Skip to main content
×
Home

Protein folding and misfolding: mechanism and principles

  • S. Walter Englander (a1), Leland Mayne (a1) and Mallela M. G. Krishna (a1) (a2)
Abstract
Abstract

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.

Copyright
Corresponding author
*Author for correspondence: Dr S. W. Englander, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, USA. Tel.: 215-898-4509; Fax: 215-898-2415; Email: engl@mail.med.upenn.edu
References
Hide All
Anfinsen C. B. (1973). Principles that govern the folding of protein chains. Science 181, 223230.
Anfinsen C. B., Haber E., Sela M. & White F. H. (1961). Kinetics of formation of native ribonuclease during oxidation of reduced polypeptide chain. Proceedings of the National Academy of Sciences USA 47, 13091314.
Bahar I., Wallqvist A., Covell D. G. & Jernigan R. L. (1998). Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 37, 10671075.
Bai Y., Englander J. J., Mayne L., Milne J. S. & Englander S. W. (1995a). Thermodynamic parameters from hydrogen exchange measurements. Methods in Enzymology 259, 344356.
Bai Y. & Englander S. W. (1996). Future directions in folding: the multi-state nature of protein structure. Proteins: Structure, Function, Genetics 24, 145151.
Bai Y., Milne J. S., Mayne L. & Englander S. W. (1993). Primary structure effects on peptide group hydrogen exchange. Proteins: Structure, Function, Genetics 17, 7586.
Bai Y., Milne J. S., Mayne L. & Englander S. W. (1994). Protein stability parameters measured by hydrogen exchange. Proteins: Structure, Function, Genetics 20, 414.
Bai Y., Sosnick T. R., Mayne L. & Englander S. W. (1995b). Protein folding intermediates: native-state hydrogen exchange. Science 269, 192197.
Baum J., Dobson C. M., Evans P. A. & Hanley C. (1989). Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin. Biochemistry 28, 713.
Bédard S., Mayne L., Peterson R. W., Wand A. J. & Englander S. W. (2008). The foldon substructure of staphylococcal nuclease. Journal of Molecular Biology 376, 11421154.
Bertagna A. M. & Barrick D. (2004). Nonspecific hydrophobic interactions stabilize an equilibrium intermediate of apomyoglobin at a key position within the AGH region. Proceedings of the National Academy of Sciences USA 101, 1251412519.
Bieri O. & Kiefhaber T. (2001). Origin of apparent fast and non-exponential kinetics of lysozyme folding measured in pulsed hydrogen exchange measurements. Journal of Molecular Biology 310, 919935.
Bieri O., Wildegger G., Bachmann A., Wagner C. & Kiefhaber T. (1999). A salt-induced kinetic intermediate is on a new parallel pathway of lysozyme folding. Biochemistry 38, 1246012470.
Bilsel O., Zitzewitz J. A., Bowers K. E. & Matthews C. R. (1999). Folding mechanism of the a-subunit of tryptophan synthase, an a/b barrel protein: global analysis highlights the interconversion of multiple native, intermediate, and unfolded forms through parallel channels. Biochemistry 38, 10181029.
Bollen Y. J. M., Kamphuis M. B. & van Mierlo C. P. M. (2006). The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates. Proceedings of the National Academy of Sciences USA 103, 40954100.
Bryngelson J. D., Onuchic J. N., Socci N. D. & Wolynes P. G. (1995). Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins: Structure, Function, and Genetics 21, 167195.
Capaldi A. P., Kleanthous C. & Radford S. E. (2002). Im7 folding mechanism: misfolding on a path to the native state. Nature Structural Biology 9, 209216.
Cavagnero S., Dyson H. J. & Wright P. E. (1999). Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. Journal of Molecular Biology 285, 269282.
Cecconi C., Shank E. A., Bustamante C. & Marqusee S. (2005). Direct observation of the three-state folding of a single protein molecule. Science 309, 20572060.
Cellitti J., Bernstein R. & Marqusee S. (2007). Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway. Protein Science 16, 852862.
Chamberlain A. K., Fischer K. F., Reardon D., Handel T. M. & Marqusee A. S. (1999). Folding of an isolated ribonuclease H core fragment. Protein Science 8, 22512257.
Chamberlain A. K., Handel T. M. & Marqusee S. (1996). Detection of rare partially folded molecules in equilibrium with the native conformation of RNase H. Nature Structural Biology 3, 782787.
Chamberlain A. K. & Marqusee S. (2000). Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. Advances in Protein Chemistry 53, 283328.
Chan H. S., Shimizu S. & Kaya H. (2004). Cooperativity principles in protein folding. Methods in Enzymology 380, 350379.
Chi E. Y., Krishnan S., Randolph T. W. & Carpenter J. F. (2003). Physical stability of proteins in aqueous solution: mechanism and driving forces in nonnative protein aggregation. Pharmaceutical Research 20, 13251336.
Chu R., Pei W., Takei J. & Bai Y. (2002). Relationship between native-state hydrogen exchange and the folding pathway of a four-helix bundle protein. Biochemistry 41, 79988003.
Clarke J. & Fersht A. R. (1996). An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Folding & Design 1, 243254.
Colon W., Elove G. A., Wakem L. P., Sherman F. & Roder H. (1996). Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding. Biochemistry 35, 55385549.
Connelly G. P., Bai Y., Jeng M.-F., Mayne L. & Englander S. W. (1993). Isotope effects in peptide group hydrogen exchange. Proteins: Structure, Function, Genetics 17, 8792.
Creighton T. E. (1986). Disulfide bonds as probes of protein folding pathways. Methods in Enzymology 131, 83106.
Dabora J. M., Pelton J. G. & Marqusee S. (1996). Structure of the acid state of Escherichia coli ribonuclease HI. Biochemistry 35, 1195111958.
De Lorenzo F., Goldberger R., Steers E. J., Givol D. & Anfinsen C. B. (1966). Purification and properties of an enzyme from beef liver which catalyzes sulfhydryl-disulfide interchange in proteins. Journal of Biological Chemistry 241, 15621567.
Dill K. A. (1985). Theory for the folding and stability of globular proteins. Biochemistry 24, 15011509.
Dyson H. J. & Wright P. E. (2002). Coupling of folding and binding for unstructured proteins. Current Opinion in Structural Biology 12, 5460.
Eliezer D., Chung J., Dyson H. J. & Wright P. E. (2000). Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. Biochemistry 39, 28942901.
Elöve G. A., Bhuyan A. K. & Roder H. (1994). Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry 33, 69256935.
Englander J. J., Del Mar C., Li W., Englander S. W., Kim J. S., Stranz D. D., Hamuro Y. & Woods V. L. J. (2003). Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Proceedings of the National Academy of Sciences USA 100, 70577062.
Englander J. J., Louie G., McKinnie R. E. & Englander S. W. (1998a). Energetic components of the allosteric machinery in hemoglobin measured by hydrogen exchange. Journal of Molecular Biology 284, 16951706.
Englander J. J., Rogero J. R. & Englander S. W. (1985). Protein hydrogen exchange studied by the fragment separation method. Analytical Biochemistry 147, 234244.
Englander S. W. (1963). A hydrogen exchange method using tritium and Sephadex. Application to ribonuclease. Biochemistry 2, 798807.
Englander S. W. (2006). Hydrogen exchange and mass spectrometry: a historical perspective. Journal of the American Society for Mass Spectrometry 17, 14811489.
Englander S. W. & Kallenbach N. R. (1983). Hydrogen exchange and structural dynamics of proteins and nucleic-acids. Quarterly Reviews of Biophysics 16, 521655.
Englander S. W., Mayne L., Bai Y. & Sosnick T. R. (1997). Hydrogen exchange: the modern legacy of Linderstrom-Lang. Protein Science 6, 11011109.
Englander S. W., Sosnick T. R., Mayne L. C., Shtilerman M., Qi P. X. & Bai Y. W. (1998b). Fast and slow folding in cytochrome c. Accounts of Chemical Research 31, 737744.
Eyles S. J. & Kaltashov I. A. (2004). Methods to study protein dynamics and folding by mass spectrometry. Methods 34, 8899.
Feng H., Takei J., Lipsitz R., Tjandra N. & Bai Y. (2003a). Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding. Biochemistry 42, 1246112465.
Feng H., Takei J., Lipsitz R., Tjandra N. & Bai Y. (2004). The high-resolution structure of a protein intermediate state: implications for protein folding. Protein Science 13, 219220.
Feng H., Zhou Z. & Bai Y. (2005a). A protein folding pathway with multiple folding intermediates at atomic resolution. Proceedings of the National Academy of Sciences USA 102, 50265031.
Feng H. Q., Vu N. D. & Bai Y. W. (2005b). Detection of a hidden folding intermediate of the third domain of PDZ. Journal of Molecular Biology 346, 345353.
Feng Y., Liu D. & Wang J. (2003b). Native-like partially folded conformations and folding process revealed in the N-terminal large fragments of staphylococcal nuclease: a study by NMR spectroscopy. Journal of Molecular Biology 330, 821837.
Fersht A. R. & Daggett V. (2007). Folding and binding: implementing the game plan. Current Opinion in Structural Biology 17, 12.
Fetrow J. S. & Baxter S. M. (1999). Assignment of 15N chemical shifts and 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c. Biochemistry 38, 44804492.
Fetrow J. S., Dreher U., Wiland D. J., Schaak D. L. & Boose T. L. (1998). Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c. Protein Science 7, 9941005.
Fine R., Dimmler G. & Levinthal C. (1991). Fastrun – a special purpose, hardwired computer for molecular simulation. Proteins: Structure, Function, Genetics 11, 242253.
Fischer K. F. & Marqusee S. (2000). A rapid test for identification of autonomous folding units in proteins. Journal of Molecular Biology 302, 701712.
Fuentes E. J. & Wand A. J. (1998a). Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange. Biochemistry 37, 36873698.
Fuentes E. J. & Wand A. J. (1998b). Local stability and dynamics of apocytochrome b562 examined by the dependence of hydrogen exchange on hydrostatic pressure. Biochemistry 37, 98779883.
Garcia A. E. & Hummer G. (1999). Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins: Structure, Function, Genetics 36, 175191.
Garcia C., Nishimura C., Cavagnero S., Dyson H. J. & Wright P. E. (2000). Changes in the apomyoglobin folding pathway caused by mutation of the distal histidine residue. Biochemistry 39, 1122711237.
Gualfetti P. J., Bilsel O. & Matthews C. R. (1999). The progressive development of structure and stability during the equilibrium folding of the alpha subunit of tryptophan synthase from Escherichia coli. Protein Science 8, 16231635.
Hernandez G., Jenney F. E., Adams M. W. W. & LeMaster D. M. (2000). Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature. Proceedings of the National Academy of Sciences USA 97, 31663170.
Hilser V. J., Garcia-Moreno B. E., Oas T. G., Kapp G. & Whitten S. T. (2006). A statistical thermodynamic model of the protein ensemble. Chemical Reviews 106, 15451558.
Hoang L., Bédard S., Krishna M. M. G., Lin Y. & Englander S. W. (2002). Cytochrome c folding pathway: kinetic native-state hydrogen exchange. Proceedings of the National Academy of Sciences USA 99, 1217312178.
Hoang L., Maity H., Krishna M. M., Lin Y. & Englander S. W. (2003). Folding units govern the cytochrome c alkaline transition. Journal of Molecular Biology 331, 3743.
Hollien J. & Marqusee S. (1999). A thermodynamic comparison of mesophilic and thermophilic ribonucleases H. Biochemistry 38, 38313836.
Hughson F. M., Wright P. E. & Baldwin R. L. (1990). Structural characterization of a partly folded apomyoglobin intermediate. Science 249, 15441548.
Huyghues-Despointes B. M., Pace C. N., Englander S. W. & Scholtz J. M. (2001). Measuring the conformational stability of a protein by hydrogen exchange. Methods in Molecular Biology 168, 6992.
Hvidt A. (1964). A discussion of the pH dependence of the hydrogen-deuterium exchange of proteins. Comptes Rendus des Travaux du Laboratoire Carlsberg Séries Chimique 34, 299317.
Hvidt A. & Nielsen S. O. (1966). Hydrogen exchange in proteins. Advances in Protein Chemistry 21, 287386.
Jamin M., Yeh S. R., Rousseau D. L. & Baldwin R. L. (1999). Submillisecond unfolding kinetics of apomyoglobin and its pH 4 intermediate. Journal of Molecular Biology 292, 731740.
Jemmerson R., Liu J., Hausauer D., Lam K.-P., Mondino A. & Nelson R. D. (1999). A conformational change in cytochrome c of apoptotic and necrotic cells is detected by monoclonal antibody binding and mimicked by association of the native antigen with synthetic phospholipid vesicles. Biochemistry 38, 35993609.
Jeng M. F., Englander S. W., Elöve G. A., Wand A. J. & Roder H. (1990). Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry 29, 1043310437.
Jennings P. A. & Wright P. E. (1993). Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262, 892896.
Kamagata K., Sawano Y., Tanokura M. & Kuwajima K. (2003). Multiple parallel-pathway folding of proline-free staphylococcal nuclease. Journal of Molecular Biology 332, 11431153.
Kato H., Vu N. D., Feng H. Q., Zhou Z. & Bai Y. W. (2007). The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate. Journal of Molecular Biology 365, 881891.
Kelly J. W., Colon W., Lai Z., Lashuel H. A., McCulloch J., McCutchen S. L., Miroy G. J. & Peterson S. A. (1997). Transthyretin quaternary and tertiary structural changes facilitate misassembly into amyloid. Advances in Protein Chemistry 50, 161181.
Kiefhaber T. (1995). Kinetic traps in lysozyme folding. Proceedings of the National Academy of Sciences USA 92, 90299033.
Kiefhaber T., Bachmann A., Wildegger G. & Wagner C. (1997). Direct measurement of nucleation and growth rates in lysozyme folding. Biochemistry 36, 51085112.
Kihara H., Saigo S., Nakatani H., Hiromi K., Ikeda-Saito M. & Iizuka T. (1976). Kinetic study of isomerization of ferricytochrome c at alkaline pH. Biochimica et Biophysica Acta 430, 225243.
Kim K. S., Fuchs J. A. & Woodward C. K. (1993). Hydrogen exchange identifies native-state motional domains important in protein folding. Biochemistry 32, 96009608.
Kim P. S. & Baldwin R. L. (1982a). Influence of charge on the rate of amide proton exchange. Biochemistry 21, 15.
Kim P. S. & Baldwin R. L. (1982b). Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annual Review of Biochemistry 51, 459489.
Kim P. S. & Baldwin R. L. (1990). Intermediates in the folding reactions of small proteins. Annual Review of Biochemistry 59, 631660.
Korzhnev D. M., Neudecker P., Zarrine-Afsar A., Davidson A. R. & Kay L. E. (2006). Abp1p and Fyn SH3 domains fold through similar low-populated intermediate states. Biochemistry 45, 1017510183.
Korzhnev D. M., Religa T. L., Lundstrom P., Fersht A. R. & Kay L. E. (2007). The folding pathway of an FF domain: characterization of an on-pathway intermediate state under folding conditions by (15)N, (13)C(alpha) and (13)C-methyl relaxation dispersion and (1)H/(2)H-exchange NMR spectroscopy. Journal of Molecular Biology 372, 497512.
Korzhnev D. M., Salvatella X., Vendruscolo M., Nardo A. A. D., Davidson A. R., Dobson C. M. & Kay L. E. (2004). Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430, 586590.
Krantz B. A., Dothager R. S. & Sosnick T. R. (2004). Discerning the structure and energy of multiple transition states in protein folding using y-analysis. Journal of Molecular Biology 337, 463475.
Krishna M. M. G. & Englander S. W. (2005). The N-terminal to C-terminal motif in protein folding and function. Proceedings of the National Academy of Sciences USA 102, 10531058.
Krishna M. M. G. & Englander S. W. (2007). A unified mechanism for protein folding: predetermined pathways with optional errors. Protein Science 16, 449464.
Krishna M. M. G., Hoang L., Lin Y. & Englander S. W. (2004a). Hydrogen exchange methods to study protein folding. Methods 34, 5164.
Krishna M. M. G., Lin Y. & Englander S. W. (2004b). Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity. Journal of Molecular Biology 343, 10951109.
Krishna M. M. G., Lin Y., Mayne L. & Walter Englander S. (2003a). Intimate view of a kinetic protein folding intermediate: residue-resolved structure, interactions, stability, folding and unfolding rates, homogeneity. Journal of Molecular Biology 334, 501513.
Krishna M. M. G., Lin Y., Rumbley J. N. & Englander S. W. (2003b). Cooperative omega loops in cytochrome c: role in folding and function. Journal of Molecular Biology 331, 2936.
Krishna M. M. G., Maity H., Rumbley J. N. & Englander S. W. (2007). Branching in the sequential folding pathway of cytochrome c. Protein Science 16, 19461956.
Krishna M. M. G., Maity H., Rumbley J. N., Lin Y. & Englander S. W. (2006). Order of steps in the cytochrome c folding pathway: evidence for a sequential stabilization mechanism. Journal of Molecular Biology 359, 14111420.
Leopold P. E., Montal M. & Onuchic J. N. (1992). Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proceedings of the National Academy of Sciences USA 89, 87218725.
Leszczynski J. F. & Rose G. D. (1986). Loops in globular proteins: a novel category of secondary structure. Science 234, 849855.
Levinthal C. (1969). How to fold graciously. In Mossbauer Spectroscopy in Biological Systems. Proceedings, University of Illinois Bulletin, vol. 67, pp. 2224. Urbana, IL: University of Illinois Press.
Lifson S. & Roig A. (1961). On the theory of the helix-coil transition in polypeptides. Journal of Chemical Physics 34, 19631974.
Linderstrøm-Lang K. (1958). Deuterium exchange and protein structure. In Symposium on Protein Structure (edNeuberger A.). London: Methuen.
Linderstrøm-Lang K. U. & Schellman J. A. (1959). Protein structure and enzyme activity. In The Enzymes (edsBoyer P. D., Lardy H. and Myrback K.), pp. 443510. New York: Academic Press.
Loh S. N., Kay M. S. & Baldwin R. L. (1995). Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway. Proceedings of the National Academy of Sciences USA 92, 54465450.
Loh S. N., Prehoda K. E., Wang J. & Markley J. L. (1993). Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry 32, 1102211028.
Maity H., Lim W. K., Rumbley J. N. & Englander S. W. (2003). Protein hydrogen exchange mechanism: local fluctuations. Protein Science 12, 153160.
Maity H., Maity M. & Englander S. W. (2004). How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. Journal of Molecular Biology 343, 223233.
Maity H., Maity M., Krishna M. M. G., Mayne L. & Englander S. W. (2005). Protein folding: the stepwise assembly of foldon units. Proceedings of the National Academy of Sciences USA 102, 47414746.
Maity H., Rumbley J. N. & Englander S. W. (2006). Functional role of a protein foldon: an W-loop foldon controls the alkaline transition in ferricytochrome c. Proteins: Structure, Function, Genetics 63, 349355.
Mayne L. & Englander S. W. (2000). Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchange. Protein Science 9, 18731877.
Milne J. S., Mayne L., Roder H., Wand A. J. & Englander S. W. (1998). Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Science 7, 739745.
Milne J. S., Xu Y., Mayne L. C. & Englander S. W. (1999). Experimental study of the protein folding landscape: unfolding reactions in cytochrome c. Journal of Molecular Biology 290, 811822.
Molday R. S., Englander S. W. & Kallen R. G. (1972). Primary structure effects on peptide group hydrogen exchange. Biochemistry 11, 150158.
Moult J., Fidelis K., Kryshtafovych A., Rost B., Hubbard T. & Tramontano A. (2007). Critical assessment of methods of protein structure prediction – round VII. Proteins: Structure Function and Bioinformatics 69, 39.
Myers J. K., Pace C. N. & Scholtz J. M. (1995). Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Science 4, 21382148.
Neudecker P., Zarrine-Afsar A., Davidson A. R. & Kay L. E. (2007). Phi-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy. Proceedings of the National Academy of Sciences USA 104, 1571715722.
Nishimura C., Dyson H. J. & Wright P. E. (2006). Identification of native and non-native structure in kinetic folding intermediates of apomyoglobin. Journal of Molecular Biology 355, 139156.
Oas T. G. & Kim P. S. (1988). A peptide model of a protein folding intermediate. Nature 336, 4248.
Ozkan S. B., Wu G. A., Chodera J. D. & Dill K. A. (2007). Protein folding by zipping and assembly. Proceedings of the National Academy of Sciences USA 104, 1198711992.
Pace C. N. (1975). The stability of globular proteins. CRC Critical Reviews in Biochemistry 3, 143.
Panchenko A. R., Luthey schulten Z. & Wolynes P. G. (1996). Foldons, protein structural modules, and exons. Proceedings of the National Academy of Sciences USA 93, 20082013.
Pettigrew G. W. & Moore G. R. (1987). Cytochromes c. Biological Aspects. Berlin Heidelberg, Germany: Springer-Verlag.
Plaxo K. W., Simons K. T. & Baker D. (1998). Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology 277, 985994.
Pletneva E. V., Gray H. B. & Winkler J. R. (2005). Snapshots of cytochrome c folding. Proceedings of the National Academy of Sciences USA 102, 1839718402.
Plotkin S. S. & Onuchic J. N. (2002a). Understanding protein folding with energy landscape theory. Part I: Basic concepts. Quarterly Reviews of Biophysics 35, 111167.
Plotkin S. S. & Onuchic J. N. (2002b). Understanding protein folding with energy landscape theory. Part II: Quantitative concepts. Quarterly Reviews of Biophysics 35, 205286.
Ptitsyn O. B. (1995). Molten globule and protein folding. Advances in Protein Chemistry 47, 83229.
Radford S. E., Dobson C. M. & Evans P. A. (1992). The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 358, 302307.
Raschke T. M., Kho J. & Marqusee S. (1999). Confirmation of the hierarchical folding of RNase H: a protein engineering study. Nature Structural Biology 6, 825831.
Raschke T. M. & Marqusee S. (1997). The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions. Nature Structural Biology 4, 298304.
Roder H., Elove G. A. & Englander S. W. (1988). Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature 335, 700704.
Rosenberg A. & Chakravarti K. (1968). Studies of hydrogen exchange in proteins. I. The exchange kinetics of bovine carbonic anhydrase. Journal of Biological Chemistry 243, 51935201.
Rumbley J., Hoang L., Mayne L. C. & Englander S. W. (2001). An amino acid code for protein folding. Proceedings of the National Academy of Sciences USA 105, 105112.
Schlunegger M. P., Bennett M. J. & Eisenberg D. (1997). Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Advances in Protein Chemistry 50, 61122.
Schmid F. X. & Baldwin R. L. (1979). Detection of an early intermediate in the folding of ribonuclease A by protection of amide protons against exchange. Journal of Molecular Biology 135, 199215.
Silverman J. A. & Harbury P. B. (2002a). The equilibrium unfolding pathway of a (b/a)8 barrel. Journal of Molecular Biology 324, 10311040.
Silverman J. A. & Harbury P. B. (2002b). Rapid mapping of protein structure, interactions, and ligand binding by misincorporation proton-alkyl exchange. Journal of Biological Chemistry 277, 3096830975.
Sosnick T. R., Krantz B. A., Dothager R. S. & Baxa M. (2006). Characterizing the protein folding transition state using psi analysis. Chemical Reviews 106, 18621876.
Sosnick T. R., Mayne L. & Englander S. W. (1996). Molecular collapse: the rate-limiting step in two-state cytochrome c folding. Proteins: Structure, Function, Genetics 24, 413426.
Sosnick T. R., Mayne L., Hiller R. & Englander S. W. (1994). The barriers in protein folding. Nature Structural Biology 1, 149156.
Spolaore B., Bermejo R., Zambonin M. & Fontana A. (2001). Protein interactions leading to conformational changes monitored by limited proteolysis: Apo form and fragments of horse cytochrome c. Biochemistry 40, 94609468.
Sugase K., Dyson H. J. & Wright P. E. (2007). Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447, 10211025.
Takei J., Pei W., Vu D. & Bai Y. (2002). Populating partially unfolded forms by hydrogen exchange-directed protein engineering. Biochemistry 41, 1230812312.
Udgaonkar J. B. & Baldwin R. L. (1988). NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature 335, 694699.
Vendrusculo M., Paci E., Dobson C. M. & Karplus M. (2003). Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. Journal of the American Chemical Society 125, 1568615687.
Vu N. T., Feng H. & Bai Y. (2004). The folding pathway of barnase: the rate-limiting transition state and a hidden intermediate under native conditions. Protein Science 13, 220220.
Wagner G. & Wüthrich K. (1982). Amide proton exchange and surface conformation of BPTI in solution: studies with 2D NMR. Journal of Molecular Biology 160, 343361.
Wallace L. A. & Matthews C. R. (2002). Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions. Biophysical Chemistry 101, 113131.
Wand A. J. & Englander S. W. (1996). Protein complexes studied by NMR spectroscopy. Current Opinion in Biotechnology 7, 403408.
Wang L. & Kallenbach N. R. (1998). Proteolysis as a measure of the free energy difference between cytochrome c and its derivatives. Protein Science 7, 24602464.
Watson J. D. & Crick F. H. C. (1953). Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. Nature 171, 737738.
Weinkam P., Zong C. & Wolynes P. G. (2005). A fu-nneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proceedings of the National Academy of Sciences USA 102, 1240112406.
Wildegger G. & Kiefhaber T. (1997). Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate. Journal of Molecular Biology 270, 294304.
Wolynes P. G., Onuchic J. N. & Thirumalai D. (1995). Navigating the folding routes. Science 267, 16191620.
Woodward C. K. (1994). Hydrogen exchange rates and protein folding. Current Opinion in Structural Biology 4, 112116.
Woodward C. K. & Hilton B. D. (1979). Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. Annual Review of Biophysics & Bioengineering 8, 99127.
Woodward C. K., Hilton B. D. & Tuchsen E. (1982). Hydrogen exchange and the dynamic structure of proteins. Molecular and Cellular Biochemistry 48, 135160.
Wu Y. & Matthews C. R. (2002). Parallel channels and rate-limiting steps in complex protein folding reactions: prolyl isomerization and the alpha subunit of Trp synthase, a TIM barrel protein. Journal of Molecular Biology 323, 309325.
Wu Y. & Matthews C. R. (2003). Proline replacements and the simplification of the complex, parallel channel folding mechanism for the alpha subunit of Trp synthase, a TIM barrel protein. Journal of Molecular Biology 330, 11311144.
Xu Y., Mayne L. & Englander S. W. (1998). Evidence for an unfolding and refolding pathway in cytochrome c. Nature Structural Biology 5, 774778.
Yan S., Gawlak G., Smith J., Silver L., Koide A. & Koide S. (2004). Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis. Journal of Molecular Biology 338, 811825.
Yan S., Kennedy S. D. & Koide S. (2002). Thermodynamic and kinetic exploration of the energy landscape of Borrelia budgdorferi OspA by native-state hydrogen exchange. Journal of Molecular Biology 323, 363375.
Yewdell J. W. (2005). Serendipity strikes twice: the discovery and rediscovery of defective ribosomal products (DRiPS). Cell and Molecular Biology 51, 635641.
Zhang Z. & Smith D. L. (1993). Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Science 2, 522531.
Zhou Z., Feng H. & Bai Y. (2006). Detection of a hidden folding intermediate in the focal adhesion target domain: implications for its function and folding. Proteins: Structure, Function, Genetics 65, 259265.
Zimm G. H. & Bragg J. K. (1959). Theory of the phase transition between helix and random coil in polypeptide chains. Journal of Chemical Physics 31, 526535.
Zwanzig R., Szabo A. & Bagchi B. (1992). Levinthal's paradox. Proceedings of the National Academy of Sciences USA 89, 2022.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Full text views

Total number of HTML views: 5
Total number of PDF views: 82 *
Loading metrics...

Abstract views

Total abstract views: 390 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 25th November 2017. This data will be updated every 24 hours.