Understanding enzymic catalysis: The importance of short, strong hydrogen bonds

Chemistry and Biology

Volumn 4, Issue 4, 1997, Pages 259-267

  Gerlt, John A ^a   Kreevoy, Maurice M ^b   Cleland, W W ^c,d   Frey, Perry A ^c,d  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Minnesota   (United States)

^c UNIVERSITY OF WISCONSIN   (United States)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031127432     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(97)90069-7     Document Type: Review

References (63)

1. Gerlt, J.A. & Gassman, P.G. (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.
2. Gerlt, J.A. & Gassman, P.G. (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.
3. Cleland, W.W. & Kreevoy, M.M. (1994). Low-barrier hydrogen bonds and enzymic catalysis. Science 264, 1887-1890.
4. Frey, P., Whitt, S. & Tobin, J. (1994). A low barrier hydrogen bond in the catalytic triad of serine proteases. Science 264, 1927-1930.
5. Guthrie, J.P. (1996). Short strong hydrogen bonds: can they explain enzymic catalysis? Chem. Biol. 3, 163-170.
6. Scheiner, S. & Kar, T. (1995). The nonexistence of specially stabilized hydrogen bonds in enzymes. J. Am. Chem. Soc. 117, 6970-6975.
7. Shan, S., Loh, S. & Herschlag, D. (1996). The energetics of hydrogen bonds in model systems: implications for enzymic catalysis. Science 272, 97-101.
8. 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.
9. Warshel, A., Papazyan, A. & Kollman, P.A. (1995). On low-barrier hydrogen bonds and enzyme catalysis. Science 269, 102-104.
10. Speakman, J.C. (1949). The crystal structures of the acid salts of some monobasic acids. Part I. Potassium hydrogen bisphenylacetate. J. Chem. Soc. 3357-3356.
11. Hadzi, D. (1965). Infrared spectra of strongly hydrogen-bonded systems. Pure Appl. Chem. 11, 435-453.
12. Zundel, G. (1976). In The Hydrogen Bond. II. (Schuster, P., Zundel, G. & Sandorfy, C., eds), North Holland, Amsterdam, pp. 683-766.
13. -. J. Am. Chem. Soc. 102, 3315-3322.
14. Pauling, L. (1960). The Nature of the Chemical Bond, 3rd Edition. Cornell University Press, Ithaca, USA.
15. Gilli, P., Bertolase, 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.
16. Levine, I.N. (1988). Physical Chemistry, Third Edition. McGraw Hill, New York, USA. pp. 162-164.
17. Brown, I.D. (1994). In Structure Correlation, Vol. 2. (Bürgi, H.-B. & Dunitz, J.D., eds), VCH Publishers, New York, USA. pp. 405-429.
18. Scheiner, S. (1994). Relationship between strength of hydrogen bond and barrier to proton transfer. J. Mol. Struct. (Theochem.) 307, 65-71.
19. Scheiner, S. & Redfern, P. (1986). Quantum mechanical test of Marcus theory. Effects of alkylation upon proton transfer. J. Phys. Chem. 90, 2969-2974.
20. Garcia-Viloca, M., González-Lafont, A. & Lluch, J.M. (1997). Theoretical study of the low barrier hydrogen bond in the hydrogen maleate anion in the gas phase. Comparison with normal hydrogen bonds. J. Am. Chem. Soc. 119, 1081-1086.
21. 2H acid. J. Phys. Chem. 92, 3379-3386.
22. Jeffrey, G.A. & Saenger, W. (1991). Hydrogen Bonding in Biological Structures. Springer-Verlag, Berlin, Germany, pp. 111-116.
23. Steiner, T. & Saenger, W. (1994). Lengthening of the covalent O-H bond in O-H⋯O hydrogen bonds re-examined from low-temperature neutron diffraction data of organic compounds. Acta Crystallogr. B 50, 348-357.
24. Speakman, J.C. (1972). Acid salts of carboxylic acids. Crystals with some "very short" hydrogen bonds. Struct. Bonding (Berlin) 12, 141-199.
25. Hadzi, D. Novak, A. & Gordon, J.E. (1963). Infrared spectra of, and hydrogen bonding in, some adducts of phenols with their phenoxides and other oxygen bases. J. Phys. Chem. 67, 1118-1124.
26. Marimanikkuppam, S.S., Binder, D.A., Lee, I-S., Young, V.G. & Kreevoy, M.M. (1996). The effect of ordered water on a short, strong (Speakman-Hadzi) hydrogen bond. Croatica Chem. Acta 69, 1661-1674.
27. + complexes in acetonitrile. Adv. Mol. Relaxation Processes 5, 99-106.
28. Altman, L.J., Laungani, D., Gunnarsson, G., Wennerstrom, H. & Forsen, S. (1978) Proton, deuterium, and tritium nuclear magnetic resonance of intramolecular hydrogen bonds. Isotope effects and the shape of the potential energy function. J. Am, Chem. Soc. 100, 8264-8266.
29. a <1. Can. J. Chem. 58, 311-322.
30. Hadzi, D. & Smerkolj, R. (1976). Hydrogen bonding in some adducts of oxygen bases with acids. Part 8. Proton chemical shifts and thermodynamic data on the association of chloroacetic acids with some oxygen bases. J. Chem. Soc. Faraday Trans. 72, 1188-1191.
31. Benoit, R.L., Rinfret, M., & Domain, R. (1972). Calorimetric studies in the halide-hydrogen chloride systems, Inorg. Chem. 11, 2603-2605.
32. Levine, I.N. (1988). Physical Chemistry, 3rd Edition. McGraw Hill, New York, USA. p. 240.
33. Schwartz, B. & Drueckhammer, D.G. (1995). A simple method for determining the relative strengths of normal and low-barrier hydrogen bonds in solution: implications to enzyme catalysis. J. Am. Chem. Soc. 117, 11902-11905.
34. Küppers, H. (1978). Lithium hydrogen phthalate monohydrate. Acta Cryst. B 34, 3763-3765.
35. Küppers, H. (1978). The crystal structure of lithium hydrogen phthalate dihydrate, containing a very short hydrogen bond. Acta Cryst. B 31, 1068-1072.
36. Orel, B., Hadzi, D. & Cabassi, F. (1975). Infrared and raman spectra of potassium hydrogen phthalate. Spectrochim. Acta 31 A, 169-182.
37. Shan, S. & Herschlag, D. (1996). Energetic effects of multiple hydrogen bonds. Implications for enzymic catalysis. J. Am. Chem. Soc. 118, 5515-5518.
38. Magnoli, D.E. & Murdoch, J.R. (1981). Kinetic and thermodynamic contributions to energy barriers and energy wells: application to proton-bound dimers in gas-phase proton-transfer reactions. J. Am. Chem. Soc. 103, 7465-7469.
39. + analogues. J. Am. Chem. Soc. 110, 524-530.
40. Shan, S. & Herschlag, D. (1996). The change in hydrogen bond strength accompanying charge rearrangement. Implications for enzymic catalysis. Proc. Natl Acad. Sci. USA, 93, 14474-14479.
41. Abraham, M.H., Grellier, P.L., Prior, D.V., Duce, P.P., Morris, J.J. & Taylor, P.J. (1989). Hydrogen bonding. Part 7. A scale of solute hydrogen-bond acidity based on log k values for complexation in tetrachloromethane. J. Chem. Soc. Perkin Trans. II, 699-711.
42. Clatman, D. & Zeegers-Huyskens, Th. (1967). Application des relations de taft à la complexation. Spectrochim. Acta 23 A, 1627-1639.
43. Stymne, B., Stymne, H. & Wettermark, G. (1973). Substituent effects in the thermodynamics of hydrogen bonding as obtained by infrared spectrometry. J. Am. Chem. Soc. 95, 3490-3494.
44. Hopkins, H.P. Jr., Alexander, C.J. & Ali, S.Z. (1978). A quantitative comparison of the relative hydrogen bonding basicities and the gas-phase proton affinities of substituted pyridines. J. Phys. Chem. 82, 1268-1272.
45. Bordwell, F.R., McCallum, R.J. & Olmstead, W.N. (1984) Acidities and hydrogen bonding of phenols in dimethyl sulfoxide. J. Org. Chem. 49, 1424-1427.
46. Perrin, C.L. (1994). Symmetries of hydrogen bonds in solution. Science 266, 1665-1668.
47. Mangel, W.F., et al., & Sweet, R.M. (1991). Structure of an acyl-enzyme intermediate during catalysis: (guanidinobenzoyl)trypsin. Biochemistry 29, 8351-8357.
48. Sekikawa, T., Miyakubo, K., Takeda, S. & Kobayashi, T. (1996). Charge-transfer effects in a strongly hydrogen-bonded system: potassium salts of acetylenedicarboxylic acid. J. Phys. Chem. 100, 5844-5848.
49. Anderson, G.R. & Lippincott, E.R. (1971). Vibronic effects in hydrogen bonding. J. Chem. Phys. 55, 4077-4087.
50. Reed, A.E., Curtiss, L.A. & Weinhold, F. (1988). Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem. Rev. 88, 899-926.
51. Xiang, S., Short, S.A., Wolfenden, R. & Carter, C.W. (1995). Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase. Biochemistry 34, 4516-4523.
52. Bondi, A. (1964). van der Waals volumes and radii. J. Phys. Chem. 68, 441-451.
53. Carlow, D.C., Smith, A.A., Yang, C.C., Short, S.A. & Wolfenden, R. (1995). Major contribution of a carboxymethyl group to transition-state stabilization by cytidine deaminase: mutation and rescue. Biochemistry 34, 4220-4224.
54. Liang, T.-C. & Abeles, R.H. (1987). Complex of ct-chymotrypsin and N-acetyl-L-leucyl-L-phenylalanyl trifluoromethyl ketone: structural studies with NMR spectroscopy. Biochemistry 26, 7603-7608.
55. Brady, K., Wei, A., Ringe, D. & Abeles, R.H. (1990). Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors. Biochemistry 29, 7600-7607.
56. Cassidy, C., Lin, J. & Frey, P.A. (1997). A new concept for the mechanism of action of chymotrypsin: the role of the low barrier hydrogen bond. Biochemistry 36, 4576-4584.
57. Gandour, R.D., Nabulsi, N.A.R. & Fronczek, F.R. (1990). Structural model of a short carboxyl-imidazole hydrogen bond with a nearly central located proton: implications for the Asp-His dyad in serine proteases. J. Am. Chem. Soc. 112, 7816-7817.
58. Candour, R.D. (1981). On the importance of orientation in general base catalysis by carboxylate. Bioorg. Chem. 10, 169-176.
59. 5-3-ketosteroid isomerase. Proc. Natl Acad. Sci. USA 93, 8220-8224.
60. Usher, K.C., Remington, S.J., Martin, D.P. & Drueckhammer, D.G. (1994). A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase. Biochemistry 33, 7753-7759.
61. a balance: the case of triose phosphate isomerase (TIM)? J. Am. Chem. Soc. 117, 9855-9862.
62. Guo, H. & Salahub, D.R. (1996). Large cooperative effects of hydrogen bonding involving a peptide linkage and an imidazole ring: implications for the enzymic action of triosephosphate isomerase (TIM). In press.
63. Messmore, J., Fuchs, D. & Raines, R.T. (1995). Ribonuclease A: revealing structure-function relationships with semisynthesis. J. Am. Chem. Soc. 117, 8057-8060.