Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Taking Ockham's razor to enzyme dynamics and catalysis

Nature Chemistry volume 4, pages 169–176 (2012)Cite this article

Subjects

Abstract

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution — where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Transition-state structure for the rate-determining step in the AADH–tryptamine iminoquinone complex.
Figure 2: Multidimensional schematic of the potential-energy surface for the two-state kinetic model used to fit experimental data for SLO, MADH, AADH and DHFR.
Figure 3: Fits to experimental data using our simple two-state TST model.

Similar content being viewed by others

References

  1. Nagel, Z. D. & Klinman, J. P. A 21st century revisionist's view at a turning point in enzymology. Nature Chem. Biol. 5, 543–550 (2009).

    Article  CAS  Google Scholar 

  2. 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 

  3. Rothlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190–194 (2008).

    Article  PubMed  Google Scholar 

  4. Siebrand, W. & Smedarchina, Z. Model for the analysis of enzymatic proton-transfer reactions with an application to soybean lipoxygenase-1 and six mutants. J. Phys. Org. Chem. 23, 620–631 (2010).

    Article  CAS  Google Scholar 

  5. 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).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  8. Cha, Y., Murray, C. J. & Klinman, J. P. Hydrogen tunneling in enzyme reactions. Science 243, 1325–1330 (1989).

    Article  CAS  PubMed  Google Scholar 

  9. Basran, J., Sutcliffe, M. J. & Scrutton, N. S. Enzymatic H-transfer requires vibration-driven extreme tunneling. Biochemistry 38, 3218–3222 (1999).

    Article  CAS  PubMed  Google Scholar 

  10. Glickman, M. H. & Klinman, J. P. Nature of rate-limiting steps in the soybean lipoxygenase-1 reaction. Biochemistry 34, 14077–14092 (1995).

    Article  CAS  PubMed  Google Scholar 

  11. Forrest, L. R. et al. Mechanism for alternating access in neurotransmitter transporters. Proc. Natl Acad. Sci. USA 105, 10338–10343 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Pentikainen, U., Pentikainen, O. T. & Mulholland, A. J. Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations. Proteins 70, 498–508 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Strickland, N., Mulholland, A. J. & Harvey, J. N. The Fe-CO bond energy in myoglobin: A QM/MM study of the effect of tertiary structure. Biophys. J. 90, L27–L29 (2006).

    Article  CAS  PubMed  Google Scholar 

  14. Koshland, D. E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98–104 (1958).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ma, B. Y. & Nussinov, R. Enzyme dynamics point to stepwise conformational selection in catalysis. Curr. Opin. Chem. Biol. 14, 652–659 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zhou, H. X. From induced fit to conformational selection: A continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys. J. 98, L15–L17 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Vértessy, B. G. & Orosz, F. From “fluctuation fit” to “conformational selection”: Evolution, rediscovery, and integration of a concept. BioEssays 33, 30–34 (2011).

    Article  PubMed  Google Scholar 

  18. Van der Kamp, M. W., Perruccio, F. & Mulholland, A. J. High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase. Chem. Commun. 1874–1876 (2008).

  19. Henzler-Wildman, K. A. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838–813 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Venkitakrishnan, R. P. et al. Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry 43, 16046–16055 (2004).

    Article  CAS  PubMed  Google Scholar 

  21. Min, W. et al. Fluctuating enzymes: Lessons from single-molecule studies. Accounts Chem. Res. 38, 923–931 (2005).

    Article  CAS  Google Scholar 

  22. Lodola, A. et al. Conformational effects in enzyme catalysis: Reaction via a high energy conformation in fatty acid amide hydrolase. Biophys. J. 92, L20–L22 (2007).

    Article  CAS  PubMed  Google Scholar 

  23. Chouard, T. Breaking the protein rules. Nature 471, 151–153 (2011).

    Article  CAS  PubMed  Google Scholar 

  24. Tokuriki, N. & Tawfik, D. S. Protein dynamism and evolvability. Science 324, 203–207 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Wolf-Watz, M. et al. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nature Struct. Mol. Biol. 11, 945–949 (2004).

    Article  CAS  Google Scholar 

  26. Daggett, V. Protein folding-simulation. Chem. Rev. 106, 1898–1916 (2006).

    Article  CAS  PubMed  Google Scholar 

  27. Warshel, A. Bicycle-pedal model for the first step in the vision process. Nature 260, 679–683 (1976).

    Article  CAS  PubMed  Google Scholar 

  28. Van der Kamp, M. W., Shaw, K. E., Woods, C. J. & Mulholland, A. J. Biomolecular simulation and modelling: status, progress and prospects. J. R. Soc. Interface 5, S173–S190 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Lonsdale, R., Harvey, J. N., Manby, F. R. & Mulholland, A. J. Comment on “A stationary-wave model of enzyme catalysis” by Carlo Canepa. J. Comput. Chem. 32, 368–369 (2011).

    Article  CAS  PubMed  Google Scholar 

  30. McGeagh, J. D., Ranaghan, K. E. & Mulholland, A. J. Protein dynamics and enzyme catalysis: Insights from simulations. Biochim. Biophys. Acta 1814, 1077–1092 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Hammes-Schiffer, S. & Benkovic, S. J. Relating protein motion to catalysis. Annu. Rev. Biochem. 75, 519–541 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Benkovic, S. J. & Hammes-Schiffer, S. A perspective on enzyme catalysis. Science 301, 1196–1202 (2003).

    Article  CAS  PubMed  Google Scholar 

  33. Garcia-Viloca, M., Gao, J., Karplus, M. & Truhlar, D. G. How enzymes work: Analysis by modern rate theory and computer simulations. Science 303, 186–195 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Pu, J. Z., Gao, J. L. & Truhlar, D. G. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem. Rev. 106, 3140–3169 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Gilbert, R. G. & Smith, S. C. Theory of Unimolecular and Recombination Reactions (Blackwell, 1990).

    Google Scholar 

  37. Bowman, G. R. & Pande, V. S. Protein folded states are kinetic hubs. Proc. Natl Acad. Sci. USA 107, 10890–10895 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Huang, R. et al. Direct observation of the full transition from ballistic to diffusive Brownian motion in a liquid. Nature Phys. 7, 576–580 (2011).

    Article  CAS  Google Scholar 

  39. Laidler, K. J. Chemical Kinetics 3rd edn (Harper International, 1987).

    Google Scholar 

  40. Lourderaj, U. & Hase, W. L. Theoretical and computational studies of non-RRKM unimolecular dynamics. J. Phys. Chem. A 113, 2236–2253 (2009).

    Article  CAS  PubMed  Google Scholar 

  41. Heazlewood, B. R. et al. Near-threshold H/D exchange in CD3CHO photodissociation. Nature Chem. 3, 443–448 (2011).

    Article  CAS  Google Scholar 

  42. Glowacki, D. R. & Pilling, M. J. Unimolecular reactions of peroxy radicals in atmospheric chemistry and combustion. ChemPhysChem 11, 3836–3843 (2010).

    Article  CAS  PubMed  Google Scholar 

  43. Miller, J. A. & Klippenstein, S. J. Master equation methods in gas phase chemical kinetics. J. Phys. Chem. A 110, 10528–10544 (2006).

    Article  CAS  PubMed  Google Scholar 

  44. Glowacki, D. R., Liang, C. H., Marsden, S. P., Harvey, J. N. & Pilling, M. J. Alkene hydroboration: Hot intermediates that react while they are cooling. J. Am. Chem. Soc. 132, 13621–13623 (2010).

    Article  CAS  PubMed  Google Scholar 

  45. Greaves, S. J. et al. Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution. Science 331, 1423–1426 (2011).

    Article  CAS  PubMed  Google Scholar 

  46. Glowacki, D. R., Marsden, S. P. & Pilling, M. J. Significance of nonstatistical dynamics in organic reaction mechanisms: Time-dependent stereoselectivity in cyclopentyne-alkene cycloadditions. J. Am. Chem. Soc. 131, 13896–13897 (2009).

    Article  CAS  PubMed  Google Scholar 

  47. Glowacki, D. R., Reed, S. K., Pilling, M. J., Shalashilin, D. V. & Martinez-Nunez, E. Classical, quantum and statistical simulations of vibrationally excited HOSO2: IVR, dissociation, and implications for OH + SO2 kinetics at high pressures. Phys. Chem. Chem. Phys. 11, 963–974 (2009).

    Article  CAS  PubMed  Google Scholar 

  48. Harvey, J. N. Ab initio transition state theory for polar reactions in solution. Faraday Discuss. 145, 487–505 (2010).

    Article  CAS  Google Scholar 

  49. Cooper, A. Protein heat capacity: An anomaly that maybe never was. J. Phys. Chem. Lett. 1, 3298–3304 (2010).

    Article  CAS  Google Scholar 

  50. 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).

    Article  CAS  PubMed  Google Scholar 

  51. Loveridge, E. J., Tey, L. H. & Allemann, R. K. Solvent effects on catalysis by Escherichia coli dihydrofolate reductase. J. Am. Chem. Soc. 132, 1137–1143 (2010).

    Article  CAS  PubMed  Google Scholar 

  52. Sikorski, R. S. et al. Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis. J. Am. Chem. Soc. 126, 4778–4779 (2004).

    Article  CAS  PubMed  Google Scholar 

  53. Fleming, D. G. et al. Kinetic isotope effects for the reactions of muonic helium and muonium with H2 . Science 331, 448–450 (2011).

    Article  CAS  PubMed  Google Scholar 

  54. Wu, T., Werner, H. J. & Manthe, U. First-principles theory for the H+CH4 → H2+CH3 reaction. Science 306, 2227–2229 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Claeyssens, F. et al. High-accuracy computation of reaction barriers in enzymes. Angew. Chem. Int. Ed. 45, 6856–6859 (2006).

    Article  CAS  Google Scholar 

  56. Kanaan, N., Roca, M., Tunon, I., Marti, S. & Moliner, V. Application of Grote-Hynes theory to the reaction catalyzed by thymidylate synthase. J. Phys. Chem. B 114, 13593–13600 (2010).

    Article  CAS  PubMed  Google Scholar 

  57. Alhambra, C., Sanchez, M. L., Corchado, J. C., Gao, J. & Truhlar, D. G. Quantum mechanical tunneling in methylamine dehydrogenase. Chem. Phys. Lett. 347, 512–518 (2001); Erratum ibid. 355, 388–394 (2002).

    Article  CAS  Google Scholar 

  58. Lonsdale, R., Harvey, J. N. & Mulholland, A. J. Compound I reactivity defines alkene oxidation selectivity in cytochrome P450cam. J. Phys. Chem. B 114, 1156–1162 (2010).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  60. Lodola, A. et al. Structural fluctuations in enzyme-catalyzed reactions: Determinants of reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics/molecular mechanics paths. J. Chem. Theory Comput. 6, 2948–2960 (2010).

    Article  CAS  PubMed  Google Scholar 

  61. 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).

    Article  CAS  Google Scholar 

  62. Glowacki, D. R., Paci, E. & Shalashilin, D. V. Boxed molecular dynamics: A simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems. J. Phys. Chem. B 113, 16603–16611 (2009).

    Article  CAS  PubMed  Google Scholar 

  63. Greaves, S. J. et al. Vibrational excitation through tug-of-war inelastic collisions. Nature 454, 88–91 (2008).

    Article  CAS  PubMed  Google Scholar 

  64. Glowacki, D. R., Rose, R. A., Greaves, S. J., Orr-Ewing, A. J. & Harvey, J. N. Ultrafast energy flow in the wake of solution-phase bimolecular reactions. Nature Chem. 3, 850–855 (2011).

    Article  CAS  Google Scholar 

  65. Glowacki, D. R., Orr-Ewing, A. J. & Harvey, J. N. Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases. J. Chem. Phys. 134, 214508 (2011).

    Article  PubMed  Google Scholar 

  66. Ruggiero, G. D., Williams, I. H., Roca, M., Moliner, V. & Tunon, I. QM/MM determination of kinetic isotope effects for COMT-catalyzed methyl transfer does not support compression hypothesis. J. Am. Chem. Soc. 126, 8634–8635 (2004).

    Article  CAS  PubMed  Google Scholar 

  67. Strajbl, M., Shurki, A., Kato, M. & Warshel, A. Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. J. Am. Chem. Soc. 125, 10228–10237 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  69. Dybala-Defratyka, A., Paneth, P., Banerjee, R. & Truhlar, D. G. Coupling of hydrogenic tunneling to active-site motion in the hydrogen radical transfer catalyzed by a coenzyme B-12-dependent mutase. Proc. Natl Acad. Sci. USA 104, 10774–10779 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Zuev, P. S. et al. Carbon tunneling from a single quantum state. Science 299, 867–870 (2003).

    Article  CAS  PubMed  Google Scholar 

  71. Schreiner, P. R. et al. Capture of hydroxymethylene and its fast disappearance through tunnelling. Nature 453, 906–942 (2008).

    Article  CAS  PubMed  Google Scholar 

  72. Brunton, G., Griller, D., Barclay, L. R. C. & Ingold, K. U. Kinetic applications of electron paramagnetic resonance spectroscopy. 26. Quantum-mechanical tunneling in the isomerization of sterically hindered aryl radicals. J. Am. Chem. Soc. 98, 6803–6811 (1976).

    Article  CAS  Google Scholar 

  73. Olsson, M. H. M., Siegbahn, P. E. M. & Warshel, A. Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase. J. Am. Chem. Soc. 126, 2820–2828 (2004).

    Article  CAS  PubMed  Google Scholar 

  74. Liu, H. B. & 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).

    Article  CAS  PubMed  Google Scholar 

  75. Williams, I. H. Quantum catalysis? A comment on tunnelling contributions for catalysed and uncatalysed reactions. J. Phys. Org. Chem. 23, 685–689 (2010).

    Article  CAS  Google Scholar 

  76. Masgrau, L., Ranaghan, K. E., Scrutton, N. S., Mulholland, A. J. & Sutcliffe, M. J. Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: Oxidation of tryptamine by aromatic amine dehydrogenase. J. Phys. Chem. B 111, 3032–3047 (2007).

    Article  CAS  PubMed  Google Scholar 

  77. Ranaghan, K. E., Masgrau, L., Scrutton, N. S., Sutcliffe, M. J. & Mulholland, A. J. Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase. ChemPhysChem 8, 1816–1835 (2007).

    Article  CAS  PubMed  Google Scholar 

  78. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Pang, J. Y., Pu, J. Z., Gao, J. L., Truhlar, D. G. & Allemann, R. K. Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. J. Am. Chem. Soc. 128, 8015–8023 (2006).

    Article  CAS  PubMed  Google Scholar 

  80. Agmon, N. & Hopfield, J. J. CO binding to heme proteins: A model for barrier height distributions and slow conformational changes. J. Chem. Phys. 79, 2042–2053 (1983).

    Article  CAS  Google Scholar 

  81. Knowles, J. R. Enzyme catalysis: Not different, just better. Nature 350, 121–124 (1991).

    Article  CAS  PubMed  Google Scholar 

  82. Skodje, R. T. & Truhlar, D. G. Parabolic tunneling calculations. J. Phys. Chem. 85, 624–628 (1981).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

A.J.M. is an EPSRC Leadership Fellow (EP/G007705/1). J.N.H. and D.R.G. thank EPSRC for support (Programme Grant EP/G00224X). Thanks to K.E. Ranaghan for providing Fig. 1, and for useful comments along with M. W. van der Kamp.

Author information

Authors and Affiliations

  1. Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK

    David R. Glowacki, Jeremy N. Harvey & Adrian J. Mulholland

Authors
  1. David R. Glowacki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeremy N. Harvey
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Adrian J. Mulholland
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to David R. Glowacki or Adrian J. Mulholland.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Glowacki, D., Harvey, J. & Mulholland, A. Taking Ockham's razor to enzyme dynamics and catalysis. Nature Chem 4, 169–176 (2012). https://doi.org/10.1038/nchem.1244

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.1244

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing