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Good vibrations in enzyme-catalysed reactions

Abstract

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

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Figure 1: Idealized thermally activated tunnelling and barrier compression in a model computational system, internal H-transfer in malonaldehyde (MAL).
Figure 2: Contemporary vibronic models of H-tunnelling.
Figure 3: Promoting vibrations in liver alcohol dehydrogenase and horse liver lactate dehydrogenase.
Figure 4: Barrier compression in morphinone reductase.

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References

  1. Pisliakov, A. V., Cao, J., Kamerlin, S. C. L. & Warshel, A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc. Natl Acad. Sci. USA 106, 17359–17364 (2009).

    CAS  PubMed  Google Scholar 

  2. Karplus, M. Role of conformation transitions in adenylate kinase. Proc. Natl Acad. Sci. USA 107, E71 (2010).

    CAS  PubMed  Google Scholar 

  3. Henzler-Wildman, K. A. et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913–916 (2007).

    CAS  PubMed  Google Scholar 

  4. Henzler-Wildman, K. A. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838–844 (2007).

    CAS  PubMed  Google Scholar 

  5. Agarwal, P. K., Billeter, S. R., Rajagopalan, P. T. R., Benkovic, S. J. & Hammes-Schiffer, S. Network of coupled promoting motions in enzyme catalysis. Proc. Natl Acad. Sci. USA 99, 2794–2799 (2002).

    CAS  PubMed  Google Scholar 

  6. Wang, L., Goodey, N. M., Benkovic, S. J. & Kohen, A. Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc. Natl Acad. Sci. USA 103, 15753–15758 (2006).

    CAS  PubMed  Google Scholar 

  7. Bhabha, G. et al. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332, 234–238 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Adamczyk, A. J., Cao, J., Kamerlin, S. C. L. & Warshel, A. Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc. Natl. Acad. Sci. USA 108, 14115–14120 (2011).

    CAS  PubMed  Google Scholar 

  9. Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands. Proc. Natl Acad. Sci. USA 107, 1373–1378 (2010).

    CAS  PubMed  Google Scholar 

  10. Liu, H. & Warshel, A. Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. J. Phys. Chem. B 111, 7852–7861 (2007).

    CAS  PubMed  Google Scholar 

  11. Liu, H. & Warshel, A. The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry 46, 6011–6025 (2007).

    PubMed  Google Scholar 

  12. Boekelheide, N., Salomon-Ferrer, R. & Miller, T. F. Dynamics and dissipation in enzyme catalysis. Proc. Natl Acad. Sci. USA 108, 16159–16163 (2011).

    CAS  PubMed  Google Scholar 

  13. Loveridge, E. J. & Allemann, R. K. The temperature dependence of the kinetic isotope effects of dihydrofolate reductase from Thermotoga maritima is influenced by intersubunit interactions. Biochemistry 49, 5390–5396 (2010).

    CAS  PubMed  Google Scholar 

  14. Benkovic, S. J., Hammes, G. G. & Hammes-Schiffer, S. Free-energy landscape of enzyme catalysis. Biochemistry 47, 3317–3321 (2008).

    CAS  PubMed  Google Scholar 

  15. Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638–1642 (2006).

    CAS  PubMed  Google Scholar 

  16. Pudney, C. R. et al. Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms. J. Am. Chem. Soc. 129, 13949–13956 (2007).

    CAS  PubMed  Google Scholar 

  17. Pudney, C. R. et al. Parallel pathways and free-energy landscapes for enzymatic hydride transfer probed by hydrostatic pressure. ChemBioChem 10, 1379–1384 (2009).

    CAS  PubMed  Google Scholar 

  18. Vos, M. H., Rappaport, F., Lambry, J. C., Breton, J. & Martin, J. L. Visualization of coherent nuclear motion in a membrane-protein by femtosecond spectroscopy. Nature 363, 320–325 (1993).

    CAS  Google Scholar 

  19. Hay, S., Johannissen, L. O., Sutcliffe, M. J. & Scrutton, N. S. Barrier compression and its contribution to both classical and quantum mechanical aspects of enzyme catalysis. Biophys. J. 98, 121–128 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Nagel, Z. D. & Klinman, J. P. Update 1 of: Tunneling and dynamics in enzymatic hydride transfer. Chem. Rev. 110, PR41–PR67 (2010).

    PubMed  PubMed Central  Google Scholar 

  21. Schwartz, S. D. & Schramm, V. L. Enzymatic transition states and dynamic motion in barrier crossing. Nature Chem. Biol. 5, 552–559 (2009).

    Google Scholar 

  22. Henzler-Wildman, K. & Kern, D. Dynamic personalities of proteins. Nature 450, 964–972 (2007).

    CAS  PubMed  Google Scholar 

  23. Hay, S. et al. Atomistic insight into the origin of the temperature-dependence of kinetic isotope effects and H-tunnelling in enzyme systems is revealed through combined experimental studies and biomolecular simulation. Biochem. Soc. Trans. 36, 16–21 (2008).

    CAS  PubMed  Google Scholar 

  24. Sen, A. & Kohen, A. Enzymatic tunneling and kinetic isotope effects: chemistry at the crossroads. J. Phys. Org. Chem. 23, 613–619 (2010).

    CAS  Google Scholar 

  25. Truhlar, D. G. Tunneling in enzymatic and nonenzymatic hydrogen transfer reactions. J. Phys. Org. Chem. 23, 660–676 (2010).

    CAS  Google Scholar 

  26. Kamerlin, S. C. L. & Warshel, A. At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis? Proteins 78, 1339–1375 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Kamerlin, S. C. L., Mavri, J. & Warshel, A. Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. FEBS Lett. 584, 2759–2766 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Dybala-Defratyka, A., Paneth, P. & Truhlar, D. G. in Quantum Tunnelling in Enzyme-Catalysed Reactions (eds Allemann, R. K. & Scrutton, N. S.) 36–78 (Royal Society of Chemistry, 2009).

    Google Scholar 

  29. Caratzoulas, S., Mincer, J. S. & Schwartz, S. D. Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase. J. Am. Chem. Soc. 124, 3270–3276 (2002).

    CAS  PubMed  Google Scholar 

  30. Kuznetsov, A. M. & Ulstrup, J. Proton and hydrogen atom tunnelling in hydrolytic and redox enzyme catalysis. Can. J. Chem. 77, 1085–1096 (1999).

    CAS  Google Scholar 

  31. Knapp, M. J., Rickert, K. & Klinman, J. P. Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics. J. Am. Chem. Soc. 124, 3865–3874 (2002).

    CAS  PubMed  Google Scholar 

  32. Hay, S. & Scrutton, N. S. Incorporation of hydrostatic pressure into models of hydrogen tunneling highlights a role for pressure-modulated promoting vibrations. Biochemistry 47, 9880–9887 (2008).

    CAS  PubMed  Google Scholar 

  33. Kohen, A., Cannio, R., Bartolucci, S. & Klinman, J. P. Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase. Nature 399, 496–499 (1999).

    CAS  PubMed  Google Scholar 

  34. Heyes, D. J., Sakuma, M., de Visser, S. P. & Scrutton, N. S. Nuclear quantum tunneling in the light-activated enzyme protochlorophyllide oxidoreductase. J. Biol. Chem. 284, 3762–3767 (2009).

    CAS  PubMed  Google Scholar 

  35. Maglia, G. & Allemann, R. K. Evidence for environmentally coupled hydrogen tunneling during dihydrofolate reductase catalysis. J. Am. Chem. Soc. 125, 13372–13373 (2003).

    CAS  PubMed  Google Scholar 

  36. Basner, J. E. & Schwartz, S. D. Donor-acceptor distance and protein promoting vibration coupling to hydride transfer: a possible mechanism for kinetic control in isozymes of human lactate dehydrogenase. J. Phys. Chem. B 108, 444–451 (2004).

    CAS  Google Scholar 

  37. Quaytman, S. L. & Schwartz, S. D. Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc. Natl Acad. Sci. USA 104, 12253–12258 (2007).

    CAS  PubMed  Google Scholar 

  38. Antoniou, D., Basner, J., Nunez, S. & Schwartz, S. D. Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis. Chem. Rev. 106, 3170–3187 (2006).

    CAS  PubMed  Google Scholar 

  39. Nunez, S., Antoniou, D., Schramm, V. L. & Schwartz, S. D. Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study. J. Am. Chem. Soc. 126, 15720–15729 (2004).

    CAS  PubMed  Google Scholar 

  40. Saen-oon, S., Quaytman-Machleder, S., Schramm, V. L. & Schwartz, S. D. Atomic detail of chemical transformation at the transition state of an enzymatic reaction. Proc. Natl Acad. Sci. USA 105, 16543–16548 (2008).

    CAS  PubMed  Google Scholar 

  41. Johannissen, L. O., Hay, S., Scrutton, N. S. & Sutcliffe, M. J. Proton tunneling in aromatic amine dehydrogenase is driven by a short-range sub-picosecond promoting vibration: consistency of simulation and theory with experiment. J. Phys. Chem. B 111, 2631–2638 (2007).

    CAS  PubMed  Google Scholar 

  42. Johannissen, L. O., Scrutton, N. S. & Sutcliffe, M. J. How does pressure affect barrier compression and isotope effects in an enzymatic hydrogen tunneling reaction? Angew. Chem. Int. Ed. 50, 2129–2132 (2011).

    CAS  Google Scholar 

  43. Pang, J., Hay, S., Scrutton, N. S. & Sutcliffe, M. J. Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase. J. Am. Chem. Soc. 130, 7092–7097 (2008).

    CAS  PubMed  Google Scholar 

  44. Roca, M., Oliva, M., Castillo, R., Moliner, V. & Tunon, I. Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase. Chem. Eur. J. 16, 11399–11411 (2010).

    CAS  PubMed  Google Scholar 

  45. Hatcher, E., Soudackov, A. V. & Hammes-Schiffer, S. Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects. J. Am. Chem. Soc. 129, 187–196 (2007).

    CAS  PubMed  Google Scholar 

  46. Bell, R. The Tunnel Effect in Chemistry (Chapman and Hall, 1980).

    Google Scholar 

  47. Pudney, C. R. et al. Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction. J. Am. Chem. Soc. 131, 17072–17073 (2009).

    CAS  PubMed  Google Scholar 

  48. Warshel, A. & Weiss, R. M. An empirical valence bond approach for comparing reactions in solutions and in enzymes. J. Am. Chem. Soc. 102, 6218–6226 (1980).

    CAS  Google Scholar 

  49. Pu, J. Z., Ma, S. H., Gao, J. L. & Truhlar, D. G. Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase. J. Phys. Chem. B 109, 8551–8556 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Kanaan, N. et al. Temperature dependence of the kinetic isotope effects in thymidylate synthase. A theoretical study. J. Am. Chem. Soc. 133, 6692–6702 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Hatcher, E., Soudackov, A. V. & Hammes-Schiffer, S. Proton-coupled electron transfer in soybean lipoxygenase. J. Am. Chem. Soc. 126, 5763–5775 (2004).

    CAS  PubMed  Google Scholar 

  52. Meyer, M. P., Tomchick, D. R. & Klinman, J. P. Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1. Proc. Natl Acad. Sci. USA 105, 1146–1151 (2008).

    CAS  PubMed  Google Scholar 

  53. Pudney, C. R., Johannissen, L. O., Sutcliffe, M. J., Hay, S. & Scrutton, N. S. Direct analysis of donor acceptor distance and relationship to isotope effects and the force constant for barrier compression in enzymatic H-tunneling reactions. J. Am. Chem. Soc. 132, 11329–11335 (2010).

    CAS  PubMed  Google Scholar 

  54. Hay, S., Sutcliffe, M. J. & Scrutton, N. S. Promoting motions in enzyme catalysis probed by pressure studies of kinetic isotope effects. Proc. Natl Acad. Sci. USA 104, 507–512 (2007).

    CAS  PubMed  Google Scholar 

  55. Radzicka, A. & Wolfenden, R. A proficient enzyme. Science 267, 90–93 (1995).

    CAS  PubMed  Google Scholar 

  56. Doll, K. M., Bender, B. R. & Finke, R. G. The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling. J. Am. Chem. Soc. 125, 10877–10884 (2003).

    CAS  PubMed  Google Scholar 

  57. Major, D. T. et al. Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction. Proc. Natl Acad. Sci. USA 106, 20734–20739 (2009).

    CAS  PubMed  Google Scholar 

  58. Pudney, C. R., Hay, S., Sutcliffe, M. J. & Scrutton, N. S. alpha-Secondary isotope effects as probes of 'tunneling-ready' configurations in enzymatic H-tunneling: insight from environmentally coupled tunneling models. J. Am. Chem. Soc. 128, 14053–14058 (2006).

    CAS  PubMed  Google Scholar 

  59. Hay, S., Pudney, C. R., Sutcliffe, M. J. & Scrutton, N. S. Probing active site geometry using high pressure and secondary isotope effects in an enzyme-catalysed 'deep' H-tunnelling reaction. J. Phys. Org. Chem. 23, 696–701 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Hay, S. et al. Barrier compression enhances an enzymatic hydrogen-transfer reaction. Angew. Chem. Int. Ed. 48, 1452–1454 (2009).

    CAS  Google Scholar 

  61. Masgrau, L. et al. Atomic description of an enzyme reaction dominated by proton tunneling. Science 312, 237–241 (2006).

    CAS  PubMed  Google Scholar 

  62. Johannissen, L. O., Scrutton, N. S. & Sutcliffe, M. J. The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer. J. R. Soc. Interface 5, S225–S232 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Hothi, P., Lee, M., Cullis, P. M., Leys, D. & Scrutton, N. S. Catalysis by the isolated tryptophan tryptophylquinone-containing subunit of aromatic amine dehydrogenase is distinct from native enzyme and synthetic model compounds and allows further probing of TTQ mechanism. Biochemistry 47, 183–194 (2008).

    CAS  PubMed  Google Scholar 

  64. Bandaria, J. N. et al. Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase. Proc. Natl Acad. Sci. USA 107, 17974–17979 (2010).

    CAS  PubMed  Google Scholar 

  65. Heyes, D. J., Levy, C., Sakuma, M., Robertson, D. L. & Scrutton, N. S. A twin-track approach has optimized proton and hydride transfer by dynamically coupled tunneling during the evolution of protochlorophyllide oxidoreductase. J. Biol. Chem. 286, 11849–11854 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Heyes, D. J., Sakuma, M. & Scrutton, N. S. Solvent-slaved protein motions accompany proton but not hydride tunneling in light-activated protochlorophyllide oxidoreductase. Angew. Chem. Int. Ed. 48, 3850–3853 (2009).

    CAS  Google Scholar 

  67. Sytina, O. A. et al. Conformational changes in an ultrafast light-driven enzyme determine catalytic activity. Nature 456, 1001–1004 (2008).

    CAS  PubMed  Google Scholar 

  68. Masgrau, L., Basran, J., Hothi, P., Sutcliffe, M. J. & Scrutton, N. S. Hydrogen tunneling in quinoproteins. Arch. Biochem. Biophys. 428, 41–51 (2004).

    CAS  PubMed  Google Scholar 

  69. Hay, S., Pudney, C. R. & Scrutton, N. S. Structural and mechanistic aspects of flavoproteins: probes of hydrogen tunnelling. FEBS J. 276, 3930–3941 (2009).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank the United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) for supporting this work. S.H. is a BBSRC David Phillips Fellow. N.S.S. is a BBSRC Professorial Fellow and holds a Royal Society Wolfson Research Merit Award.

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Correspondence to Sam Hay or Nigel S. Scrutton.

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Hay, S., Scrutton, N. Good vibrations in enzyme-catalysed reactions. Nature Chem 4, 161–168 (2012). https://doi.org/10.1038/nchem.1223

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