Protein folding and misfolding: mechanism and principles

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.

[1]  H. Gray,et al.  Snapshots of cytochrome c folding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Tracy M. Handel,et al.  Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH , 1996, Nature Structural Biology.

[3]  Detection of a hidden folding intermediate in the focal adhesion target domain: Implications for its function and folding , 2006, Proteins.

[4]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[5]  L Mayne,et al.  Primary structure effects on peptide group hydrogen exchange. , 1972, Proteins.

[6]  P. S. Kim,et al.  Influence of charge on the rate of amide proton exchange. , 1982, Biochemistry.

[7]  L Mayne,et al.  Determinants of protein hydrogen exchange studied in equine cytochrome c , 1998, Protein science : a publication of the Protein Society.

[8]  T. Kiefhaber,et al.  Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate. , 1997, Journal of molecular biology.

[9]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[10]  H. Dyson,et al.  Identification of native and non-native structure in kinetic folding intermediates of apomyoglobin. , 2006, Journal of molecular biology.

[11]  C. Matthews,et al.  Proline replacements and the simplification of the complex, parallel channel folding mechanism for the alpha subunit of Trp synthase, a TIM barrel protein. , 2003, Journal of molecular biology.

[12]  R. L. Baldwin,et al.  Detection of an early intermediate in the folding of ribonuclease A by protection of amide protons against exchange. , 1979, Journal of molecular biology.

[13]  Yawen Bai,et al.  Primary structure effects on peptide group hydrogen exchange , 1993, Biochemistry.

[14]  Seishi Shimizu,et al.  Cooperativity principles in protein folding. , 2004, Methods in enzymology.

[15]  C. Matthews,et al.  Parallel channels and rate-limiting steps in complex protein folding reactions: prolyl isomerization and the alpha subunit of Trp synthase, a TIM barrel protein. , 2002, Journal of molecular biology.

[16]  J. Markley,et al.  Hydrogen exchange in unligated and ligated staphylococcal nuclease. , 1993, Biochemistry.

[17]  S. Lifson,et al.  On the Theory of Helix—Coil Transition in Polypeptides , 1961 .

[18]  D. Barrick,et al.  Nonspecific hydrophobic interactions stabilize an equilibrium intermediate of apomyoglobin at a key position within the AGH region. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Leland Mayne,et al.  Evidence for an unfolding and refolding pathway in cytochrome c , 1998, Nature Structural Biology.

[20]  John F. Carpenter,et al.  Physical Stability of Proteins in Aqueous Solution: Mechanism and Driving Forces in Nonnative Protein Aggregation , 2003, Pharmaceutical Research.

[21]  T. Sosnick,et al.  Protein folding intermediates: native-state hydrogen exchange. , 1995, Science.

[22]  N. Kallenbach,et al.  Hydrogen exchange and structural dynamics of proteins and nucleic acids , 1983, Quarterly Reviews of Biophysics.

[23]  S. Englander,et al.  How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. , 2004, Journal of molecular biology.

[24]  K. Wüthrich,et al.  Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. , 1982, Journal of molecular biology.

[25]  Valerie Daggett,et al.  Folding and binding: implementing the game plan , 2007 .

[26]  S. Marqusee,et al.  A rapid test for identification of autonomous folding units in proteins. , 2000, Journal of molecular biology.

[27]  O. Bilsel,et al.  Folding Mechanism of the α-Subunit of Tryptophan Synthase, an α/β Barrel Protein: Global Analysis Highlights the Interconversion of Multiple Native, Intermediate, and Unfolded Forms through Parallel Channels† , 1999 .

[28]  L. Mayne,et al.  Intimate view of a kinetic protein folding intermediate: residue-resolved structure, interactions, stability, folding and unfolding rates, homogeneity. , 2003, Journal of molecular biology.

[29]  T. Sosnick,et al.  Molecular collapse: The rate‐limiting step in two‐state cytochrome c folding , 1996, Proteins.

[30]  A. Fersht,et al.  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. , 2007, Journal of molecular biology.

[31]  S. Marqusee,et al.  Confirmation of the hierarchical folding of RNase H: a protein engineering study , 1999, Nature Structural Biology.

[32]  G. Moore,et al.  Cytochromes c , 1987, Springer Series in Molecular Biology.

[33]  S. Englander,et al.  The N-terminal to C-terminal motif in protein folding and function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  S. Kennedy,et al.  Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. , 2002, Journal of molecular biology.

[35]  S Walter Englander,et al.  Branching in the sequential folding pathway of cytochrome c , 2007, Protein science : a publication of the Protein Society.

[36]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[37]  S. Marqusee,et al.  A thermodynamic comparison of mesophilic and thermophilic ribonucleases H. , 1999, Biochemistry.

[38]  S. Walter Englander,et al.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR , 1988, Nature.

[39]  Kunihiro Kuwajima,et al.  Multiple parallel-pathway folding of proline-free Staphylococcal nuclease. , 2003, Journal of molecular biology.

[40]  T. Creighton.  Disulfide bonds as probes of protein folding pathways. , 1986, Methods in enzymology.

[41]  C. Dobson,et al.  Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR , 2004, Nature.

[42]  S. Englander.  A HYDROGEN EXCHANGE METHOD USING TRITIUM AND SEPHADEX: ITS APPLICATION TO RIBONUCLEASE. , 1963, Biochemistry.

[43]  Robin S. Dothager,et al.  Characterizing the protein folding transition state using psi analysis. , 2006, Chemical reviews.

[44]  G. Rose,et al.  Loops in globular proteins: a novel category of secondary structure. , 1986, Science.

[45]  Anna Tramontano,et al.  Critical assessment of methods of protein structure prediction—Round VII , 2007, Proteins.

[46]  T. Kiefhaber,et al.  A salt-induced kinetic intermediate is on a new parallel pathway of lysozyme folding. , 1999, Biochemistry.

[47]  S. Englander,et al.  Cytochrome c folding pathway: Kinetic native-state hydrogen exchange , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S W Englander,et al.  Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. , 1990, Biochemistry.

[49]  D. Covell,et al.  Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. , 1998, Biochemistry.

[50]  A. Hvidt.  A DISCUSSION OF THE PH DEPENDENCE OF THE HYDROGEN-DEUTERIUM EXCHANGE OF PROTEINS. , 1964, Comptes-rendus des travaux du Laboratoire Carlsberg.

[51]  P. S. Kim,et al.  Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. , 1982, Annual review of biochemistry.

[52]  S. Englander,et al.  Hydrogen exchange methods to study protein folding. , 2004, Methods.

[53]  P. Wolynes,et al.  A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  S. Englander,et al.  Folding units govern the cytochrome c alkaline transition. , 2003, Journal of molecular biology.

[55]  J. Fetrow,et al.  Assignment of 15N chemical shifts and 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c. , 1999, Biochemistry.

[56]  Sheena E. Radford,et al.  Im7 folding mechanism: misfolding on a path to the native state , 2002, Nature Structural Biology.

[57]  P E Wright,et al.  Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. , 1999, Journal of molecular biology.

[58]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1974, Nature.

[59]  C. Anfinsen,et al.  The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Michele Vendruscolo,et al.  Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. , 2003, Journal of the American Chemical Society.

[61]  Clare Woodward,et al.  Hydrogen exchange rates and protein folding , 1994 .

[62]  O. Bagasra,et al.  Proceedings of the National Academy of Sciences , 1914, Science.

[63]  Tobin R Sosnick,et al.  Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. , 2004, Journal of molecular biology.

[64]  S. Marqusee,et al.  The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions , 1997, Nature Structural Biology.

[65]  T. Oas,et al.  A statistical thermodynamic model of the protein ensemble. , 2006, Chemical reviews.

[66]  R Fine,et al.  FASTRUN: A special purpose, hardwired computer for molecular simulation , 1991, Proteins.

[67]  S Walter Englander,et al.  Protein folding: the stepwise assembly of foldon units. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Yingang Feng,et al.  Native-like partially folded conformations and folding process revealed in the N-terminal large fragments of staphylococcal nuclease: a study by NMR spectroscopy. , 2003, Journal of molecular biology.

[69]  Yawen Bai,et al.  [15] Thermodynamic parameters from hydrogen exchange measurements , 1995 .

[70]  A. Rosenberg,et al.  Studies of hydrogen exchange in proteins. I. The exchange kinetics of bovine carbonic anhydrase. , 1968, The Journal of biological chemistry.

[71]  J. Onuchic,et al.  Understanding protein folding with energy landscape theory Part I: Basic concepts , 2002, Quarterly Reviews of Biophysics.

[72]  K. Dill,et al.  Protein folding by zipping and assembly , 2007, Proceedings of the National Academy of Sciences.

[73]  A R Panchenko,et al.  Foldons, protein structural modules, and exons. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[74]  Fast and Slow Folding in Cytochrome c , 1999 .

[75]  Carlos Bustamante,et al.  Direct Observation of the Three-State Folding of a Single Protein Molecule , 2005, Science.

[76]  J. Onuchic,et al.  Protein folding funnels: a kinetic approach to the sequence-structure relationship. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[77]  J. Fetrow,et al.  Mutagenesis of histidine 26 demonstrates the importance of loop‐loop and loop‐protein interactions for the function of iso‐1‐cytochrome c , 1998, Protein science : a publication of the Protein Society.

[78]  R. L. Baldwin,et al.  Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[79]  R. Lipsitz,et al.  Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding. , 2003, Biochemistry.

[80]  J. Yewdell.  Serendipity strikes twice: the discovery and rediscovery of defective ribosomal products (DRiPS). , 2005, Cellular and molecular biology.

[81]  S. Marqusee,et al.  Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C‐terminal subdomain as a hidden intermediate in the kinetic folding pathway , 2007, Protein science : a publication of the Protein Society.

[82]  S. Englander,et al.  Cooperative omega loops in cytochrome c: role in folding and function. , 2003, Journal of molecular biology.

[83]  Englander Sw.  A HYDROGEN EXCHANGE METHOD USING TRITIUM AND SEPHADEX: ITS APPLICATION TO RIBONUCLEASE. , 1963 .

[84]  P. Harbury,et al.  The equilibrium unfolding pathway of a (β/α)8 barrel , 2002 .

[85]  Yawen Bai,et al.  Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein. , 2002, Biochemistry.

[86]  H. Vogel,et al.  A peptide analog of the calmodulin‐binding domain of myosin light chain kinase adopts an aL‐helical structure in aqueous trifluoroethanol , 1993, Protein science : a publication of the Protein Society.

[87]  P. Harbury,et al.  The equilibrium unfolding pathway of a ( b / a ) 8 barrel , 2002 .

[88]  R. L. Baldwin,et al.  Submillisecond unfolding kinetics of apomyoglobin and its pH 4 intermediate. , 1999, Journal of molecular biology.

[89]  S. Englander,et al.  Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity. , 2004, Journal of molecular biology.

[90]  T. Kiefhaber,et al.  Kinetic traps in lysozyme folding. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[91]  S. Walter Englander,et al.  Hydrogen exchange , 2001, Nature Structural Biology.

[92]  S. Englander.  Hydrogen exchange and mass spectrometry: A historical perspective , 2006, Journal of the American Society for Mass Spectrometry.

[93]  T. Kiefhaber,et al.  Direct measurement of nucleation and growth rates in lysozyme folding. , 1997, Biochemistry.

[94]  P E Wright,et al.  Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. , 1993, Science.

[95]  T. Kiefhaber,et al.  Origin of apparent fast and non-exponential kinetics of lysozyme folding measured in pulsed hydrogen exchange experiments. , 2001, Journal of molecular biology.

[96]  T. Sosnick,et al.  Hydrogen exchange: The modern legacy of Linderstrøm‐Lang , 1997, Protein science : a publication of the Protein Society.

[97]  C M Dobson,et al.  Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin. , 1989, Biochemistry.

[98]  Scott A. Peterson,et al.  Transthyretin quaternary and tertiary structural changes facilitate misassembly into amyloid. , 1997, Advances in protein chemistry.

[99]  S. Marqusee,et al.  Folding of an isolated ribonuclease H core fragment , 2008, Protein science : a publication of the Protein Society.

[100]  A J Wand,et al.  Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange. , 1998, Biochemistry.

[101]  Yawen Bai,et al.  Detection of a hidden folding intermediate of the third domain of PDZ. , 2005, Journal of molecular biology.

[102]  S W Englander,et al.  Measuring the conformational stability of a protein by hydrogen exchange. , 2001, Methods in molecular biology.

[103]  C. V. van Mierlo,et al.  The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[104]  Robert L. Baldwin,et al.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A , 1988, Nature.

[105]  A. Bhuyan,et al.  Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. , 1994, Biochemistry.

[106]  P E Wright,et al.  Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. , 2000, Biochemistry.

[107]  S W Englander,et al.  Experimental study of the protein folding landscape: unfolding reactions in cytochrome c. , 1999, Journal of molecular biology.

[108]  Terrence G. Oas,et al.  A peptide model of a protein folding intermediate , 1988, Nature.

[109]  S W Englander,et al.  Protein complexes studied by NMR spectroscopy. , 1996, Current opinion in biotechnology.

[110]  S. Marqusee,et al.  Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. , 2000, Advances in protein chemistry.

[111]  P E Wright,et al.  Structural characterization of a partly folded apomyoglobin intermediate. , 1990, Science.

[112]  J Rumbley,et al.  An amino acid code for protein folding. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[113]  J Clarke,et al.  An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. , 1996, Folding & design.

[114]  J G Pelton,et al.  Structure of the acid state of Escherichia coli ribonuclease HI. , 1996, Biochemistry.

[115]  Virgil L. Woods,et al.  Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[116]  S W Englander,et al.  Isotope effects in peptide group hydrogen exchange , 1993, Proteins.

[117]  G. Hummer,et al.  Conformational dynamics of cytochrome c: Correlation to hydrogen exchange , 1999, Proteins.

[118]  F Sherman,et al.  Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding. , 1996, Biochemistry.

[119]  A. R. Tammar,et al.  Protein Structure and Enzyme Activity , 1985 .

[120]  A J Wand,et al.  Local stability and dynamics of apocytochrome b562 examined by the dependence of hydrogen exchange on hydrostatic pressure. , 1998, Biochemistry.

[121]  A. Zarrine-Afsar,et al.  Φ-Value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy , 2007, Proceedings of the National Academy of Sciences.

[122]  J. Onuchic,et al.  Understanding protein folding with energy landscape theory Part II: Quantitative aspects , 2002, Quarterly Reviews of Biophysics.

[123]  C. Woodward,et al.  Hydrogen exchange identifies native-state motional domains important in protein folding. , 1993, Biochemistry.

[124]  D Eisenberg,et al.  Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. , 1997, Advances in protein chemistry.

[125]  P. Neudecker,et al.  Abp1p and Fyn SH3 domains fold through similar low-populated intermediate states. , 2006, Biochemistry.

[126]  L. Mayne,et al.  Two‐state vs. multistate protein unfolding studied by optical melting and hydrogen exchange , 2000, Protein science : a publication of the Protein Society.

[127]  J. Onuchic,et al.  Navigating the folding routes , 1995, Science.

[128]  S. Englander,et al.  Functional role of a protein foldon—An Ω‐loop foldon controls the alkaline transition in ferricytochrome c , 2005, Proteins.

[129]  S Walter Englander,et al.  Protein hydrogen exchange mechanism: Local fluctuations , 2003, Protein science : a publication of the Protein Society.

[130]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[131]  Yawen Bai,et al.  Protein stability parameters measured by hydrogen exchange , 1994, Proteins.

[132]  A. Koide,et al.  Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis. , 2004, Journal of molecular biology.

[133]  Zhongqi Zhang,et al.  Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation , 1993, Protein science : a publication of the Protein Society.

[134]  Yawen Bai,et al.  The folding pathway of barnase: the rate-limiting transition state and a hidden intermediate under native conditions. , 2004, Biochemistry.

[135]  R. Zwanzig,et al.  Levinthal's paradox. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[136]  C. Matthews,et al.  The progressive development of structure and stability during the equilibrium folding of the α subunit of tryptophan synthase from Escherichia coli , 1999, Protein science : a publication of the Protein Society.

[137]  Jan Hermans,et al.  The Stability of Globular Protein , 1975 .

[138]  Yawen Bai,et al.  Fast and Slow Folding in Cytochrome c , 1998 .

[139]  S. Englander,et al.  A unified mechanism for protein folding: Predetermined pathways with optional errors , 2007, Protein science : a publication of the Protein Society.

[140]  C. Woodward,et al.  Hydrogen exchange and the dynamic structure of proteins , 1982, Molecular and Cellular Biochemistry.

[141]  O. Ptitsyn,et al.  Molten globule and protein folding. , 1995, Advances in protein chemistry.

[142]  J. R. Rogero,et al.  Protein hydrogen exchange studied by the fragment separation method. , 1985, Analytical biochemistry.

[143]  M. Ikeda-Saito,et al.  Kinetic study of isomerization of ferricytochrome c at alkaline pH. , 1976, Biochimica et biophysica acta.

[144]  P E Wright,et al.  Changes in the apomyoglobin folding pathway caused by mutation of the distal histidine residue. , 2000, Biochemistry.

[145]  S W Englander,et al.  Future directions in folding: The multi‐state nature of protein structure , 1996, Proteins.

[146]  C. Pace,et al.  The stability of globular proteins. , 1975, CRC critical reviews in biochemistry.

[147]  C. Pace,et al.  Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding , 1995, Protein science : a publication of the Protein Society.

[148]  C. Woodward,et al.  Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. , 1979, Annual review of biophysics and bioengineering.

[149]  A. Wand,et al.  The foldon substructure of staphylococcal nuclease. , 2008, Journal of molecular biology.

[150]  J. Onuchic,et al.  Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.

[151]  K. Lam,et al.  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. , 1999, Biochemistry.

[152]  R. Goldberger,et al.  Purification and properties of an enzyme from beef liver which catalyzes sulfhydryl-disulfide interchange in proteins. , 1966, The Journal of biological chemistry.

[153]  S. Eyles,et al.  Methods to study protein dynamics and folding by mass spectrometry. , 2004, Methods.

[154]  S Walter Englander,et al.  Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism. , 2006, Journal of molecular biology.

[155]  H. Dyson,et al.  Mechanism of coupled folding and binding of an intrinsically disordered protein , 2007, Nature.

[156]  C. Dobson,et al.  The folding of hen lysozyme involves partially structured intermediates and multiple pathways , 1992, Nature.

[157]  C. Matthews,et al.  Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions. , 2002, Biophysical chemistry.

[158]  A. Hvidt,et al.  Hydrogen exchange in proteins. , 1966, Advances in protein chemistry.

[159]  P. S. Kim,et al.  Intermediates in the folding reactions of small proteins. , 1990, Annual review of biochemistry.

[160]  A. Fontana,et al.  Protein interactions leading to conformational changes monitored by limited proteolysis: apo form and fragments of horse cytochrome c. , 2001, Biochemistry.

[161]  S W Englander,et al.  Energetic components of the allosteric machinery in hemoglobin measured by hydrogen exchange. , 1998, Journal of molecular biology.

[162]  Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature. , 2000 .

[163]  P. Harbury,et al.  Rapid Mapping of Protein Structure, Interactions, and Ligand Binding by Misincorporation Proton-Alkyl Exchange* , 2002, The Journal of Biological Chemistry.

[164]  N R Kallenbach,et al.  Proteolysis as a measure of the free energy difference between cytochrome c and its derivatives , 1998, Protein science : a publication of the Protein Society.

[165]  Y. Bai,et al.  Thermodynamic parameters from hydrogen exchange measurements. , 1995, Methods in enzymology.

[166]  T. Sosnick,et al.  The barriers in protein folding , 1994, Nature Structural Biology.

[167]  C. Levinthal.  How to fold graciously , 1969 .

[168]  Yawen Bai,et al.  The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate. , 2007, Journal of molecular biology.

[169]  Yawen Bai,et al.  A protein folding pathway with multiple folding intermediates at atomic resolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[170]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.