Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins

The cold shock protein CspB from Bacillus subtilis is only marginally stable, but it folds extremely fast in a simple N \[rlharr] U two-state reaction. The corresponding cold shock proteins from the thermophile Bacillus caldolyticus and the hyperthermophile Thermotoga maritima show strongly increased conformational stabilities, but unchanged very fast two-state refolding kinetics. The absence of intermediates in the folding of B. subtilis CspB is thus not a corollary of its low stability. Rather, two-state folding and an unusually native-like activated state of folding seem to be inherent properties of these small all-β proteins. There is no link between stability and folding rate, and numerous sequence positions exist which can be varied to modulate the stability without affecting the rate and mechanism of folding.

[1]  A Ikai,et al.  Kinetics of unfolding and refolding of proteins. 3. Results for lysozyme. , 1973, Journal of molecular biology.

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

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

[4]  A. Fersht,et al.  Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis. , 1993, Biochemistry.

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

[6]  R. L. Baldwin The nature of protein folding pathways: The classical versus the new view , 1995, Journal of biomolecular NMR.

[7]  H. Dyson,et al.  Absence of a stable intermediate on the folding pathway of protein A , 1997, Protein science : a publication of the Protein Society.

[8]  T. Oas,et al.  Submillisecond folding of monomeric lambda repressor. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[9]  H Nakatani,et al.  Test reactions for a stopped-flow apparatus. Reduction of 2,6-dichlorophenolindophenol and potassium ferricyanide by L-ascorbic acid. , 1978, Analytical biochemistry.

[10]  A Ikai,et al.  Kinetics of unfolding and refolding of proteins. I. Mathematical analysis. , 1973, Journal of molecular biology.

[11]  M. Marahiel,et al.  Extremely rapid protein folding in the absence of intermediates , 1995, Nature Structural Biology.

[12]  Matthews Cr PATHWAYS OF PROTEIN FOLDING , 1993 .

[13]  Hermann Schindelin,et al.  Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein , 1993, Nature.

[14]  H. Roder,et al.  Kinetic role of early intermediates in protein folding. , 1997, Current opinion in structural biology.

[15]  C. Pace,et al.  How to measure and predict the molar absorption coefficient of a protein , 1995, Protein science : a publication of the Protein Society.

[16]  R. L. Baldwin,et al.  On-pathway versus off-pathway folding intermediates. , 1996, Folding & design.

[17]  L. Serrano,et al.  Non-native local interactions in protein folding and stability: introducing a helical tendency in the all beta-sheet alpha-spectrin SH3 domain. , 1997, Journal of molecular biology.

[18]  M A Daugherty,et al.  Microsecond protein folding through a compact transition state. , 1996, Journal of molecular biology.

[19]  S. Khorasanizadeh,et al.  Folding and stability of a tryptophan-containing mutant of ubiquitin. , 1993, Biochemistry.

[20]  Terrence G. Oas,et al.  The energy landscape of a fast-folding protein mapped by Ala→Gly Substitutions , 1997, Nature Structural Biology.

[21]  M. Karplus,et al.  How does a protein fold? , 1994, Nature.

[22]  A Ikai,et al.  Kinetics of unfolding and refolding of proteins. II. Results for cytochrome c. , 1973, Journal of molecular biology.

[23]  C. Pace Determination and analysis of urea and guanidine hydrochloride denaturation curves. , 1986, Methods in enzymology.

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

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

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

[27]  F. Neidhardt,et al.  Induction of proteins in response to low temperature in Escherichia coli , 1987, Journal of bacteriology.

[28]  S. Khorasanizadeh,et al.  Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues , 1996, Nature Structural Biology.

[29]  A. Fersht,et al.  Protein folding and stability: the pathway of folding of barnase , 1993 .

[30]  Luis Serrano,et al.  Different folding transition states may result in the same native structure , 1996, Nature Structural Biology.

[31]  M. Marahiel,et al.  Overproduction, crystallization, and preliminary X‐ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB , 1992, Proteins.

[32]  D. Laurents,et al.  Protein folding: matching theory and experiment. , 1998, Biophysical journal.

[33]  D. W. Bolen,et al.  Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. , 1988, Biochemistry.

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

[35]  R. Jaenicke,et al.  Folding and association of proteins. , 1982, Biophysics of structure and mechanism.

[36]  L Serrano,et al.  Evidence for a two-state transition in the folding process of the activation domain of human procarboxypeptidase A2. , 1995, Biochemistry.

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

[38]  T. Schindler,et al.  Thermodynamic properties of an extremely rapid protein folding reaction. , 1996, Biochemistry.

[39]  P. Kraulis A program to produce both detailed and schematic plots of protein structures , 1991 .

[40]  L Serrano,et al.  Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. , 1994, Biochemistry.

[41]  L A Mirny,et al.  Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. , 1996, Folding & design.

[42]  F M Poulsen,et al.  Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein. , 1995, Biochemistry.

[43]  J. Onuchic,et al.  Protein folding funnels: the nature of the transition state ensemble. , 1996, Folding & design.

[44]  A. Fersht,et al.  Movement of the position of the transition state in protein folding. , 1995, Biochemistry.

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

[46]  P. V. von Hippel,et al.  Calculation of protein extinction coefficients from amino acid sequence data. , 1989, Analytical biochemistry.

[47]  M. Marahiel,et al.  Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperatures , 1992, Journal of bacteriology.

[48]  T. Apostol Mathematical Analysis , 1957 .

[49]  T. Kiefhaber,et al.  Folding of the disulfide-bonded beta-sheet protein tendamistat: rapid two-state folding without hydrophobic collapse. , 1997, Journal of molecular biology.

[50]  J. Onuchic,et al.  Toward an outline of the topography of a realistic protein-folding funnel. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[51]  M. Czisch,et al.  Structure in solution of the major cold-shock protein from Bacillus subtilis , 1993, Nature.

[52]  F M Poulsen,et al.  Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family. , 1996, Journal of molecular biology.

[53]  H. Scheraga,et al.  Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme. , 1996, Biochemistry.

[54]  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.