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Simulation of enzyme–substrate encounter with gated active sites

Nature Structural & Molecular Biologyvolume 1pages6569 (1994) | Download Citation



We describe a brownian dynamics simulation method that allows investigation of the effects of receptor flexibility on ligand binding rates. The method is applied to the encounter of substrate, glyceraldehyde 3–phosphate, with triose phosphate isomerase, a diffusion–controlled enzyme with flexible peptide loops at its active sites. The simulations show that while the electrostatic field surrounding the enzyme steers the substrate into its active sites, the flexible loops appear to have little influence on the substrate binding rate. The dynamics of the loops may therefore have been optimized during evolution to minimize their interference with the substrate's access to the active sites. The calculated and experimental rate constants are in good agreement.

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  1. 1

    Blacklow, S., Raines, R., Lim, W., Zamore, P. & Knowles, J. Triosephosphate isomerase catalysis is diffusion controlled. Biochemistry 27, 1158–1167 (1988).

  2. 2

    Calef, D. & Deutch, J. Diffusion-controlled reactions. A. Rev. phys. Chem. 34, 493–524 (1983).

  3. 3

    Pompliano, D., Peyman, A. & Knowles, J. Stabilization of a reaction intermediate as a catalytic device: Definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry 29, 3186–3194 (1990).

  4. 4

    Sampson, N. & Knowles, J. Segmental motion in catalysis: Investigation of a hydrogen bond critical for loop closure in the reaction triose phosphate isomerase. Biochemistry 31, 8488–8494 (1992).

  5. 5

    Clarke, A. et al. Site-directed mutagenesis reveals role of mobile arginme residue in lactate dehydrogenase catalysis. Nature 324, 699–702 (1986).

  6. 6

    Fry, D., Kuby, S. & Mildvan, A. ATP-binding site of adenylate kinase: Mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc. natn. Acad. Sci U.S.A. 83, 907–911 (1986).

  7. 7

    Kempner, E. Movable lobes and flexible loops in proteins. FEBS Lett. 326, 4–10 (1993).

  8. 8

    Northrup, S., Allinson, S. & McCammon, J. Brownian dynamics simulation of diffusion-influenced bimolecular reactions, J. chem. Phys. 80, 1517–1524 (1984).

  9. 9

    Zhou, H.-X. On the calculation of diffusive reaction rates using brownian dynamics simulations. J. chem. Phys. 92, 3092–3095 (1990).

  10. 10

    Smoluchowski, M. Versuch einer machematischen theorie der koagulationskinetik kolloider loesungen. Z. phys. Chem. 92, 129–168 (1917).

  11. 11

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

  12. 12

    Plaut, B. & Knowles, J. pH-dependence of the triose phosphate isomerase reaction. Biochem. J. 129, 311–320 (1972).

  13. 13

    Wierenga, R. et al. The crystal structure of the open and the closed conformation of the flexible loop of trypanosomal triosephosphate isomerase. Proteins 10, 33–49 (1991).

  14. 14

    Madura, J. & McCammon, J. Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and d-glyceraldehyde phosphate. J. phys. Chem. 93, 7285–7287 (1989).

  15. 15

    Luty, B. et al. Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: Electrostatic steering of glyceraldehyde phosphate. J. phys. Chem. 97, 233–237 (1993).

  16. 16

    Wade, R., Davis, M., Luty, B., Madura, J. & McCammon, J. Gating of the active site of triose phsophate isomerase: Brownian dynamics simulations of flexible peptide loops in the enyzme. Biophys. J. 64, 9–15 (1993).

  17. 17

    Getzoff, E. et al. Faster superoside dismutase mutants designed by enhancing electorstatic guidance. Nature 358, 357–351 (1992).

  18. 18

    McCammon, J. Superperfect enzymes. Curr. Biol. 2, 585–586 (1992).

  19. 19

    Bernstein, F. et al. The protein data base: a computer-based archival file for macromolecular structures. J. molec. Biol. 112, 535–542 (1977).

  20. 20

    Molecular Simulations Inc. QUANTA. Burlington, MA.

  21. 21

    Jorgensen, W. & Tirado-Rives, J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambm. J. Am. chem. Soc. 110, 1657–1666 (1988).

  22. 22

    Davis, M., Madura, J., Luty, B. & McCammon, J. Electrostatics and diffusion of molecules in solution: Simulations with the university of Houston Brownian dynamics program. Comp. Phys. Comm. 62, 187–197 (1990).

  23. 23

    Davis, M. & McCammon, J. Solving the finite difference linearized poisson-boltzmann equation: A comparison of relaxation of conjugate gradient methods. J. comput. Chem. 10, 386–391 (1989).

  24. 24

    Davis, M. & McCammon, J. Dielectric boundary smoothing infinite difference solutions of the poisson eguation: An approach to improve accuracy and convergence. J. comput. Chem. 7, 909–912 (1991).

  25. 25

    McCammon, J., Northrup, S., Karplus, M. & Levy, R. Helix-coil transitions in a simple polypeptide model. Biopolymers 19, 2033–2045 (1980).

  26. 26

    Levitt, M. & Warshel, A. Computer simulation of protein folding. Nature 253, 694–698 (1975).

  27. 27

    Levitt, M. A simplified representation of protein conformations for rapid simulation of protein folding. J. molec. Biol. 104, 59–107 (1976).

  28. 28

    Ermak, D. & McCammon, J. Brownian dynamics with hydrodynamic interactions. J. chem. Phys. 69, 1352–1360 (1978).

  29. 29

    Luty, B., McCammon, J. & Zhou, H.-X. Diffusive reaction rates from Brownian dynamics simulations: Replacing the outer cutoff surface by an analytical treatment. J. chem. Phys. 97, 5682–5686 (1992).

  30. 30

    Lolis, E. & Petsko, G. Crystallography analysis of the complex between triosephosphate isomerase and 2- phosphoglycolate at 2.5 Å resolution: Implications for catalysis. Biochemistry 29, 6619–6625 (1990).

  31. 31

    Banner, D. et al. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 resolution using amino acid sequence data. Nature 255, 609–614 (1975).

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Author information


  1. European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 , Heidelberg, Germany

    • Rebecca C. Wade
    •  & Eugene Demchuk
  2. Department of Chemistry, University of Houston, Houston, TX, 77204-5641, USA

    • Brock A. Luty
    • , James M. Briggs
    •  & J. Andrew McCammon
  3. Department of Chemistry, University of South Alabama, Mobile, AL, 36688

    • Jeffry D. Madura
  4. Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, New Jersey, 08543, USA

    • Malcolm E. Davis


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