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Proc Natl Acad Sci U S A. 1996 March 19; 93(6): 2539–2544.
PMCID: PMC39833
Least activation path for protein folding: investigation of staphylococcal nuclease folding by stopped-flow circular dichroism.
Z D Su, M T Arooz, H M Chen, C J Gross, and T Y Tsong
Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
Abstract
Is the pathway of protein folding determined by the relative stability of folding intermediates, or by the relative height of the activation barriers leading to these intermediates? This is a fundamental question for resolving the Levinthal paradox, which stated that protein folding by a random search mechanism would require a time too long to be plausible. To answer this question, we have studied the guanidinium chloride (GdmCl)-induced folding/unfolding of staphylococcal nuclease [(SNase, formerly EC 3.1.4.7; now called microbial nuclease or endonuclease, EC 3.1.31.1] by stopped-flow circular dichroism (CD) and differential scanning microcalorimetry (DSC). The data show that while the equilibrium transition is a quasi-two-state process, kinetics in the 2-ms to 500-s time range are triphasic. Data support the sequential mechanism for SNase folding: U3 <--> U2 <--> U1 <--> N0, where U1, U2, and U3 are substates of the unfolded protein and N0 is the native state. Analysis of the relative population of the U1, U2, and U3 species in 2.0 M GdmCl gives delta-G values for the U3 --> U2 reaction of +0.1 kcal/mol and for the U2 --> U1 reaction of -0.49 kcal/mol. The delta-G value for the U1 --> N0 reaction is calculated to be -4.5 kcal/mol from DSC data. The activation energy, enthalpy, and entropy for each kinetic step are also determined. These results allow us to make the following four conclusions. (i) Although the U1, U2, and U3 states are nearly isoenergetic, no random walk occurs among them during the folding. The pathway of folding is unique and sequential. In other words, the relative stability of the folding intermediates does not dictate the folding pathway. Instead, the folding is a descent toward the global free-energy minimum of the native state via the least activation path in the vast energy landscape. Barrier avoidance leads the way, and barrier height limits the rate. Thus, the Levinthal paradox is not applicable to the protein-folding problem. (ii) The main folding reaction (U1 --> N0), in which the peptide chain acquires most of its free energy (via van der Waals' contacts, hydrogen bonding, and electrostatic interactions), is a highly concerted process. These energy-acquiring events take place in a single kinetic phase. (iii) U1 appears to be a compact unfolded species; the rate of conversion of U2 to U1 depends on the viscosity of solution. (iv) All four relaxation times reported here depend on GdmCl concentrations: it is likely that none involve the cis/trans isomerization of prolines. Finally, a mechanism is presented in which formation of sheet-like chain conformations and a hydrophobic condensation event precede the main-chain folding reaction.
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Selected References
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  • Anfinsen CB. Principles that govern the folding of protein chains. Science. 1973 Jul 20;181(96):223–230. [PubMed]
  • Tanford C. Protein denaturation. Adv Protein Chem. 1968;23:121–282. [PubMed]
  • Kim PS, Baldwin RL. Intermediates in the folding reactions of small proteins. Annu Rev Biochem. 1990;59:631–660. [PubMed]
  • Matthews CR. Pathways of protein folding. Annu Rev Biochem. 1993;62:653–683. [PubMed]
  • Ellis J. Proteins as molecular chaperones. Nature. 328(6129):378–379. [PubMed]
  • Ellis RJ, van der Vies SM. Molecular chaperones. Annu Rev Biochem. 1991;60:321–347. [PubMed]
  • Wetlaufer DB, Ristow S. Acquisition of three-dimensional structure of proteins. Annu Rev Biochem. 1973;42:135–158. [PubMed]
  • Kanehisa MI, Tsong TY. Mechanism of the multiphasic kinetics in the folding and unfolding of globular proteins. J Mol Biol. 1978 Sep 5;124(1):177–194. [PubMed]
  • Schechter AN, Chen RF, Anfinsen CB. Kinetics of folding of staphylococcal nuclease. Science. 1970 Feb 6;167(3919):886–887. [PubMed]
  • Epstein HF, Schechter AN, Chen RF, Anfinsen CB. Folding of staphylococcal nuclease: kinetic studies of two processes in acid renaturation. J Mol Biol. 1971 Sep 28;60(3):499–508. [PubMed]
  • Davis A, Parr GR, Taniuchi H. A kinetic study of the folding of nuclease B, a possible precursor of staphylococcal nuclease A. Biochim Biophys Acta. 1979 Jun 19;578(2):505–510. [PubMed]
  • Sugawara T, Kuwajima K, Sugai S. Folding of staphylococcal nuclease A studied by equilibrium and kinetic circular dichroism spectra. Biochemistry. 1991 Mar 12;30(10):2698–2706. [PubMed]
  • Fox RO, Evans PA, Dobson CM. Multiple conformations of a protein demonstrated by magnetization transfer NMR spectroscopy. Nature. 1986 Mar 13;320(6058):192–194. [PubMed]
  • Evans PA, Kautz RA, Fox RO, Dobson CM. A magnetization-transfer nuclear magnetic resonance study of the folding of staphylococcal nuclease. Biochemistry. 1989 Jan 10;28(1):362–370. [PubMed]
  • Alexandrescu AT, Ulrich EL, Markley JL. Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: effects of mutations and solution conditions on their distribution. Biochemistry. 1989 Jan 10;28(1):204–211. [PubMed]
  • Chen HM, You JL, Markin VS, Tsong TY. Kinetic analysis of the acid and the alkaline unfolded states of staphylococcal nuclease. J Mol Biol. 1991 Aug 5;220(3):771–778. [PubMed]
  • Chen HM, Markin VS, Tsong TY. pH-induced folding/unfolding of staphylococcal nuclease: determination of kinetic parameters by the sequential-jump method. Biochemistry. 1992 Feb 11;31(5):1483–1491. [PubMed]
  • Chen HM, Markin VS, Tsong TY. Kinetic evidence of microscopic states in protein folding. Biochemistry. 1992 Dec 15;31(49):12369–12375. [PubMed]
  • Griko YV, Privalov PL, Sturtevant JM, Venyaminov SYu Cold denaturation of staphylococcal nuclease. Proc Natl Acad Sci U S A. 1988 May;85(10):3343–3347. [PubMed]
  • Kuwajima K. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins. 1989;6(2):87–103. [PubMed]
  • Fuchs S, Cuatrecasas P, Anfinsen CB. An improved method for the purification of staphylococcal nuclease. J Biol Chem. 1967 Oct 25;242(20):4768–4770. [PubMed]
  • Chang CT, Wu CS, Yang JT. Circular dichroic analysis of protein conformation: inclusion of the beta-turns. Anal Biochem. 1978 Nov;91(1):13–31. [PubMed]
  • Shortle D, Meeker AK. Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins. 1986 Sep;1(1):81–89. [PubMed]
  • Tsong TY. Ferricytochrome c chain folding measured by the energy transfer of tryptophan 59 to the heme group. Biochemistry. 1976 Dec 14;15(25):5467–5473. [PubMed]
  • Lattman EE, Fiebig KM, Dill KA. Modeling compact denatured states of proteins. Biochemistry. 1994 May 24;33(20):6158–6166. [PubMed]
  • Gottfried DS, Haas E. Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor. Biochemistry. 1992 Dec 15;31(49):12353–12362. [PubMed]
  • Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding. Nat Struct Biol. 1994 Mar;1(3):149–156. [PubMed]
  • Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 1994 May 19;369(6477):248–251. [PubMed]
  • Baldwin RL. Protein folding. Matching speed and stability. Nature. 1994 May 19;369(6477):183–184. [PubMed]