Abstract
Here we used the cold-shock protein CspB from Bacillus subtilis to study protein folding at an elementary level. The thermodynamic stability of this small five-stranded β-barrel protein is low, but unfolding and refolding are extremely rapid reactions. In 0.6 M urea the time constant of refolding is about 1.5 ms, and at the transition midpoint (4 M urea) the folded and unfolded forms equilibrate in less than 100 ms. Both the equilibrium unfolding transition and the folding kinetics are perfectly described by a N⇌U two-state model. The validity of this model was confirmed by several kinetic tests. Folding intermediates could neither be detected at equilibrium nor in the folding kinetics. We suggest that the extremely rapid folding of CspB and the absence of folding intermediates are related phenomena.
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References
Levinthal, C.J. Are there pathways for protein folding? J. Chem. Phys. 65, 44–45 (1968).
Karplus, M. & Weaver, D.L. Protein-folding dynamics. Nature 260, 404–406 (1976).
Woodward, C.K. Hydrogen exchange rates and protein folding. Curr. Opin. Struct. Biol. 4, 112–116 (1994).
Creighton, T.E. The energetic ups and downs of protein folding. Nature struct Biology 1, 135–138 (1994).
Baldwin, R.L. The nature of protein folding pathways: The classical versus the new view. J. biomol. NMR 5, 103–109 (1995).
Sosnick, T.R., Mayne, L., Hiller, R. & Englander, S.W. The barriers in protein folding. Nature struct. Biology 1, 149–156 (1994).
Darby, N.J., van Mierlo, C.P.M., Scott, G.H.E., Neuhaus, D. & Creighton, T.E. Kinetic roles and conformational properties of the non-native two-disulphide intermediates in the refolding of bovine pancreatic trypsin inhibitor. J. molec. Biol. 224, 905–911 (1992).
Weissman, J.S. & Kim, P.S. Reexamination of the folding of BPTI: predominance of native intermediates. Science 253, 1386–1393 (1991).
Mücke, M. & Schmid, F.X. Intact disulfide bonds decelerate the folding of ribonuclease T1. J. molec. Biol. 239, 713–725 (1994).
Herzberg, O. & Moult, J. Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins: Struct. Funct. Genet. 11, 223–229 (1991).
Janin, J., Wodak, S., Levitt, M. & Maigret, B. Conformations of amino acid sidechains in proteins. J. molec. Biol. 125, 357–386 (1978).
Orengo, C.A., Jones, D.T. & Thornton, J.M. Protein superfamilies and domain superfolds. Nature 372, 631–634 (1994).
Ponder, J.W. & Richards, F.M. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. molec. Biol. 193, 775–792 (1987).
Dyson, H.J. & Wright, P.E. Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3, 60–65 (1993).
Mayr, L.M., Kiefhaber, T. & Schmid, F.X. Prolyl isomerizations as rate-determining steps in the folding of ribonuclease T1 in Protein folding: in vivo and in vitro (ed. Cleland, J.L.) 142–155 (American Chemical Society, Washington, 1993).
Odefey, C., Mayr, L.M. & Schmid, F.X., Non-prolyl cis-trans peptide bond isomerization as a rate-determining step in protein unfolding and refolding. J. molec. Biol. 245, 69–78 (1995).
Schmid, F.X. Kinetics of unfolding and refolding of single-domain proteins. in Protein folding (ed. Creighton, T.E.) 197–241 (Freeman, New York, 1992).
Creighton, T.E. Folding pathways determined using disulfide bonds. in Protein folding (ed. Creighton, T.E.) 301–351 (Freeman, New York, 1992).
Kiefhaber, T., Grunert, H.P., Hahn, U. & Schmid, F.X. Folding of RNase T1 is decelerated by a specific tertiary contact in a folding intermediate. Proteins: Struct. Funct. Genet. 12, 171–179 (1992).
Jones, P.G., van Bogelen, R.A. & Neidhardt, F.C. Induction of proteins in response to low temperature in Escherichia coli. J. Bacteriol. 169, 2092–2095 (1987).
Willimsky, G., Bang, H., Fischer, G. & Marahiel, M.A. Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperature. J. Bacteriol. 174, 6326–6335 (1992).
Schnuchel, A., Wiltschek, R., Czisch, M., Herrler, M., Willimsky, G., Graumann, P., Marahiel, M.A. & Holak, T.A. Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature 364, 169–171 (1993).
Schindelin, H., Marahiel, M.A. & Heinemann, U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature 364, 164–168 (1993).
Woody, R.W. Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins. Biopolymers 17, 1451–1467 (1978).
Manning, M.C. & Woody, R.W. Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor. Biochemistry 28, 8609–8613 (1989).
Perczel, A., Park, K. & Fasman, G.D. Deconvolution of the circular dichroism spectra of proteins: the circular dichroism spectra of the antiparallel β-sheet in proteins. Proteins: Struct. Funct. Genet. 13, 57–69 (1992).
Graumann, P. & Marahiel, M.A. The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT-sequences in single stranded oligonucleotides. FEBS Lett. 338, 157–160 (1995).
Chatterjee, S., Jiang, W., Emerson, S.D. & Inouye, M. The backbone structure of the major cold-shock protein CS7.4 of Escherichia coli in solution includes extensive β-sheet structure. J. Biochem. 114, 663–669 (1993).
Schindelin, H., Jiang, W., Inouye, M. & Heinemann, U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc. natn. Acad. Sci. U.S.A. 91, 5119–5123 (1994).
Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S.D., Inouye, M. & Montelione, G.T. Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: Identification of a binding epitope for DNA. Proc. natn. Acad. Sci. U.S.A. 91, 5114–5118 (1994).
Pace, C.N. The stability of globular proteins. CRC Crit. Rev. Biochem. 3, 1–43 (1975).
Pace, C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Meths Enzymol. 131, 266–280 (1986).
Santoro, M.M. & Bolen, D.W. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl a-chymotrypsin using different denaturants. Biochemistry 27, 8063–8068 (1988).
Scholtz, J.M., Barrick, D., York, E.J., Stewart, J.M. & Baldwin, R.L. Urea unfolding of peptide helices as a model for interpreting protein unfolding. Proc. natn. Acad. Sci. U.S.A. 92, 185–189 (1995).
Tanford, C. Protein denaturation Part C. Adv. Protein Chem. 24, 1–95 (1970).
Schmid, F.X. Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates. Biochemistry 22, 4690–4696 (1983).
Kiefhaber, T., Quaas, R., Hahn, U. & Schmid, F.X. Folding of Ribonuclease T1. 1. Existence of multiple unfolded states created by proline isomerization. Biochemistry 29, 3053–3061 (1990).
Mayr, L.M., Landt, O., Hahn, U. & Schmid, F.X. Stability and folding kinetics of ribonuclease T1 are strongly altered by the replacement of cis-proline 39 with alanine. J. molec. Biol. 231, 897–912 (1993).
Mayr, L.M., Willbold, D., Landt, O. & Schmid, F.X. Role of the Cys 2-Cys 10 disulfide bond for the structure, stability, and folding kinetics of ribonuclease T1. Prot. Sci. 3, 227–239 (1994).
Schreiber, G. & Fersht, A.R. The refolding of cis- and trans- peptidylprolyl isomers of Barstar. Biochemistry 32, 11195–11203 (1993).
Mücke, M. & Schmid, F.X. A kinetic method to evaluate the two-state character of solvent-induced protein denaturation. Biochemistry 33, 12930–12935 (1994).
Varley, P., Gronenborn, A.M., Christensen, H., Wingfield, P.T., Pain, R.H. & Clore, G.M. Kinetics of folding of the all beta-sheet protein lnterleukin-1β. Science 260, 1110–1113 (1993).
Goto, Y. & Hamaguchi, K. Formation of the intrachain disulphide bond in the constant fragment of immunoglobulin light chain. J. molec. Biol. 146,321–340 (1981).
Viguera, A.R., Martinez, J.C., Filimonov, V.V., Mateo, P.L. & Serrano, L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 32, 2142–2150 (1994).
Khorasanizadeh, S., Peters, I.D., Butt, T.R. & Roder, H. Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry 32, 7054–7063 (1993).
Jackson, S.E. & Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428–10435 (1991).
Kuszewski, J., Clore, G.M. & Gronenborn, A.M. Fast folding of a prototypic polypeptide: The immunoglobulin binding domain of streptococcal protein G. Prot. Sci. 3, 1945–1952 (1994).
Finkelstein, A.V. Rate of β-structure formation in polypeptides. Proteins: Struct. Funct. Genet. 9, 23–27 (1991).
Alexander, P., Orban, J. & Bryan, P. Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G. Biochemistry 32, 7243–7248 (1992).
Schellman, J.A. Solvent denaturation. Biopolymers 17, 1305–1322 (1978).
Honeycutt, J.D. & Thirumalai, D. Metastability of the folded states of globular proteins. Proc. natn. Acad. Sci. U.S.A. 87, 3526–3529 (1990).
Sali, A., Shakhnovich, E. & Karplus, M. How does a protein fold? Nature 369, 248–251 (1994).
Go, N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12, 183–210 (1983).
Schindelin, H., Herrler, M., Willimsky, G., Marahiel, M.A. & Heinemann, U. Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB. Proteins: Struct. Funct. Genet. 14, 120–124 (1992).
Schägger, H. & von Jagow, G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Analyt. Biochem. 166, 368–379 (1987).
Gill, S.C. & von Hippel, P.H. Calculation of protein extinction coefficients from amino acid sequence data. Analyt. Biochem. 182, 319–326 (1989).
Tonomura, B., Nakatani, H., Ohnishi, M., Yamaguchi-lto, J. & Hiromi, K. Test reaction for a stopped-flow apparatus. Analyt. Biochem. 84, 370–383 (1978).
Kragelund, B.B., Robinson, C.V., Knudsen, J., Dobson, C.M. & Poulsen, F.M. Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein. Biochemistry 34, 7117–7224 (1995).
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Schindler, T., Herrler, M., Marahiel, M. et al. Extremely rapid protein folding in the absence of intermediates. Nat Struct Mol Biol 2, 663–673 (1995). https://doi.org/10.1038/nsb0895-663
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DOI: https://doi.org/10.1038/nsb0895-663
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