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.

  • Article
  • Published:

Simulation of enzyme–substrate encounter with gated active sites

Nature Structural Biology volume 1, pages 65–69 (1994)Cite this article

Abstract

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.

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

Similar content being viewed by others

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  20. Molecular Simulations Inc. QUANTA. Burlington, MA.

  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).

    Article  CAS  Google Scholar 

  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).

    Article  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  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

Authors
  1. Rebecca C. Wade
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brock A. Luty
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eugene Demchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jeffry D. Madura
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Malcolm E. Davis
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. James M. Briggs
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Andrew McCammon
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wade, R., Luty, B., Demchuk, E. et al. Simulation of enzyme–substrate encounter with gated active sites. Nat Struct Mol Biol 1, 65–69 (1994). https://doi.org/10.1038/nsb0194-65

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0194-65

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