W., Downer, N.W. & Teitelbaum, H. Hydrogen exchange. Annu. Rev. Biochem. 41, 903–924 (1972).
Woodward, C.K. & Hilton, B.D. Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. Annu. Rev. Biophys. Bioeng. 8, 99–127 (1979).
Bai, Y., Sosnick, T.R., Mayne, L. & Englander, S.W. Protein folding intermediates: Native-state hydrogen exchange. Science 269, 192–197 (1995).
Bai, Y. & Englander, S.W. Future directions in folding: The multi-state nature of protein structure. Proteins: Struct. Funct. Genet. 24, 145–151 (1996).
Balbach, J. et al. Following protein folding in real time using NMR spectroscopy. Nature Struct. Biol. 2, 865–870 (1995).
Udgaonkar, J.B. & Baldwin, R.L. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature 335, 694–699 (1988).
Roder, H., Elöve, G.A. & Englander, S.W. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature 335, 700–704 (1988).
Radford, S.E., Dobson, C.M. & Evans, P.A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 358, 302–307 (1992).
Miranker, A., Robinson, C.V., Radford, S.E., Aplin, R.T. & Dobson, C.M. Detection of transient protein folding populations by mass spectrometry. Science 262, 896–900 (1993).
Radford, S.E. & Dobson, C.M. Insights into protein folding using physical techniques: Studies of lysozyme and α-lactalbumin. Phil. Trans. R. Soc. Lond. B348, 17–25 (1995).
Miranker, A., Robinson, C.V., Radford, S.E. & Dobson, C.M. Investigation of protein folding by mass spectrometry. Faseb J. 10, 93–101 (1996).
Chen, B.-L., Baase, W.A. & Schellman, J.A. Low-temperature unfolding of a mutant of phage T4 lysozyme. 2. Kinetic investigations. Biochemistry 28, 691–699 (1989).
Matouschek, A., Kellis, J.T. Jr., Serrano, L., Bycroft, M. & Fersht, A.R. Transient folding intermediates characterized by protein engineering. Nature 346, 440–445 (1990).
Fersht, A.R. Characterizing transition states in protein folding: An essential step in the puzzle. Curr. Opin. Struct. Biol. 5, 79–84 (1995).
Neira, J.L. et al. Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary fragments of cleaved chymotrypsin inhibitor 2. Direct evidence for a nucleation-condensation mechanism. Folding & Design 1, 189–208 (1996).
Jones, C.M. et al. Fast events in protein folding initiated by nanosecond laser photolysis. Proc. Natl. Acad. Sci. USA 90, 11860–11864 (1993).
Williams, S. et al. Fast events in protein folding: Helix melting and formation in a small peptide. Biochemistry 35, 691–697 (1996).
Pascher, T., Chesick, J.P., Winkler, J.R. & Gray, H.B. Protein folding triggered by electron transfer. Science 271, 1558–1560 (1996).
Miranker, A.D. & Dobson, C.M. Collapse and cooperativity in protein folding. Curr. Opin. Struct Biol. 6, 31–42 (1996).
Jackson, S.E. & Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428–10435 (1991).
Fersht, A.R. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA 92, 10869–10873 (1995).
Sosnick, T.R., Mayne, L., Hiller, R. & Englander, S.W. The barriers in protein folding. Nature Struct. Biol. 1, 149–156 (1994).
Huang, G.S. & Oas, T.G. Submillisecond folding of monomeric λ represser. Proc. Natl. Acad. Sci. USA 92, 6878–6882 (1995).
Schindler, T., Herrler, M., Marahiel, M.A. & Schmid, F.X. Extremely rapid protein folding in the absence of intermediates. Nature Struct. Biol. 2, 663–673 (1995).
Sosnick, T.R., Mayne, L. & Englander, S.W. Molecular collapse: The rate-limiting step in two-state cytochrome c folding. Proteins: Struct. Funct. Genet. 24, 413–426 (1996).
Chan, H.S. & Dill, K.A. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20, 447–490 (1991).
Chan, H.S. & Dill, K.A. Comparing folding codes for proteins and polymers. Proteins: Struct. Funct. Genet. 24, 335–344 (1996).
Bryngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. Funnels, pathways and the energy landscape of protein folding: A synthesis. Proteins: Struct. Funct. Genet. 21, 167–195 (1995).
Wolynes, P.G., Onuchic, J.N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619–1620 (1995).
Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z. & Socci, N.D. Towards an outline of the topography of a realistic protein folding funnel. Proc. Natl. Acad. Sci. USA 92, 3626–3630 (1995).
Socci, N.D., Onuchic, J.N. & Wolynes, P.G. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104, 5860–5868 (1996).
Dill, K.A. The stabilities of globular proteins. In Protein Engineering (eds Oxender, D. L. & Fox, C. F.) 187–192 (Alan R. Liss, Inc., New York, 1987).
Bryngelson, J.D. & Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93, 6902–6915 (1989).
Shakhnovich, E.I., Farztdinov, G., Gutin, A.M. & Karplus, M. Protein folding bottlenecks: A lattice Monte Carlo simulation. Phys. Rev. Lett. 67, 1665–1668 (1991).
Camacho, C.J. & Thirumalai, D. Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 90, 6369–6372 (1993).
Chan, H.S. & Dill, K.A. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100, 9238–9257 (1994).
Socci, N.D. & Onuchic, J.N. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101, 1519–1528 (1994).
Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101, 6052–6062 (1994).
Šali, A., Shakhnovich, E. & Karplus, M. How does a protein fold? Nature 369, 248–251 (1994).
Dill, K.A. et al. Principles of protein folding—A perspective from simple exact models. Protein Sci. 4, 561–602 (1995).
Hao, M.-H. & Scheraga, H.A. Statistical thermodynamics of protein folding: Sequence dependence. J. Phys. Chem. 98, 9882–9893 (1994).
Hao, M.-H. & Scheraga, H.A. How optimization of potential functions affects protein folding. Proc. Natl. Acad. Sci. USA 93, 4984–4989 (1996).
Bryngelson, J.D. & Wolynes, P.G. Spin-glass and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84, 7524–7528 (1987).
Leopold, P.E., Montal, M. & Onuchic, J.N. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA 89, 8721–8725 (1992).
Guo, Z. & Thirumalai, D. Kinetics of protein folding: Nucleation mechanism, time scales, and pathways. Biopolymers 36, 83–102 (1995).
Socci, N.D. & Onuchic, J.N. Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103, 4732–4744 (1995).
Thirumalai, D. From minimal models to real proteins: Time scales for protein folding kinetics. J. Phys. 15, 1457–1467 (1995).
Mirny, L.A., Abkevich, V. & Shakhnovich, E.I. Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model. Folding & Design 1, 103–116 (1996).
Thirumalai, D. & Woodson, S.A. Kinetics of folding of proteins and RNA. Ace. Chem. Res. 29, 433–439 (1996).
Chan, H.S. & Dill, K.A. Protein folding kinetics from the perspectives of simple models. Proteins: Struct. Funct. Genet. in the press.
Chan, H.S. & Dill, K.A. Energy landscapes and the collapse dynamics of homopolymers. J. Chem. Phys. 99, 2116–2127 (1993).
Kuroda, Y., Hamada, D., Tanaka, T. & Goto, Y. High helicity of peptide fragments corresponding to β-strand regions of β-lactoglobulin observed by 2D-NMR spectroscopy. Folding & Design 1, 243–251 (1996).
Hamada, D., Segawa, S.-I. & Goto, Y. Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet protein. Nature Struct. Biol. 3, 868–873 (1996).
Landry, S.J. & Gierasch, L.M. Polypeptide interactions with molecular chaperones and their relationship to in vivo protein folding. Annu. Rev. Biophys. Biomol. Struct. 23, 645–669 (1994).
Hlodan, R. & Hartl, F.U. in Mechanisms of Protein Folding (ed. R.H. Pain) 194–228 (Oxford University Press, New York, 1994).
Thirumalai, D. in Statistical Mechanics, Protein Structure, and Protein-Substrate Interactions (ed. S. Doniach) 115–134 (Plenum, New York, 1994).
Chan, H.S. & Dill, K.A. A simple model of chaperonin-mediated protein folding. Proteins: Struct. Funct. Genet. 24, 345–351 (1996).
Todd, M.J., Lorimer, G.H. & Thirumalai, D. Chaperonin-facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism. Proc. Natl. Acad. Sci. USA 93, 4030–4035 (1996).
Sfatos, C.D., Gutin, A.M., Abkevich, V.I. & Shakhnovich, E.I. Simulations of chaperone-assisted folding. Biochemistry 35, 334–339 (1996).
Gutin, A.M., Abkevich, V.I. & Shakhnovich, E.I. Is burst hydrophobic collapse necessary for protein folding? Biochemistry 34, 3066–3076 (1995).
Shrivastava, I., Vishveshwara, S., Cieplak, M., Maritan, A. & Banavar, J.R. Lattice model for rapidly folding protein-like heteropolymers. Proc. Natl. Acad. Sci. USA 92, 9206–9209 (1995).
Klimov, D.K. & Thirumalai, D. A criterion that determines the foldability of proteins. Phys. Rev. Lett. 76, 4070–4073 (1996).
Klimov, D.K. & Thirumalai, D. Factors governing the foldability of proteins. Proteins: Struct. Funct. Genet. In the press.
Hill, T.L. Effect of rotation on the diffusion-controlled rate of ligand-protein association. Proc. Natl. Acad. Sci. USA 72, 4918–4922 (1975).
Hill, T.L. Diffusion frequency factors in some simple examples of transition-state rate theory. Proc. Natl. Acad. Sci. USA 73, 679–683 (1976).
Steinfeld, J.I., Francisco, J.S. & Hase, W.L. Chemical Kinetics and Dynamics (Prentice-Hall, Englewood Cliffs, New Jersey, 1989).
Zhou, H.-X. & Zwanzig, R. A rate process with an entropy barrier. J. Chem. Phys. 94, 6147–6152 (1991).
Tanford, C. Protein denaturation. Adv. Protein Chem. 23, 121–282 (1968).
Matthews, C.R., Crisanti, M.M., Manz, J.T. & Gepner, G.L. Effects of a single amino acid substitution on the folding of the α-subunit of tryptophan synthase. Biochemistry 22, 1445–1452 (1983).
Segawa, S.-I. & Sugihara, M. Characterization of the transition state of lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state. Biopolymers 23, 2473–2488 (1984).
Chen, B.-L., Baase, W.A., Nicholson, H. & Schellman, J.A. Folding kinetics of T4 lysozyme and nine mutants at 12 °C. Biochemistry 31, 1464–1476 (1992).
Shortle, D., Chan, H.S. & Dill, K.A. Modeling the effects of mutations on the denatured states of proteins. Protein Sci. 1, 201–215 (1992).
Chan, H.S. Kinetics of protein folding. Nature 373, 664–665 (1995).
Unger, R. & Moult, J. Local interactions dominate folding in a simple protein model. J. Mol. Biol. 259, 988–994 (1996).
Fukugita, M., Lancaster, D. & Mitchard, M.G. A heteropolymer model study for the mechanism of protein folding. Biopolymers, in the press.
Dill, K.A., Fiebig, K.M. & Chan, H.S. Cooperativity in protein folding kinetics. Proc. Natl. Acad. Sci. USA 90, 1942–1946 (1993).
Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33, 10026–10036 (1994).
Onuchic, J.N., Socci, N.D., Luthey-Schulten, Z. & Wolynes, P.G. Protein folding funnels: The nature of the transition state ensemble. Folding & Design, in the press.
Kiefhaber, T. & Baldwin, R.L. Kinetics of hydrogen bond breakage in the process of unfolding of ribonuclease A measured by pulsed hydrogen exchange. Proc. Natl. Acad. Sci. USA 92, 2657–2661 (1995).
Hoeltzli, S.D. & Frieden, C. Stopped-flow NMR spectroscopy: Real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. Proc. Natl. Acad. Sci. USA 92, 9318–9322 (1995).
Hvidt, A. & Nielsen, S.O. Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287–386 (1966).
Miller, D.W. & Dill, K.A. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 4, 1860–1873 (1995).
Alonso, D.O.V. & Dill, K.A. Solvent denaturation and stabilization of globular proteins. Biochemistry 30, 5974–5985 (1991).
Dill, K.A., Alonso, D.O.V. & Hutchinson, K. Thermal stabilities of globular proteins. Biochemistry 28, 5439–5449 (1989).
Hagen, S.J., Hofrichter, J., Szabo, A. & Eaton, W.A. Diffusion-limited contact formation in unfolded cytochrom c: Estimating the maximum rate of protein folding. Proc. Natl. Acad. Sci. USA 93, 11615–11617 (1996).
McCammon, J.A. A speed limit for protein folding. Proc. Natl. Acad. Sci. USA 93, 11426–11427 (1996).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Dill, K., Chan, H. From Levinthal to pathways to funnels. Nat Struct Mol Biol 4, 10–19 (1997). https://doi.org/10.1038/nsb0197-10
Issue Date:
DOI: https://doi.org/10.1038/nsb0197-10
This article is cited by
-
Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease
Scientific Reports (2023)
-
Monitoring protein unfolding transitions by NMR-spectroscopy
Journal of Biomolecular NMR (2022)
-
Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH
The Protein Journal (2022)
-
Optical tweezers in single-molecule biophysics
Nature Reviews Methods Primers (2021)