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1995 | 42 | 4 |

Tytuł artykułu

Simulation of enzyme-substrate interactions: the diffusional encounter step

Autorzy

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
Enzymes are targets for structure-based redesign and drug design. One potentially important design strategy is to create molecules — enzymes and ligands — with desired diffusional encounter properties. Rates of diffusive bimolecular encounter can be calculated by Brownian dynamics simulation. This methodology and its appli­cation to study the factors influencing the rates of diffusion-influenced enzymes are described here.

Wydawca

-

Rocznik

Tom

42

Numer

4

Opis fizyczny

p.419-425,fig.

Twórcy

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

Bibliografia

  • 1. Albery, J.W. & Knowles, J.R. (1976) Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15,5631-5640.
  • 2. Cudd, A. & Fridovich, I. (1982) Electrostatic interactions in the reaction mechanisms of bovine erythrocyte superoxide dismutase. /. Biol. Chan. 257,11443-11447.
  • 3. Blacklow, S.C., Raines, R.T., Lim, WA., Zamore, P.D. & Knowles, J.R. (1988) Triosephosphate iso- merase catalysis is diffusion controlled. Bio­chemistry 27,1158-1167.
  • 4. Baxelyansky, M., Robey, C. & Kirsch, J.F. (1986) Fractional diffusion-limited component of reactions catalyzed by acetylcholinesterase. Biochemistry 25,125-130.
  • 5. Simopoulos, T.T. & Jencks, W.P. (1994) Alkaline phosphatase is an almost perfect enzyme. Biochemistry 33,10375-10380.
  • 6. Hardy, L.W. & Kirsch, J.F. (1984) Diffusion- -limited component of reactions catalyzed by Bacillus cereus (3-lactamase I. Biochemistry 23, 1275-1282.
  • 7. Christensen, H., Martin, M.T. & Waley, S.G. (1990) ^-Lactamase as fully efficient enzymes. Determination of all the rate constants in the acyl-erizyme mechanism. Biochem. }. 266, 853- -861.
  • 8. Guha, MX, Vander Jagt, D.L. & Creighton, D.J. (1988) Diffusion-dependent rates for the hydrolysis reactions catalyzed by glyoxalase II from rat erythrocytes. Biochemistry 27, 8818- -8822.
  • 9. Caldwell S.R., Newcomb, J.R., Schlecht, K.A. & Raushel, F.M. (1991) Limits of diffusion in the hydrolysis of substrates by the phosphodies­terase from Pseudomonas diminuta. Biochemistry 30,7438-7444.
  • 10. Kurz, L.C., Weitkamp, E. & Frieden, C. (1987) Adenosine deaminase: Viscosity studies and the mechanism of binding of substrate and of ground- and transition-state analogue inhi­bitors. Biochemistry 26,3027-3032.
  • 11. McCammon, J.A. (1992) Superperfect enzymes. Curr, Biol 2,585-586.
  • 12. Getzoff, E.D., Cabelli, D.E., Fisher, C.L., Parge, H.E., Viezzoli, M.S., Banci, L. & Hallewell, R.A. (1992) Faster superoxide dismutase mutants designed by enhancing electrostatic guidance. Nature (London) 358,347-351.
  • 13. Allinson, S.A., Bacquet, R.J. & McCammon, J.A. (1988) Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models. Biopolymers 27, 251-269.
  • 14. Sharp, K., Fine, R. & Honig, B.H. (1987) Computer simulations of the diffusion of a substrate to an active site of an enzyme. Science 236,1460-1463.
  • 15. Sines, J.J., Allison, S.A. & McCammon, J.A. (1990) Point charge distributions and electro­static steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases. Biochemistry 29, 9403- -9412.
  • 16. Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R. & McCammon, J.A. (1995) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comp. Phys. Commun. (in press).
  • 17. Northrup, S.H., Allison, S.A. & McCammon, J.A. (1984) Brownian dynamics simulation of diffusion influenced bimolecular reactions. /. Chem. Phys. 97,5682-5686.
  • 18. Luty, B.A., McCammon, J.A. & Zhou, H.-X. (1992) Diffusive reaction rates from Brownian dynamics simulations: Replacing the outer cutoff surface by an analytical treatment. /. Chem. Phys. 97,5682-5686.
  • 19. Smoluchowski, M.V. (1916) Drei Vortraege ueber Diffusion, Brownische Molekularbe- vegung und Koagulation von Kolloidteilchen. Phys. Z. 17,557-571.
  • 20. Smoluchowski, M.V. (1917) Versuch einer mathematischen Theorie der Koagulation- skinetik kolloider Loesungen. Z, Phys. Chem. 92, 129-168.
  • 21. Ermak, D.L. & McCammon, J.A. (1978) Brow­nian dynamics with hydrodynamic inter­actions. /. Chem. Phys. 69,1352-1360.
  • 22. Davis, M.E., Madura, J.D., Luty, B.A. & McCa­mmon, J.A. (1990) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comp. Phys. Commun. 62,187-197.
  • 23. Davis, M.E. & McCammon, J.A. (1989) Solving the finite difference linearized Poisson-Boltz- mann equation: A comparison of relaxation and conjugate gradient method. /. Comput. Chem. 10, 386-391.
  • 24. Brune, D. & Kim, S. (1994) Hydrodynamic steering effects in protein association. Proc. Natl. Acad. Sci. U.S.A. 91,2930-2934.
  • 25. Antosiewicz, J. & McCammon, J.A. (1995) Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association. Biophys./. 69,57-65.
  • 26. Garcia de al Torre, J. & Bloomfield, V. (1981) Hydrodynamic properties of complex, rigid, biological macromolecules: Theory and appli­cations. Quart. Rev. Biophys. 14,81-139.
  • 27. Levitt, M. (1976) A simplified representation of protein conformations for rapid simulation of protein folding./. Mol. Biol. 104,59-107.
  • 28. McCammon, J.A., Northrup, S.H., Karplus, M. & Levy, R.M. (1980) Helix-coil transitions in a simple polypeptide model. Biopolymers 19, 2033-2045.
  • 29. Wade,R.C., Davis, M.E., Luty, B.A., Madura,J.D. & McCammon, J.A. (1993) Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys.}. 64,9-15.
  • 30. Madura, J.D. & McCammon, J.A. (1989) Brow­nian dynamics simulation of diffusional en­counters between triose phosphate isomerase and d-glyceraldehyde phosphate. /. Phys. Chem. 93,7285-7287.
  • 31. Tan, R.C., Truong, T.N., McCammon, J.A. & Su- ssman, J.L. (1993) Acetylcholinesterase: Electro­static steering increases the rate of ligand bin­ding. Biochemistry 32,401-403.
  • 32. Antosiewicz, J., McCammon, J.A., Wlodek, S.T. & Gilson, M.K. (1995) Simulation of charge--mutant acetylcholinesterases. Biochemistry 34, 4211^219.
  • 33. Luty, B.A., Wade, R.C., Madura, J.D., Davis, M.E., Briggs, J.M. & McCammon, J.A. (1993) Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: Electrostatic steering of glyceraldehyde phosphate. /. Phys. Chem. 97,233-237.
  • 34. Antosiewicz, J., Gilson, M.K., Lee, I.H. & McCa­mmon, J.A. (1995) Acetylcholinesterase: Diffu­sional encounter rate constants for dumb- bell models of ligands. Biophys. J. 68,62-68.
  • 35. Luty, B.A. & McCammon, J.A. (1993) Simula­tions of bimolecular reactions: Synthesis of the encounter and reaction steps. Molecular Simu­lation 10,61-65.
  • 36. Luty, B.A., El Amrani, S. & McCammon, J.A. (1993) Simulation of the bimolecular reaction between superoxide and superoxide dismutase: Synthesis of the encounter and reaction steps. /. Am. Chem. Soc. 115,11874-11877.
  • 37. Wade, R.C., Luty B.A., Demchuk, E., Madura, J.D., Davis, M.E., Briggs, J. & McCammon, J.A. (1994) Simulation of enzyme-substrate encoun­ter with gated active sites. Nature struct. Biol. 1, 65-69.
  • 38. Northrup, S.H., Boles, J.O. & Reynolds, J.C.L. (1988) Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science 241,67-70.
  • 39. Kozack, R.E. & Subramaniam, S. (1993) Brow­nian dynamics simulations of molecular reco­gnition in an antibody-antigen system. Protein Science 2, 915-926.

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

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