Short strong hydrogen bonds: Can they explain enzymic catalysis?

Chemistry and Biology

Volumn 3, Issue 3, 1996, Pages 163-170

  Guthrie, J Peter ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

CATALYSIS; CHEMISTRY; HYDROGEN BOND; METABOLISM; REVIEW;

CATALYSIS; ENZYMES; HYDROGEN BONDING;

EID: 0030090490     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/s1074-5521(96)90258-6     Document Type: Review

References (57)

1. Cleland, W. & Kreevoy, M. (1994). Low-barrier hydrogen bonds and enzymic catalysis. Science 264, 1887-1890.
2. Warshel, A., Papazyan, A., Kollman, P., Cleland, W., Kreevoy, M. & Frey, P. (1995). On low barrier hydrogen bonds and enzyme catalysis. Science 269, 102.
3. Scheiner, S. & Kar, T. (1995). The nonexistence of specially stabilized hydrogen bonds in enzymes. J. Am. Chem. Soc. 117, 6970-6975.
4. Gerlt, J. & Gassman, P. (1993). An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids - importance of late transition states in concerted mechanisms. J. Am. Chem. Soc. 115, 11552-11568.
5. Gerlt, J. & Gassman, P. (1993). Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl transfer reactions, and displacement reactions of phosphodiesters. Biochemistry 32, 11943-11952.
6. Tobin, J., Whitt, S., Cassidy, C. & Frey, P. (1995). Low barrier hydrogen bonding in molecular complexes analogous to histidine and aspartate in the catalytic triad of serine proteases. Biochemistry 34, 6919-6924.
7. Mock, W. & Chua, D. (1995). Exceptional active site H-bonding in enzymes? Significance of the 'oxyanion hole' in the serine proteases from a model study. J. Chem. Soc. Perkin II, 2069-2074.
8. Frey, P., Whitt, S. & Tobin, J. (1994). A low barrier hydrogen bond in the catalytic triad of serine proteases. Science 264, 1927-1930.
9. Xiang, S., Short, S., Wolfenden, R. & Carter, C. (1995). Transition state selectivity for a single hydroxyl group during catalysis by cytidine deaminase. Biochemistry 34, 4516-4523.
10. Tong, H. & Davis, L. (1995). 2-Amino-3-ketobutyrate-CoA ligase from beef liver mitochondria: an NMR spectroscopic study of low barrier bonds of a pyridoxal 5′-phosphate-dependent enzyme. Biochemistry 34, 3362-3367.
11. 5-3-ketosteroid isomerase. Biochemistry 34, 426-434.
12. Messmore, J., Fuchs, D. & Raines, R. (1995). Ribonuclease A; revealing structure function relations with semisynthesis. J. Am. Chem. Soc. 117, 8057-8060.
13. Schwartz, B. & Drueckhammer, D. (1995). A simple method for determining the relative strengths of normal and low barrier hydrogen bonds in solution: implications for enzyme catalysis. J. Am. Chem. Soc. 117, 11902-11905.
14. Usher, K., Remington, S., Marton, D. & Drueckhammer, D. (1994). Affinities of acid and amide analogs of acetylCoA to citrate synthase. Biochemistry 33, 7753.
15. O'Connell, T. & Malthouse, J. (1995). A study of the stabilization of the oxyanion of tetrahedral adducts by trypsin, chymotrypsin, and subtilisin. Biochem. J. 307, 353-359.
16. Perrin, C. (1994). Symmetries of hydrogen bonds in solution. Science 266, 1665-1668.
17. Usher, K., Remington, S., Martin, D. & Drueckhammer, D. (1994). A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase. Biochemistry 33, 7753-7759.
18. a balance: the case of triose phosphate isomerase (TIM)? J. Am. Chem. Soc. 117, 9855-9862.
19. -. J. Am. Chem. Soc. 102, 3315-3322.
20. Emsley, J. (1980). Very strong hydrogen bonds. Chem. Soc. Rev. 9, 91-124.
21. Hibbert, F. & Emsley, J. (1990). Hydrogen bonding and chemical reactivity. Adv. Phys. Org. Chem. 26, 255-379.
22. -. J. Am. Chem. Soc. 104, 5848-5849.
23. -. A gas phase experimental and G2 theoretical study. J. Phys. Chem. 99, 2002-2005.
24. Broene, H. & DeVries, T. (1947). The thermodynamics of aqueous hydrofluoric acid solutions. J. Am. Chem. Soc. 69, 1644-1646.
25. Baumann, E.W. (1969). Determination of stability constants of hydrogen and aluminum fluorides with a fluoride-selective electrode. J. Inorg. Nucl. Chem. 31, 3155-3162.
26. Ellis, A.J. (1966). The effect of temperature on the ionization of hydrofluoric acid. J. Chem. Soc., 4300-4304.
27. Kresge, A.J. & Chiang, Y. (1973). Solvent isotope effects on the ionization of hydrofluoric acid. J. Phys. Chem. 77, 822-825.
28. Larson, J.W. & McMahon, T.B. (1982). Formation, thermochemistry, and relative stabilities of proton-bound dimers of oxygen n-donor bases from ion cyclotron resonance solvent-exchange equilibria measurements. J. Am. Chem. Soc. 104, 6255-6261.
29. Larson, J.W. & McMahon, T.B. (1983). Strong hydrogen bonding in gas-phase anions. An ion cyclotron resonance determination of fluorid binding energetics to Bronsted acids from gas phase fluoride exchange equilibria measurements. J. Am. Chem. Soc. 105, 2944-2950.
30. Larson, J.W. & McMahon, T.B. (1984). Hydrogen bonding in gas-phase anions. An experimental investigation of the interaction between chloride ion and Bronsted acids from ion cyclotron resonance chloride exchange equilibria. J. Am. Chem. Soc. 106, 517-521.
31. Gilli, P., Bertolasi, V., Ferretti, V. & Gilli, G. (1994). Covalent nature of the strong homonuclear hydrogen bond - study of the O-H - O system by crystal structure correlation methods. J. Am. Chem. Soc. 116, 909-915.
32. Bartmess, J.E., Scott, J.A. & McIver, R.T. (1979). Scale of acidities in the gas phase from methanol to phenol. J. Am. Chem. Soc. 101, 6046-6056.
33. Aue, D.H., Webb, H.M. & Bowers, M.T. (1976). Quantitative proton affinities, ionization potentials, and hydrogen affinities of alkylamines. J. Am. Chem. Soc. 98, 311-317.
34. Albrecht, G. & Zundel, G. (1984) Carboxylic acid-N base hydrogen bonds with large proton polarizability in acetonitrile as a function of the basicity of hydrogen bond donors. Z. Naturforsch. 39A 986-992.
35. Magonski, J., Pawlak, Z. & Jasinski, T. (1993). Dissociation constants of substituted phenols and homoconjugation constants of the corresponding phenol-phenolate systems in acetonitrile. J. Chem. Soc., Faraday Trans. 89, 119-122.
36. Hand, E.S. & Jencks, W.P. (1975). Nonlinearity in buffer-rate relationships. The significance of carboxylate-acid complexes. J. Am. Chem. Soc. 97, 6221-6230.
37. Bordwell, F.G., Branca, J.C. & Hughes, D L. (1980). Equilibria involving organic anions in dimethyl sulfoxide and N-methylpyrrolidin-2-one: acidities, ion pairing, and hydrogen bonding. J. Org. Chem. 45, 3305-3313.
38. Coetzee, J. (1967). Ionic reactions in acetonitrile. Prog. Phys. Org. Chem. 4, 45-92.
39. Stahl, N. & Jencks, W.P. (1986). Hydrogen bonding between solutes in aqueous solution. J. Am. Chem. Soc. 108, 4196-4205.
40. Kolthoff, I.M., and Chantooni, M. (1975). Intramolecular hydrogen bonding in monoanions of o-phthalic acid and the homologous oxalic acid series in acetonitrile. J. Am. Chem. Soc. 97, 1376-1381.
41. Kolthoff, I.M. & Chantooni, M. (1976). Intramolecular hydrogen bonding involving hydroxyl groups in mono- and dianions of diprotic acids in acetonitrile and dimethyl sulfoxide. J. Am. Chem. Soc. 98, 5063-5068.
42. Chantooni, M. & Kolthoff, IM (1975). Acid-base equilibria in methanol, acetonitrile, and dimethyl sulfoxide in acids and salts of oxalic acid and homologs, furmaric and o-phthalic acids. Transfer activity coefficients of acids and ions. J. Phys. Chem. 79, 1178-1182.
43. Kolthoff, I.M & Chantooni, M. (1969). Some hydrogen bond relations between homoconjugates and heteroconjugates of phenols and phenolates in acetonitrile. J. Am. Chem. Soc. 91, 4621-4625.
44. Harlow, G. & Bruss, B. (1958). Titration of weak acids in nonaqueous solvents. Potentiometric studies in inert solvents. Anal. Chem. 30, 1833-1836.
45. Bruss, B. & Harlow, G. (1958). Titration of weak acids in nonaqueous solvents. Conductimetric studies. Anal. Chem. 30, 1836-1839.
46. Hadzi, D. & Rajnvajn, J. (1973). Hydrogen bonding in some adducts of oxygen bases with acids. 7. Thermodynamic study by infra-red spectroscopy of the association of chloroacetic acids with some oxygen bases. J. Chem. Soc., Faraday Trans. 1 69, 151-155.
47. Alder, R.W., Bowman, P.S., Steele, W.R.S. & Winterman, D.R. (1968). The remarkable basicity of 1,8-bis(dimethylamino)naphthalene. Chem. Commun., 723-724.
48. 2O mixtures with hydroxide ion. J. Chem. Soc. [II], 1895-1899.
49. Wepster, B. (1952). The basic strength of benzoquinuclidine and its bearing on the basic strength and the mesomeric energy of aromatic amines. Recl. Trav. Chim. Pays-Bas 71, 1171-1178.
50. Shan, S.-O., Loh, S. & Herschlag, D. (1996). The energetics of hydrogen bonds in model systems. Implication for enzymatic catalysis. Science, in press.
51. Gerlt, J.A., Kozarich, J.W., Kenyon, G.L. & Gassman, P.G. (1991). Electrophilic catalysis can explain the unexpected acidity of carbon acids in enzyme catalyzed reactions. J. Am. Chem. Soc. 113, 9667-9669.
52. Gerlt, J.A. & Gassman, P.G. (1992). Understanding enzyme catalyzed proton abstraction from carbon acids: details of stepwise mechanisms for β-elimination reactions. J. Am. Chem. Soc. 114, 5928-5934.
53. Guthrie, J.P. & Kluger, R. (1993). Electrostatic stabilization can explain the unexpected acidity of carbon acids in enzyme catalyzed reactions. J. Am. Chem. Soc. 115, 11569-11572.
54. Kresge, A. (1991). Generation and study of enols and other reactive species. Pure Appl. Chem. 63, 213-221.
55. Bryan, P., Pantoliano, M., Quill, S., Hsiao, H. & Poulos, T. (1986). Site directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc. Natl. Acad. Sci. USA 83, 3743-3745.
56. Herschlag, D. (1994). Ribonuclease revisited: catalysis via the classical general acid-base mechanism or a triester-like mechanism? J. Am. Chem. Soc. 116, 11631-11635.
57. Jencks, W.P. & Regenstein, J. (1976). Physical and chemical data. In Handbook of Biochemistry and Molecular Biology (G. Fassman, Ed.), vol. 1, pp. 305-451. Chemical Rubber Company, Cleveland.