How does protein synthesis give rise to the 3D‐structure?

The recent experimental data on stages and kinetic intermediates in protein folding are reviewed. It is emphasized that these data are consistent with the ‘framework model’ proposed by the author in 1973. The model implies that protein folds by stage mechanism (secondary structure — molten globule state — native state) in such a way that the results of previous stages are not reconsidered in subsequent ones. Arguments are presented that both these hypotheses and available experimental data do not contradict the assumption that native structures of at least small proteins are nevertheless under thermodynamic rather than kinetic control, i.e. correspond to global minima of free energy.

[1]  J. Szulmajster.  Protein folding , 1988, Bioscience reports.

[2]  O. Ptitsyn.  Protein folding: Hypotheses and experiments , 1987 .

[3]  E I Shakhnovich,et al.  Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition , 1989, Biopolymers.

[4]  R. L. Baldwin,et al.  Use of site-directed mutagenesis to destabilize native apomyoglobin relative to folding intermediates. , 1989, Biochemistry.

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

[6]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[7]  M. Goldberg,et al.  Kinetics of appearance of an early immunoreactive species during the refolding of acid-denatured Escherichia coli tryptophan synthase beta 2 subunit. , 1988, Biochemistry.

[8]  O. Ptitsyn,et al.  α‐lactalbumin: compact state with fluctuating tertiary structure? , 1981, FEBS letters.

[9]  E. Rowe,et al.  Multiparameter kinetic study on the unfolding and refolding of bovine carbonic anhydrase B. , 1980, Biochemistry.

[10]  K. Kuwajima,et al.  Folding of carp parvalbumin studied by equilibrium and kinetic circular dichroism spectra , 1988 .

[11]  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.

[12]  S. Blond,et al.  Kinetic characterization of early intermediates in the folding of E. coli tryptophan‐synthase β2 subunit , 1986, Proteins.

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

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

[15]  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.

[16]  J. Rothman.  Polypeptide chain binding proteins: Catalysts of protein folding and related processes in cells , 1989, Cell.

[17]  R. Woody,et al.  Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor. , 1989, Biochemistry.

[18]  D. Sears,et al.  23 – Circular Dichroism , 1973 .

[19]  C. Mitchinson,et al.  Effects of sulphate and urea on the stability and reversible unfolding of beta-lactamase from Staphylococcus aureus. Implications for the folding pathway of beta-lactamase. , 1985, Journal of molecular biology.

[20]  S Sugai,et al.  Rapid formation of secondary structure framework in protein folding studied by stopped‐flow circular dichroism , 1987, FEBS letters.

[21]  A. Ikai,et al.  Reactivation of kinetics of guanidine denatured bovine carbonic anhydrase B. , 1978, Archives of biochemistry and biophysics.

[22]  M. Goldberg,et al.  Kinetic characterization of early immunoreactive intermediates during the refolding of guanidine-unfolded Escherichia coli tryptophan synthase beta 2 subunits. , 1990, Biochemistry.

[23]  A. Fersht,et al.  Detection and characterization of a folding intermediate in barnase by NMR , 1990, Nature.

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

[25]  O. Ptitsyn,et al.  An early intermediate of refolding α‐lactalbumin forms within 20 ms , 1987 .

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

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

[28]  B. Robson,et al.  The mechanism of folding of globular proteins. Equilibria and kinetics of conformational transitions of penicillinase from Staphylococcus aureus involving a state of intermediate conformation. , 1976, The Biochemical journal.

[29]  O. Ptitsyn,et al.  Sequential mechanism of refolding of carbonic anhydrase B , 1987, FEBS letters.

[30]  J. C. Kendrew,et al.  Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence , 1965 .

[31]  M. Desmadril,et al.  Kinetic studies of the unfolding-refolding of horse muscle phosphoglycerate kinase induced by guanidine hydrochloride. , 1985, Biochemistry.

[32]  Ken A. Dill,et al.  Conformations and Forces in Protein Folding , 1991 .

[33]  S Sugai,et al.  An early immunoreactive folding intermediate of the tryptophan synthase β2 subunit is a ‘molten globule’ , 1990, FEBS letters.

[34]  O. Ptitsyn,et al.  Evidence for a molten globule state as a general intermediate in protein folding , 1990, FEBS letters.

[35]  F. Schmid,et al.  The mechanism of protein folding. Implications of in vitro refolding models for de novo protein folding and translocation in the cell. , 1990, Biochemistry.

[36]  R. L. Baldwin,et al.  Early folding intermediate of ribonuclease A. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[37]  C. Levinthal.  Are there pathways for protein folding , 1968 .

[38]  A. Finkelstein,et al.  Theory of protein secondary structure and algorithm of its prediction , 1983, Biopolymers.

[39]  O. Ptitsyn,et al.  Why do globular proteins fit the limited set of folding patterns? , 1987, Progress in biophysics and molecular biology.

[40]  D I Stuart,et al.  Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme. , 1989, Journal of molecular biology.

[41]  O. Ptitsyn,et al.  ‘Molten‐globule“ state accumulates in carbonic anhydrase folding , 1984, FEBS letters.

[42]  M. Nadeau.  Proteins : Structure , Function , and Genetics , 2022 .

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

[44]  A. Wada,et al.  ‘Molten‐globule state’: a compact form of globular proteins with mobile side‐chains , 1983, FEBS letters.

[45]  E. Shakhnovich,et al.  [The theory of cooperative transitions in protein globules]. , 1982, Doklady Akademii nauk SSSR.

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

[47]  T. Creighton,et al.  Circular and circularly permuted forms of bovine pancreatic trypsin inhibitor. , 1983, Journal of molecular biology.

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