Molecular mechanic study of nerve agent O-ethyl S-[2- (diisopropylamino)ethyl]methylphosphonothioate (VX) bound to the active site of Torpedo californica acetylcholinesterase

Proteins: Structure, Function and Genetics

Volumn 28, Issue 4, 1997, Pages 543-555

  Albaret, Christine ^a   Lacoutière, Stéphane ^a   Ashman, William P ^b   Froment, Daniel ^a   Fortier, Pierre Louis ^a  

^a CENTRE D ETUDES DU BOUCHET   (France)

^b US Army Edgewood Res Devmt E   (United States)

Author keywords

Ab initio calculations; Enantiomeric inhibition; Serine esterase; Stochastic dynamics

Indexed keywords

ACETYLCHOLINESTERASE; METHYLPHOSPHONOTHIOIC ACID S (2 DIISOPROPYLAMINOETHYL) O ETHYL ESTER;

AMINO ACID SEQUENCE; ARTICLE; DRUG PROTEIN BINDING; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; TORPEDO CALIFORNICA;

ACETYLCHOLINESTERASE; ANIMALS; BINDING SITES; CHEMICAL WARFARE AGENTS; CHOLINESTERASE INHIBITORS; MOLECULAR STRUCTURE; ORGANOTHIOPHOSPHORUS COMPOUNDS; SERINE; TORPEDO;

TORPEDO CALIFORNICA;

EID: 0030795240     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199708)28:4<543::AID-PROT8>3.0.CO;2-A     Document Type: Article

References (48)

1. Rosenberry, T.L. Acetylcholineserase. Adv. Enzymol. 43:103-218, 1975.
2. Taylor, P. "Pharmacological Basis of Therapeutics." New York: Macmillan, 1985:110-129.
3. Sussman, J.L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L., Silman, I. Atomic structure of acetylcholinesterase from Torpedo californica: A prototypic acetylcholine-binding protein. Science 253:872-879, 1991.
4. Barak, D., Kronman, C., Ordentlich, A., Ariel, N., Bromberg, A., Marcus, D., Lazar, A., Velan, B., Shafferman, A. Acetylcholinesterase peripheral anionic site degeneracy conferred by amino acid arrays sharing a common core. J. Biol. Chem. 264:6296-6305, 1994.
5. Barak, D., Ordentlich, A., Bromberg, A., Kronman, C., Marcus, D., Lazar, A., Ariel, N., Velan, B., Shafferman, A. Allosteric modulation of acetylcholinesterase activity by peripheral ligands involves a conformational transition of the anionic subsite. Biochemistry 34:15444-15452, 1995.
6. Harel, M., Schalk, I., Ehret-Sabatier, L., Bouet, F., Goeldner, M., Hirth, C., Axelsen, P.H., Silman, I., Sussman, J.L. Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase. Proc. Natl. Acad. Sci. U.S.A. 90:9031-9035, 1993.
7. de Jong, L.P.A., Benschop, H.P. Biochemical and toxicological implications of chirality in anticholinesterase organophosphates. In "Stereoselectivity of Pesticides: Biological and Chemical Problems." Ariëns, E.J., van Rensen, J.J.S., Welling, W. (eds.). Amsterdam: Elsevier, 1988:109-147.
8. Nair, H.K., Lee, K., Quinn, D.M. m-(N,N,N-Trimethylammonio)trifluoroacetophenone: A femtomolar inhibitor of acetylcholinesterase. J. Am. Chem. Soc. 115:9939-9941, 1993.
9. de Jong, L.P.A., van Dijk, C. Inhibition of acetylcholinesterase by the enantiomers of isopropyl S-2-trimethylammonio-ethyl methylphosphonothiate iodide: Affinity and phosphorylation constants. Biochem. Biophys. Acta 268:680-689, 1972.
10. Wustner, D.A., Fukoto, T.R. Affinity and phosphonylation constants for the inhibition of cholinesterases by the optical isomers of O-2-butyl S-2-(dimethylammonium)ethyl ethylphosphonothioate hydrogen oxalate. Pestic. Biochem. Physiol. 4:365-376, 1974.
11. Berman, H.A., Leonard, K. Chiral reactions of acetylcholinesterase probed with enantiomeric methylphosphonothioates. J. Biol. Chem. 264:3942-3950, 1989.
12. Benschop, H.P., de Jong, L.P.A. Nerve agent stereoisomers: Analysis, isolation, and toxicology. Acct. Chem. Res. 21:368-374, 1988.
13. Berman, H.A., Decker, M.M. Chiral nature of covalent methylphosphonyl conjugates of acetylcholinesterase. J. Biol. Chem. 264:3951-3956, 1989.
14. Hosea, N.A., Berman, H.A., Taylor, P. Specificity and orientation of trigonal carboxyl esters and tetrahedral alkylphosphonyl esters in cholinesterase. Biochemistry 34:11528-11536, 1995.
15. Ordentlich, A., Barak, D., Kronman, C., Flashner, Y., Leitner, M., Segall, Y., Ariel, N., Cohen, S., Velan, B., Shafferman, A. Dissection of the human acetylcholinesterase active center determinants of substrate specificity. J. Biol. Chem. 268:17083-17095, 1993.
16. Harel, M., Kleywegt, G.J., Ravelli, R.B.G., Silman, I., Sussman, J.L. Crystal structure of an acetylcholinesterase-fasciculin complex: Interaction of a three-fingered toxin from snake venom with its target. Structure 3:1355-1366, 1995.
17. Harel, M., Quinn, D.M., Nair, H.K., Silman, I., Sussman, J.L. The X-ray structure of a transition state analog complex reveals the molecular origins of the catalytic power and substrate specificity of acetylcholinesterase. J. Am. Chem. Soc. 118:2340-2346, 1996.
18. Berstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rogers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
19. Gilson, M.K., Straastsma, T.P., McCammon, J.A., Ripoll, D.R., Faerman, C.H., Axelsen, P.H., Silman, I., Sussman, J.L. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science 263:1276-1278, 1994.
20. Daggett, V., Schröder, S., Koolman, P. Catalytic pathway of serine proteases: Classical and quantum mechanical calculations. J. Am. Chem. Soc. 113:8926-8935, 1991.
21. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217, 1983.
22. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
23. Brooks III, C.L., Karplus, M. Solvent effects on protein motion and protein effects on solvent motion. J. Mol. Biol. 208:159-181, 1989.
24. Ollis, D.L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S.M., Harel, M., Remington, S.J., Silman, I., Schrag, J., Sussman, J.L., Verschueren, K.H.G., Goldman, A. The α/β hydrolase fold. Protein Eng. 5:197-211, 1992.
25. Brooks III, C.L., Brünger, A., Karplus, M. Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach. Biopolymers 24:843-865, 1985.
26. Brünger, A.T., Brooks III, C.L., Karplus, M. Active site dynamics of ribonuclease. Proc. Natl. Acad. Sci. U.S.A. 82:8458-8462, 1985.
27. Nakagawa, S., Yu, H.-A., Karplus, M., Umeyama, H. Active site dynamics of acyl-chymotrypsin. Proteins 16:172-194, 1993.
28. Brooks III, C.L., Karplus, M., Pettitt, B.M. "Proteins. A Theoritical Perspective of Dynamics, Structure, and Thermodynamics." New York: Wiley-Interscience, 1988.
29. Brünger, A.T., Brooks III, C.L., Karplus, M. Stochastic boundary conditions for molecular dynamic simulations of ST2 water. Chem. Phys. Lett. 105:495-500, 1984.
30. Ryckaert, J.-P., Ciccotti, G., Berendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. comput. Phys. 23:327-341, 1977.
31. Mulholland, A.J., Grant, G.H., Richards, W.G. Computer modelling of enzyme catalysed reaction mechanisms. Protein Eng. 6:133-147, 1993.
32. Benscura, A., Enyedy, I.Y., Kovach, I.M. Probing the active site of acetylcholinesterase by molecular dynamics of its phosphonate ester adducts. J. Am. Chem. Soc. 118:8531-8541, 1996.
33. Ordentlich, A., Barak, D., Kronman, C., Ariel, N., Segall, Y., Velan, B., Shaffermann, A. Contribution of aromatic moities of tyrosine 133 and of the anionic subsite tryptophan 86 to catalytic efficiency and allosteric modulation of acetylcholinesterase. J. Biol. Chem. 270:2082-2091, 1995.
34. Sussman, J.L., Harel, M., Silman, I. Three-dimensional structure of acetylcholinesterase and of its complexes with anticholinesterase drugs. Chem. Biol. Interact. 87:187-197, 1993.
35. Ordentlich, A., Barak, D., Kronman, C., Ariel, N., Segall, Y., Velan, B., Shafferman, A. The architecture of human acetylcholinesterase active center probed by interactions with selected organophosphate inhibitors. J. Biol. Chem. 271:11953-11962, 1996.
36. Quian, N., Kovach, I.M. Key active site residues in the inhibition of acetylcholinesterase by soman. FEBS Lett. 336:263-266, 1993.
37. Radic, Z., Pickering, N.A., Vellom, D.C., Camp, S., Taylor, P. Three distinct domains in the cholinesterase module confer selectivity for acetyl- and butyrylcholinesterase inhibitors. Biochemistry 32:12074-12084, 1993.
38. Bencsura, A., Enyedy, I., Kovach, I.M. Origins and diversity of the aging reaction in phosphonate adducts of serine hydrolase enzymes: What characteristics of the active site do they probe? Biochemistry 34:8989-8999, 1995.
39. Höltje, H.-D., Kier, L.B. Nature of anionic or α-site of cholinesterase. J. Pharm. Sci. 64:418-420, 1975.
40. Dougherty, D.A., Stauffer, D.A. Acetylcholine binding by a synthetic receptor: implications for biological recognition. Science 250:1558-1560, 1990.
41. Berry, R.S. Correlations of rates of intramolecular tunneling processes, with application of some group V compounds. J. Chem. Phys. 32:933-938, 1960.
42. Ugi, I., Marquarding, D., Klusacek, H., Gillespie, P., Ramirez, F. Berry pseudorotation and turnstile rotation. Acct. Chem. Res. 4:288-296, 1971.
43. Gillespie, P., Ramirez, F., Ugi, I., Marquarding, D. Displacement reactions of phosphorus (V) compounds and their pentacoordinate intermediates. Angew. Chem. Int. Ed. Engl. 12:91-119, 1973.
44. Hosea, N.A., Radic, Z., Tsigelny, I., Berman, H.A., Quinn, D.M., Taylor, P. Aspartate 74 as a primary determinant in acetylcholinesterase governing specificity to cationic organophosphoriales. Biochemistry 35:10995-11004, 1996.
45. Fersht, A. "Enzyme Structure and Mechanism." New York: W.H. Freeman, 1985:221-247.
46. Dougherty, D.A. Cation-π interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp. Science 271:163-168, 1996.
47. Nair, H.K., Seravalli, J., Arbuckle, T., Quinn, D.M. Molecular recognition in acetylcholinesterase catalysis: Free-energy correlations for substrate turnover and inhibition by trifluoro ketone transition-state analogs. Biochemistry 33:8566-8576, 1994.
48. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr. 24:946-950, 1991.