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. 1989 Aug;86(15):5820–5824. doi: 10.1073/pnas.86.15.5820

Enzymes work by solvation substitution rather than by desolvation.

A Warshel 1, J Aqvist 1, S Creighton 1
PMCID: PMC297722  PMID: 2762299

Abstract

Considerable attention has recently been drawn to the hypothesis that enzymes catalyze their reactions by displacing solvent and creating an environment similar to the gas phase for the reacting substrates. This "desolvation hypothesis" is reexamined in this paper by defining a common reference energy for reactions in various environments. It is argued that consistent attempts to describe the actual energetics of enzymatic reactions, taking either gas phase or solution as a reference, would contradict the above hypothesis. That is, the enzyme does remove water molecules from its substrate, but substitutes these molecules for another polar environment (namely, its active site). By taking amide hydrolysis as an example, we use experimentally estimated solvation energies and analyze the reaction profile in the gas phase, in solution, and in enzyme active sites. We show that the gas-phase reaction is characterized by an enormous activation barrier (associated with forming the charged nucleophile from neutral fragments), although the nucleophilic attack is essentially barrierless. On the other hand, the enzyme and solution reactions are found to have similar reaction profiles, with a lower activation barrier for the enzymatic reaction. Presumably, the fact that previous analyses of this problem did not involve the construction of the relevant thermodynamic cycles (and quantitative estimates of the corresponding solvation energies) led to the desolvation hypothesis. Our conclusion is that enzyme active sites provide specific polar environments that do not resemble the gas phase but that are designed for electrostatic stabilization of ionic transition states and that "solvate" these states more than water does.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bryan P., Pantoliano M. W., Quill S. G., Hsiao H. Y., Poulos T. Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3743–3745. doi: 10.1073/pnas.83.11.3743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cohen S. G., Vaidya V. M., Schultz R. M. Active Site of alpha-Chymotrypsin Activation by Association-Desolvation. Proc Natl Acad Sci U S A. 1970 Jun;66(2):249–256. doi: 10.1073/pnas.66.2.249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Crosby J., Stone R., Lienhard G. E. Mechanisms of thiamine-catalyzed reactions. Decarboxylation of 2-(1-carboxy-1-hydroxyethyl)-3,4-dimethylthiazolium chloride. J Am Chem Soc. 1970 May 6;92(9):2891–2900. doi: 10.1021/ja00712a048. [DOI] [PubMed] [Google Scholar]
  4. Dewar M. J., Dieter K. M. Mechanism of the chain extension step in the biosynthesis of fatty acids. Biochemistry. 1988 May 3;27(9):3302–3308. doi: 10.1021/bi00409a027. [DOI] [PubMed] [Google Scholar]
  5. Dewar M. J. New ideas about enzyme reactions. Enzyme. 1986;36(1-2):8–20. doi: 10.1159/000469274. [DOI] [PubMed] [Google Scholar]
  6. Dewar M. J., Storch D. M. Alternative view of enzyme reactions. Proc Natl Acad Sci U S A. 1985 Apr;82(8):2225–2229. doi: 10.1073/pnas.82.8.2225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fersht A. R. Acyl-transfer reactions of amides and esters with alcohols and thiols. A reference system for the serine and cysteine proteinases. Concerning the N protonation of amides and amide-imidate equilibria. J Am Chem Soc. 1971 Jul 14;93(14):3504–3515. doi: 10.1021/ja00743a035. [DOI] [PubMed] [Google Scholar]
  8. Hunkapiller M. W., Smallcombe S. H., Whitaker D. R., Richards J. H. Carbon nuclear magnetic resonance studies of the histidine residue in alpha-lytic protease. Implications for the catalytic mechanism of serine proteases. Biochemistry. 1973 Nov 6;12(23):4732–4743. doi: 10.1021/bi00747a028. [DOI] [PubMed] [Google Scholar]
  9. Hwang J. K., Warshel A. Semiquantitative calculations of catalytic free energies in genetically modified enzymes. Biochemistry. 1987 May 19;26(10):2669–2673. doi: 10.1021/bi00384a003. [DOI] [PubMed] [Google Scholar]
  10. Kossiakoff A. A., Spencer S. A. Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: neutron structure of trypsin. Biochemistry. 1981 Oct 27;20(22):6462–6474. doi: 10.1021/bi00525a027. [DOI] [PubMed] [Google Scholar]
  11. Kraut J. How do enzymes work? Science. 1988 Oct 28;242(4878):533–540. doi: 10.1126/science.3051385. [DOI] [PubMed] [Google Scholar]
  12. Kraut J. Serine proteases: structure and mechanism of catalysis. Annu Rev Biochem. 1977;46:331–358. doi: 10.1146/annurev.bi.46.070177.001555. [DOI] [PubMed] [Google Scholar]
  13. Page M. I., Jencks W. P. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc Natl Acad Sci U S A. 1971 Aug;68(8):1678–1683. doi: 10.1073/pnas.68.8.1678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Rao S. N., Singh U. C., Bash P. A., Kollman P. A. Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin. Nature. 1987 Aug 6;328(6130):551–554. doi: 10.1038/328551a0. [DOI] [PubMed] [Google Scholar]
  15. Scheiner S., Kleier D. A., Lipscomb W. N. Molecular orbital studies of enzyme activity: I: Charge relay system and tetrahedral intermediate in acylation of serine proteinases. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2606–2610. doi: 10.1073/pnas.72.7.2606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Umeyama H., Imamura A., Nagata C. A molecular orbital study on the enzymic reaction mechanism of alpha-chymotrypsin. J Theor Biol. 1973 Oct;41(3):485–502. doi: 10.1016/0022-5193(73)90057-x. [DOI] [PubMed] [Google Scholar]
  17. Warshel A. Energetics of enzyme catalysis. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5250–5254. doi: 10.1073/pnas.75.11.5250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Warshel A., Naray-Szabo G., Sussman F., Hwang J. K. How do serine proteases really work? Biochemistry. 1989 May 2;28(9):3629–3637. doi: 10.1021/bi00435a001. [DOI] [PubMed] [Google Scholar]
  19. Warshel A., Russell S. T. Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys. 1984 Aug;17(3):283–422. doi: 10.1017/s0033583500005333. [DOI] [PubMed] [Google Scholar]
  20. Weiner S. J., Seibel G. L., Kollman P. A. The nature of enzyme catalysis in trypsin. Proc Natl Acad Sci U S A. 1986 Feb;83(3):649–653. doi: 10.1073/pnas.83.3.649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Wolfenden R. Waterlogged molecules. Science. 1983 Dec 9;222(4628):1087–1093. doi: 10.1126/science.6359416. [DOI] [PubMed] [Google Scholar]

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