Mechanism of protein folding

The high structural resolution of the main transition states for the formation of native structure for the six small proteins of which Φ‐values for a large set of mutants have become available, barstar, barnase, chymotrypsin inhibitor 2, Arc repressor, the src SH3 domain, and a tetrameric p53 domain reveals that for the first 5 of these proteins: (1) Residues that belong to regular secondary structure have a significantly larger average fraction of native structural consolidation than residues in loops; (2) on the other hand, secondary and tertiary structures have built up to the same degree, or at least a high degree, but nonuniformly distributed over the molecule; (3) the most consolidated parts of each protein molecule in the transition state cluster together, and these clusters contain a significantly higher percentage of residues that belong to regular secondary structure than the rest of the molecule. These observations further reconcile the framework model with the nucleation‐condensation mechanism for folding: The amazing speed of protein folding can be understood as caused by the catalytic effect of the formation of clusters of residues which have particularly high preferences for the early formation of regular secondary structure in the presence of significant amounts of tertiary structure interactions. Proteins 2000;41:288–298. © 2000 Wiley‐Liss, Inc.

[1]  K. Dill.  Dominant forces in protein folding. , 1990, Biochemistry.

[2]  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.

[3]  P. Wolynes,et al.  Symmetry and the energy landscapes of biomolecules. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[4]  L. Mirny,et al.  Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. , 1999, Journal of molecular biology.

[5]  O. Ptitsyn,et al.  A model of myoglobin self-organization. , 1975, Biophysical chemistry.

[6]  R. Sauer,et al.  Evolution of a protein fold in vitro. , 1999, Science.

[7]  S. Rackovsky,et al.  Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Fersht,et al.  Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[9]  K. Kuwajima,et al.  The burst-phase intermediate in the refolding of beta-lactoglobulin studied by stopped-flow circular dichroism and absorption spectroscopy. , 1996, Journal of molecular biology.

[10]  L Serrano,et al.  The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. , 1992, Journal of molecular biology.

[11]  C. Batt,et al.  Is folding of β-lactoglobulin non-hierarchic? intermediate with native-like β-sheet and non-native α-helix , 2000 .

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

[13]  Christopher M. Dobson,et al.  Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding , 1999, Nature Structural Biology.

[14]  T. Kiefhaber,et al.  Protein folding kinetics. , 1995, Methods in molecular biology.

[15]  M. Gruebele,et al.  Direct observation of fast protein folding: the initial collapse of apomyoglobin. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[16]  D. Hamada,et al.  The equilibrium intermediate of beta-lactoglobulin with non-native alpha-helical structure. , 1997, Journal of molecular biology.

[17]  R. Carrell,et al.  Conformational changes and disease--serpins, prions and Alzheimer's. , 1998, Current opinion in structural biology.

[18]  E. Shakhnovich,et al.  A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. , 1998, Folding & design.

[19]  K A Dill,et al.  The meaning of hydrophobicity. , 1990, Science.

[20]  A. Fersht,et al.  Mapping the transition state and pathway of protein folding by protein engineering , 1989, Nature.

[21]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[22]  L Serrano,et al.  The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure. , 1992, Journal of molecular biology.

[23]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[24]  H. Chan.  Protein folding: Matching speed and locality , 1998, Nature.

[25]  K. Breslauer,et al.  Volumetric characterizations of the native, molten globule and unfolded states of cytochrome c at acidic pH. , 1995, Journal of molecular biology.

[26]  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.

[27]  A. Fersht,et al.  Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution. , 1994, Biochemistry.

[28]  C. Masters,et al.  Spongiform encephalopathies: Tracking turncoat prion proteins , 1997, Nature.

[29]  L. Serrano,et al.  Obligatory steps in protein folding and the conformational diversity of the transition state , 1998, Nature Structural &Molecular Biology.

[30]  Luis Serrano,et al.  The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved , 1999, Nature Structural Biology.

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

[32]  C. Arrowsmith,et al.  Solution structure of the tetrameric minimum transforming domain of p53 , 1995, Nature Structural Biology.

[33]  Michael J. Eck,et al.  Three-dimensional structure of the tyrosine kinase c-Src , 1997, Nature.

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

[35]  K. Kuwajima.  The molten globule state of α‐lactalbumin , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[36]  R. Dyer,et al.  Fast events in protein folding: the time evolution of primary processes. , 1998, Annual review of physical chemistry.

[37]  M Karplus,et al.  Protein folding dynamics: The diffusion‐collision model and experimental data , 1994, Protein science : a publication of the Protein Society.

[38]  M Karplus,et al.  The fundamentals of protein folding: bringing together theory and experiment. , 1999, Current opinion in structural biology.

[39]  R. A. Goldbeck,et al.  Multiple pathways on a protein-folding energy landscape: kinetic evidence. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Gruebele,et al.  Observation of strange kinetics in protein folding. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  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.

[42]  E. Shakhnovich.  Folding by association , 1999, Nature Structural Biology.

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

[44]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[45]  L Serrano,et al.  The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure. , 1992, Journal of molecular biology.

[46]  Serrano,et al.  Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. , 1995, Folding & design.

[47]  A. Fersht,et al.  The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. , 1992, Journal of molecular biology.

[48]  A. Fersht,et al.  Submillisecond events in protein folding. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Fersht,et al.  Three-dimensional solution structure and 13C assignments of barstar using nuclear magnetic resonance spectroscopy. , 1994, Biochemistry.

[50]  L Serrano,et al.  The folding of an enzyme. VI. The folding pathway of barnase: comparison with theoretical models. , 1992, Journal of molecular biology.

[51]  A. Fersht,et al.  Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

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

[53]  R. Sauer,et al.  P22 Arc repressor: transition state properties inferred from mutational effects on the rates of protein unfolding and refolding. , 1995, Biochemistry.

[54]  J. Hofrichter,et al.  Fast events in protein folding. , 1996, Structure.

[55]  A. Fersht.  Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Alan R. Fersht,et al.  Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53 , 1999, Nature Structural Biology.

[57]  M Karplus,et al.  "New view" of protein folding reconciled with the old through multiple unfolding simulations. , 1997, Science.

[58]  B. Nölting.  Analysis of the Folding Pathway of Chymotrypsin Inhibitor by Correlation of Φ-values with Inter-residue Contacts , 1999 .

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

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

[61]  A. Fersht,et al.  Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments. , 1999, Journal of molecular biology.

[62]  Christopher M Dobson,et al.  From Computer Simulations to Human Disease Emerging Themes in Protein Folding , 1999, Cell.

[63]  G Schreiber,et al.  The folding pathway of a protein at high resolution from microseconds to seconds. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Benjamin A. Shoemaker,et al.  Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble. , 1999, Journal of molecular biology.

[65]  K. Kuwajima,et al.  The molten globule state as a clue for understanding the folding and cooperativity of globular‐protein structure , 1989, Proteins.

[66]  William H. Woodruff,et al.  Fast events in protein folding: structures and fast folding dynamics of the native and acid forms of apomyoglobin , 1997 .

[67]  A V Finkelstein,et al.  Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. , 1997, Folding & design.

[68]  C. Dobson,et al.  Detection of transient protein folding populations by mass spectrometry. , 1993, Science.

[69]  M. James,et al.  Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. , 1988, Biochemistry.

[70]  A. Fersht,et al.  Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. , 1997, Journal of molecular biology.

[71]  D. Rousseau,et al.  Folding intermediates in cytochrome c , 1998, Nature Structural Biology.

[72]  D. Wetlaufer.  Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[73]  A. Fersht,et al.  Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus. , 1998, Biochemistry.

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

[75]  R. Kaptein,et al.  Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. , 1994, Journal of molecular biology.

[76]  C. Batt,et al.  alpha-->beta transition of beta-lactoglobulin as evidenced by heteronuclear NMR. , 1998, Journal of molecular biology.

[77]  V. Daggett,et al.  Mapping the interactions present in the transition state for unfolding/folding of FKBP12. , 1999, Journal of molecular biology.

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

[79]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[80]  W. A. Eaton,et al.  Optical Triggers of Protein Folding , 1996, Science.

[81]  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.

[82]  R. Dyer,et al.  Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[83]  E. Shakhnovich,et al.  Conserved residues and the mechanism of protein folding , 1996, Nature.