The folding of single domain proteins--have we reached a consensus?

Rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. These topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.

[1]  Vijay S Pande,et al.  Progress and challenges in the automated construction of Markov state models for full protein systems. , 2009, The Journal of chemical physics.

[2]  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.

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

[4]  Distinguishing between smooth and rough free energy barriers in protein folding. , 2009, Biochemistry.

[5]  S. Marqusee,et al.  Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues. , 2010, Biochemistry.

[6]  Vijay S Pande,et al.  Solvent viscosity dependence of the protein folding dynamics. , 2008, The journal of physical chemistry. B.

[7]  Jeanette Tångrot,et al.  Complete change of the protein folding transition state upon circular permutation , 2002, Nature Structural Biology.

[8]  Sheena E Radford,et al.  Intermediates: ubiquitous species on folding energy landscapes? , 2007, Current opinion in structural biology.

[9]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[10]  E. Kondrashkina,et al.  Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein , 2008, Proceedings of the National Academy of Sciences.

[11]  Kevin W Plaxco,et al.  The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics , 2003, Protein science : a publication of the Protein Society.

[12]  R. Best,et al.  Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water. , 2010, Biophysical journal.

[13]  Abhishek K. Jha,et al.  Statistical coil model of the unfolded state: resolving the reconciliation problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Tobin R Sosnick,et al.  Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  V. Pande,et al.  Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. , 2003, Journal of Molecular Biology.

[16]  Satoshi Takahashi,et al.  Specifically collapsed intermediate in the early stage of the folding of ribonuclease A. , 2005, Journal of molecular biology.

[17]  The denatured state of N-PGK is compact and predominantly disordered. , 2009, Journal of molecular biology.

[18]  Lisa J Lapidus,et al.  Extremely slow intramolecular diffusion in unfolded protein L , 2010, Proceedings of the National Academy of Sciences.

[19]  D. Thirumalai,et al.  Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. , 2009, Biochemistry.

[20]  D. Raleigh,et al.  The cold denatured state of the C-terminal domain of protein L9 is compact and contains both native and non-native structure. , 2010, Journal of the American Chemical Society.

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

[22]  J. Onuchic,et al.  Folding a protein in a computer: An atomic description of the folding/unfolding of protein A , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Alex Kentsis,et al.  D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding , 2000, Nature Structural Biology.

[24]  Pallav Kosuri,et al.  Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersion , 2009, Journal of biomolecular NMR.

[25]  Protein vivisection reveals elusive intermediates in folding. , 2010, Journal of molecular biology.

[26]  D. Goldenberg,et al.  φ-Values for BPTI folding intermediates and implications for transition state analysis , 2001, Nature Structural Biology.

[27]  Athi N. Naganathan,et al.  Direct observation of downhill folding of lambda-repressor in a microfluidic mixer. , 2009, Biophysical journal.

[28]  C. Royer,et al.  V(i)-value analysis: a pressure-based method for mapping the folding transition state ensemble of proteins. , 2007, Journal of the American Chemical Society.

[29]  Bernard R Brooks,et al.  Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model , 2008, Proceedings of the National Academy of Sciences.

[30]  Vijay S Pande,et al.  Protein folded states are kinetic hubs , 2010, Proceedings of the National Academy of Sciences.

[31]  Yawen Bai,et al.  Structural examination of Φ-value analysis in Protein folding , 2004 .

[32]  A. Kentsis,et al.  Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[33]  E. Kondrashkina,et al.  Microsecond Hydrophobic Collapse in the Folding of Escherichia coli Dihydrofolate Reductase, an α/β-Type Protein , 2007 .

[34]  B. Bowler,et al.  Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences , 2010, Proceedings of the National Academy of Sciences.

[35]  S. Marqusee,et al.  A single mutation at residue 25 populates the folding intermediate of E. coli RNase H and reveals a highly dynamic partially folded ensemble. , 2009, Journal of molecular biology.

[36]  J. Udgaonkar,et al.  Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase. , 2010, Journal of molecular biology.

[37]  K. Plaxco,et al.  Non-sequence-specific interactions can account for the compaction of proteins unfolded under "native" conditions. , 2009, Journal of molecular biology.

[38]  M. Gruebele,et al.  A survey of lambda repressor fragments from two-state to downhill folding. , 2010, Journal of molecular biology.

[39]  D Thirumalai,et al.  Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. , 2005, Journal of molecular biology.

[40]  R. Sauer,et al.  Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects , 2002, Nature Structural Biology.

[41]  Satoshi Takahashi,et al.  Specific collapse followed by slow hydrogen-bond formation of beta-sheet in the folding of single-chain monellin. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Jayant B Udgaonkar,et al.  Multiple routes and structural heterogeneity in protein folding. , 2008, Annual review of biophysics.

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

[44]  L. Serrano,et al.  Loop length, intramolecular diffusion and protein folding , 1997, Nature Structural Biology.

[45]  D. Raleigh,et al.  Phi-value analysis for ultrafast folding proteins by NMR relaxation dispersion. , 2010, Journal of the American Chemical Society.

[46]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[47]  K. Freed,et al.  Quantifying the structural requirements of the folding transition state of protein A and other systems. , 2008, Journal of molecular biology.

[48]  Robin S. Dothager,et al.  Differences in the folding transition state of ubiquitin indicated by φ and ψ analyses , 2004 .

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

[50]  J. Portman,et al.  Cooperativity and protein folding rates. , 2010, Current opinion in structural biology.

[51]  D. Engelman,et al.  Mutations can cause large changes in the conformation of a denatured protein. , 1993, Biochemistry.

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

[53]  Hue Sun Chan,et al.  Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins , 2010, Proceedings of the National Academy of Sciences.

[54]  Robert L. Baldwin,et al.  Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A , 1995, Nature.

[55]  Effect of point mutations on the folding of globular proteins. , 1987, Methods in enzymology.

[56]  P. Wolynes,et al.  Folding funnels and energy landscapes of larger proteins within the capillarity approximation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[57]  P. Harbury,et al.  The equilibrium unfolding pathway of a (beta/alpha)8 barrel. , 2002, Journal of molecular biology.

[58]  S. Marqusee,et al.  The folding trajectory of RNase H is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms. , 2009, Journal of molecular biology.

[59]  H. Chan,et al.  Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding , 2008, Proceedings of the National Academy of Sciences.

[60]  Hue Sun Chan,et al.  Desolvation is a likely origin of robust enthalpic barriers to protein folding. , 2005, Journal of molecular biology.

[61]  Bing Shan,et al.  The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure. , 2009, Biochemistry.

[62]  K. Plaxco,et al.  Is There or Isn't There? The Case for (and Against) Residual Structure in Chemically Denatured Proteins , 2005, Critical reviews in biochemistry and molecular biology.

[63]  Frank Küster,et al.  Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins , 2009, Proceedings of the National Academy of Sciences.

[64]  Abhishek K. Jha,et al.  Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. , 2005, Biochemistry.

[65]  D. Raleigh,et al.  Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein , 2009, Protein science : a publication of the Protein Society.

[66]  Ronald Wetzel,et al.  Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions , 2006, Proceedings of the National Academy of Sciences.

[67]  J. Marsh,et al.  Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints. , 2009, Journal of molecular biology.

[68]  James E. Fitzgerald,et al.  Mimicking the folding pathway to improve homology-free protein structure prediction , 2009, Proceedings of the National Academy of Sciences.

[69]  Jan Kubelka,et al.  Specificity of the initial collapse in the folding of the cold shock protein. , 2006, Journal of molecular biology.

[70]  E. Kondrashkina,et al.  Mapping the folding free energy surface for metal-free human Cu,Zn superoxide dismutase. , 2006, Journal of molecular biology.

[71]  D. Thirumalai,et al.  Viscosity Dependence of the Folding Rates of Proteins , 1997, cond-mat/9705309.

[72]  J. Onuchic,et al.  Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Ronald D. Hills,et al.  Subdomain competition, cooperativity, and topological frustration in the folding of CheY. , 2008, Journal of molecular biology.

[74]  William A Eaton,et al.  Measuring internal friction of an ultrafast-folding protein , 2008, Proceedings of the National Academy of Sciences.

[75]  Folding of the KIX domain: characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. , 2008, Journal of molecular biology.

[76]  M. Kataoka,et al.  Trifluoroethanol‐induced conformational transition of hen egg‐white lysozyme studied by small‐angle X‐ray scattering , 1997, FEBS letters.

[77]  W. Eaton,et al.  Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations , 2007, Proceedings of the National Academy of Sciences.

[78]  L. Reymond,et al.  Charge interactions can dominate the dimensions of intrinsically disordered proteins , 2010, Proceedings of the National Academy of Sciences.

[79]  R. Ghirlando,et al.  The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H. , 2008, Journal of molecular biology.

[80]  Peter L. Freddolino,et al.  Force field bias in protein folding simulations. , 2009, Biophysical journal.

[81]  T. Kiefhaber,et al.  Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. , 2003, Journal of molecular biology.

[82]  Robin S. Dothager,et al.  Early collapse is not an obligate step in protein folding. , 2004, Journal of molecular biology.

[83]  Yawen Bai,et al.  Detection and structure determination of an equilibrium unfolding intermediate of Rd-apocytochrome b562: native fold with non-native hydrophobic interactions. , 2004, Journal of molecular biology.

[84]  M. Karplus,et al.  Transition state contact orders correlate with protein folding rates. , 2005, Journal of molecular biology.

[85]  S. Hagen,et al.  Solvent friction changes the folding pathway of the tryptophan zipper TZ2. , 2009, Journal of molecular biology.

[86]  David Baker,et al.  Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain , 1998, Nature Structural &Molecular Biology.

[87]  J. Danielsson,et al.  Cooperative formation of native-like tertiary contacts in the ensemble of unfolded states of a four-helix protein , 2010, Proceedings of the National Academy of Sciences.

[88]  Haipeng Gong,et al.  Local secondary structure content predicts folding rates for simple, two-state proteins. , 2003, Journal of molecular biology.

[89]  S. Michnick,et al.  Multiple tryptophan probes reveal that ubiquitin folds via a late misfolded intermediate. , 2007, Journal of molecular biology.

[90]  Satoshi Takahashi,et al.  Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[91]  D. Baker,et al.  The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection , 2007, Cell.

[92]  Athi N. Naganathan,et al.  Insights into protein folding mechanisms from large scale analysis of mutational effects , 2010, Proceedings of the National Academy of Sciences.

[93]  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.

[94]  Yawen Bai,et al.  The folding pathway of T4 lysozyme: the high-resolution structure and folding of a hidden intermediate. , 2007, Journal of molecular biology.

[95]  S. Radford,et al.  NMR Analysis of the Conformational Properties of the Trapped on-pathway Folding Intermediate of the Bacterial Immunity Protein Im7 , 2007, Journal of molecular biology.

[96]  J. Udgaonkar,et al.  Unfolding rates of barstar determined in native and low denaturant conditions indicate the presence of intermediates. , 2002, Biochemistry.

[97]  A. Garcia,et al.  Equilibrium study of protein denaturation by urea. , 2010, Journal of the American Chemical Society.

[98]  S. Hagen,et al.  Internal friction controls the speed of protein folding from a compact configuration. , 2004, Biochemistry.

[99]  David Baker,et al.  Experiment and theory highlight role of native state topology in SH3 folding , 1999, Nature Structural Biology.

[100]  David Baker,et al.  Structural and kinetic characterization of the simplified SH3 domain FP1 , 2003, Protein science : a publication of the Protein Society.

[101]  K. Freed,et al.  Psi-constrained simulations of protein folding transition states: implications for calculating. , 2009, Journal of molecular biology.

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

[103]  Yawen Bai,et al.  Structural examination of phi-value analysis in protein folding. , 2004, Biochemistry.

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

[105]  Satoshi Takahashi,et al.  Time-resolved small-angle X-ray scattering investigation of the folding dynamics of heme oxygenase: implication of the scaling relationship for the submillisecond intermediates of protein folding. , 2006, Journal of molecular biology.

[106]  Sebastian Hansson,et al.  Folding of S6 structures with divergent amino acid composition: pathway flexibility within partly overlapping foldons. , 2006, Journal of molecular biology.

[107]  Ronald D. Hills,et al.  Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. , 2010, Journal of molecular biology.

[108]  A. Fersht,et al.  Direct observation of ultrafast folding and denatured state dynamics in single protein molecules , 2009, Proceedings of the National Academy of Sciences.

[109]  Cecilia Clementi,et al.  Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. , 2004, Journal of the American Chemical Society.

[110]  D Baker,et al.  Limited internal friction in the rate-limiting step of a two-state protein folding reaction. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[111]  M. Oliveberg,et al.  Malleability of protein folding pathways: a simple reason for complex behaviour. , 2007, Current opinion in structural biology.

[112]  G. Rose,et al.  Dry molten globule intermediates and the mechanism of protein unfolding , 2010, Proteins.

[113]  Peter G Wolynes,et al.  Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A. , 2005, Biochemistry.

[114]  Andreas Matouschek,et al.  Transient folding intermediates characterized by protein engineering , 1990, Nature.

[115]  J. Udgaonkar,et al.  Direct evidence for a dry molten globule intermediate during the unfolding of a small protein , 2009, Proceedings of the National Academy of Sciences.

[116]  Michael Wilde,et al.  Protein structure prediction enhanced with evolutionary diversity: SPEED , 2010, Protein science : a publication of the Protein Society.

[117]  Robin S. Dothager,et al.  Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[118]  T. Sosnick,et al.  Fast folding of a helical protein initiated by the collision of unstructured chains. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[119]  T. Sosnick,et al.  Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil. , 1999, Biochemistry.

[120]  Vincent A Voelz,et al.  Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. , 2010, Journal of the American Chemical Society.

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

[122]  Lewis E. Kay,et al.  Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy , 2008, Proceedings of the National Academy of Sciences.

[123]  T. Schindler,et al.  Diffusion control in an elementary protein folding reaction. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[124]  T. Sosnick,et al.  Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil , 2001, Nature Structural Biology.

[125]  Guy Ziv,et al.  Protein folding, protein collapse, and tanford's transfer model: lessons from single-molecule FRET. , 2009, Journal of the American Chemical Society.

[126]  K. Dill,et al.  Transition-states in protein folding kinetics: the structural interpretation of Phi values. , 2006, Journal of molecular biology.

[127]  A. Tokmakoff,et al.  Temperature‐dependent downhill unfolding of ubiquitin. I. Nanosecond‐to‐millisecond resolved nonlinear infrared spectroscopy , 2008, Proteins.

[128]  Athi N. Naganathan,et al.  Dynamics of one-state downhill protein folding , 2009, Proceedings of the National Academy of Sciences.

[129]  S. Radford,et al.  Single-Molecule Studies of the Im7 Folding Landscape , 2010, Journal of molecular biology.

[130]  D. Baker,et al.  Chain collapse can occur concomitantly with the rate-limiting step in protein folding , 1999, Nature Structural Biology.

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

[132]  D. Barrick,et al.  Unique features of the folding landscape of a repeat protein revealed by pressure perturbation. , 2010, Biophysical journal.

[133]  David Baker,et al.  Computer-based redesign of a protein folding pathway , 2001, Nature Structural Biology.

[134]  V. Muñoz,et al.  A simple model for calculating the kinetics of protein folding from three-dimensional structures. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[135]  Robin S. Dothager,et al.  Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature. , 2007, Journal of molecular biology.

[136]  Dmitri I Svergun,et al.  Biophysical characterization of the unstructured cytoplasmic domain of the human neuronal adhesion protein neuroligin 3. , 2008, Biophysical journal.

[137]  Benjamin Schuler,et al.  Ultrafast dynamics of protein collapse from single-molecule photon statistics , 2007, Proceedings of the National Academy of Sciences.

[138]  T. Sosnick,et al.  Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. , 2002, Journal of molecular biology.

[139]  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.

[140]  H. Dyson,et al.  Energetic frustration of apomyoglobin folding: role of the B helix. , 2010, Journal of molecular biology.

[141]  S. Radford,et al.  Desolvation and Development of Specific Hydrophobic Core Packing during Im7 Folding , 2010, Journal of molecular biology.

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

[143]  K. Lindorff-Larsen,et al.  Parallel protein-unfolding pathways revealed and mapped , 2003, Nature Structural Biology.

[144]  O. V. Galzitskaya,et al.  On the Prediction of Folding Nuclei in Globular Proteins , 2005, Molecular Biology.

[145]  Dmitry M Korzhnev,et al.  A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution , 2010, Science.

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

[147]  S M Gruner,et al.  Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[148]  William A Eaton,et al.  Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories , 2009, Proceedings of the National Academy of Sciences.

[149]  J. Berger,et al.  Contributions of folding cores to the thermostabilities of two ribonucleases H , 2002, Protein science : a publication of the Protein Society.

[150]  Daniel Boehringer,et al.  The folding transition state of the cold shock protein is strongly polarized. , 2004, Journal of molecular biology.

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

[152]  M Wilmanns,et al.  Solvation in protein folding analysis: combination of theoretical and experimental approaches. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[153]  Abhishek K. Jha,et al.  Small proteins fold through transition states with native-like topologies. , 2006, Journal of molecular biology.

[154]  A. Fersht Nucleation mechanisms in protein folding. , 1997, Current opinion in structural biology.

[155]  Hue Sun Chan,et al.  Simple two‐state protein folding kinetics requires near‐levinthal thermodynamic cooperativity , 2003, Proteins.

[156]  P. Henklein,et al.  An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain , 2010, Proceedings of the National Academy of Sciences.

[157]  A. Fersht,et al.  The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. , 1995, Journal of molecular biology.

[158]  D. Thirumalai,et al.  Kinetics of protein folding: Nucleation mechanism, time scales, and pathways , 1995 .

[159]  D. Thirumalai,et al.  Collapse transition in proteins. , 2009, Physical chemistry chemical physics : PCCP.

[160]  E I Shakhnovich,et al.  Specific nucleus as the transition state for protein folding: evidence from the lattice model. , 1994, Biochemistry.

[161]  D. Goldenberg,et al.  Small-angle X-ray scattering of reduced ribonuclease A: effects of solution conditions and comparisons with a computational model of unfolded proteins. , 2008, Journal of molecular biology.

[162]  Gerhard Hummer,et al.  Coordinate-dependent diffusion in protein folding , 2009, Proceedings of the National Academy of Sciences.

[163]  A. D. Robertson,et al.  Kinetics of unfolding and folding from amide hydrogen exchange in native ubiquitin , 2001, Nature Structural Biology.

[164]  S. Jackson,et al.  Ubiquitin folds through a highly polarized transition state. , 2005, Protein engineering, design & selection : PEDS.

[165]  Peter G Wolynes,et al.  The folding energy landscape and free energy excitations of cytochrome c. , 2010, Accounts of chemical research.

[166]  Tobin R Sosnick,et al.  Kinetic barriers and the role of topology in protein and RNA folding , 2008, Protein science : a publication of the Protein Society.

[167]  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.

[168]  C. Schütte,et al.  Supplementary Information for “ Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations ” , 2009 .

[169]  Hongyi Zhou,et al.  Critical nucleation size in the folding of small apparently two‐state proteins , 2004, Protein Science.

[170]  Jane Clarke,et al.  Experimental evidence for a frustrated energy landscape in a 3-helix bundle protein family , 2009, Nature.

[171]  A. Fersht,et al.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. , 1991, Biochemistry.

[172]  H. Chan,et al.  Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins. , 2009, Journal of molecular biology.

[173]  Robin S. Dothager,et al.  Characterizing protein folding transition States using Psi-analysis. , 2007, Methods in molecular biology.

[174]  A. Fersht,et al.  Direct observation of barrier-limited folding of BBL by single-molecule fluorescence resonance energy transfer , 2009, Proceedings of the National Academy of Sciences.

[175]  David A. C. Beck,et al.  Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate. , 2010, Biophysical journal.

[176]  Joan-Emma Shea,et al.  Probing the folding free energy landscape of the src-SH3 protein domain , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[177]  A. Garcia,et al.  Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein , 2010, Proteins.

[178]  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.

[179]  L. Kay,et al.  Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques. , 2002, Journal of molecular biology.

[180]  Hue Sun Chan,et al.  Conformational entropic barriers in topology-dependent protein folding: perspectives from a simple native-centric polymer model , 2006 .

[181]  Gerra L. Bosco,et al.  Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates. , 2009, Biochemistry.

[182]  A. Zarrine-Afsar,et al.  Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy. , 2006, Journal of molecular biology.

[183]  Yawen Bai,et al.  Probing the folding intermediate of Rd‐apocyt b562 by protein engineering and infrared T‐jump , 2007, Protein science : a publication of the Protein Society.

[184]  S. Hagen,et al.  Solvent viscosity and friction in protein folding dynamics. , 2010, Current protein & peptide science.

[185]  Kyle A. Beauchamp,et al.  Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). , 2010, Journal of the American Chemical Society.

[186]  P. Neudecker,et al.  Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding. , 2009, Biophysical journal.

[187]  A. Fersht,et al.  Time-resolved fluorescence resonance energy transfer study shows a compact denatured state of the B domain of protein A. , 2009, Biochemistry.

[188]  Caitlin L. Chicoine,et al.  Net charge per residue modulates conformational ensembles of intrinsically disordered proteins , 2010, Proceedings of the National Academy of Sciences.

[189]  Doug Barrick,et al.  Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape. , 2008, Journal of the American Chemical Society.

[190]  Temperature dependence of the free energy landscape of the src‐SH3 protein domain , 2004, Proteins.

[191]  Laura S Itzhaki,et al.  Shifting transition states in the unfolding of a large ankyrin repeat protein , 2008, Proceedings of the National Academy of Sciences.

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

[193]  A. Fersht,et al.  Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[194]  D Baker,et al.  Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. , 2000, Biochemistry.

[195]  Robin S. Dothager,et al.  Random-coil behavior and the dimensions of chemically unfolded proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[196]  Eilon Sherman,et al.  Coil-globule transition in the denatured state of a small protein. , 2006, Proceedings of the National Academy of Sciences of the United States of America.