Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies

Chemico-Biological Interactions

Volumn 187, Issue 1-3, 2010, Pages 59-63

  Lushchekina, Sofya V ^a,b   Nemukhin, Alexander V ^a,b   Morozov, Dmitry I ^b   Varfolomeev, Sergei D ^a,b  

^a EMANUEL INSTITUTE OF BIOCHEMICAL PHYSICS   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Acetylcholinesterase; Carboxylester hydrolysis; QM MM modeling; Structure property correlation

Indexed keywords

ACETYLCHOLINESTERASE; GLUTAMINE; GLYCINE; HISTIDINE; SERINE;

ARTICLE; CONTROLLED STUDY; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROLYSIS; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; MOLECULAR MECHANICS; PREDICTION; QUANTUM MECHANICS;

EID: 77955513368     PISSN: 00092797     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbi.2010.04.005     Document Type: Article

References (26)

1. Bui J.M., Henchman R.H., McCammon J.A. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys. J. 2003, 85:2267-2272.
2. Radchenko E., Makhaeva G., Malygin V., Sokolov V., Palyulin V., Zefirov N. Modeling of the relationships between the structure of O-phosphorylated oximes and their anticholinesterase activity and selectivity using molecular field topology analysis (MFTA). Dokl. Biochem. Biophys. 2008, 418:47-51.
3. Khan M.T. Molecular interactions of cholinesterases inhibitors using in silico methods: current status and future prospects. New Biotechnol. 2009, 25:331-346.
4. Fuxreiter M., Warshel A. Origin of the catalytic power of acetylcholinesterase: computer simulation studies. J. Am. Chem. Soc. 1998, 120:183-194.
5. Vagedes P., Rabenstein B., Åqvist J., Marelius J., Knapp E.-W. The deacylation step of acetylcholinesterase: computer simulation studies. J. Am. Chem. Soc. 2000, 122:12254-12262.
6. Sant'Anna C.M.R., dos Santos Viana A., do Nascimento N.M.J. A semiempirical study of acetylcholine hydrolysis catalyzed by Drosophila melanogaster acetylcholinesterase. Bioorg. Chem. 2006, 34:77-89.
7. Manojkumar T.K., Cui C., Kim K.S. Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine. J. Comput. Chem. 2005, 26:606-611.
8. Zhang Y., Kua J., McCammon J.A. Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J. Am. Chem. Soc. 2002, 124:10572-10577.
9. Warshel A., Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1976, 103:227-249.
10. Nemukhin A.V., Lushchekina S.V., Bochenkova A.V., Golubeva A.A., Varfolomeev S.D. Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. J. Mol. Model. 2008, 14:409-416.
11. Nemukhin A.V., Gariev I.A., Rogov A.V., Varfolomeev S.D. Serine hydrolase catalytic sites: geometry invariants and modeling catalytic activity. Mendeleev Commun. 2006, 16:290-292.
12. Järv J., Kesvatera T., Aaviksaar A. Structure-activity relationships in acetylcholinesterase reactions. Hydrolysis of non-ionic acetic esters. Eur. J. Biochem. 1976, 67:315-322.
13. Fujita T., Iwasa J., Hansch C. A new substituent constant, π, derived from partition coefficients. J. Am. Chem. Soc. 1964, 86:5175-5180.
14. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28:235-242.
15. Kryger G., Harel M., Giles K., Toker L., Velan B., Lazar A., Kronman C., Barak D., Ariel N., Shafferman A., Silman I., Sussman J.L. Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II. Acta Crystallogr. D: Biol. Crystallogr. 2000, 56:1385-1394.
16. Word J.M., Lovell S.C., LaBean T.H., Taylor H.C., Zalis M.E., Presley B.K., Richardson J.S., Richardson D.C. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 1999, 285:1711-1733.
17. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Am. Chem. Soc. 1998, 19:1639-1662.
18. Ponder J.W. TINKER: Software Tools for Molecular Design, Version 3.7 1999, Washington University, St. Louis.
19. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. Development and testing of a general Amber force field. J. Comput. Chem. 2004, 25:1157-1174.
20. Nemukhin A.V., Grigorenko B.L., Granovsky A.A. Molecular modeling by using the PC GAMESS program: from diatomic molecules to enzymes. Moscow Univ. Chem. Bull. 2004, 45:75-102.
21. Bakowies D., Thiel W. Hybrid models for combined quantum mechanical and molecular mechanical approaches. J. Phys. Chem. 1996, 100:10580-10594.
22. A.A. Granovsky, http://classic.chem.msu.su/gran/gamess/index.html.
23. Shafferman A., Velan B., Ordentlich A., Kronman C., Grosfeld H., Leitner M., Flashner Y., Cohen S., Barak D., Ariel N. Substrate inhibition of acetylcholinesterase: residues affecting signal transduction from the surface to the catalytic center. EMBO J. 1992, 11:3561-3568.
24. Cléry-Barraud C., Ordentlich A., Grosfeld H., Shafferman A., Masson P. Pressure and heat inactivation of recombinant human acetylcholinesterase. Eur. J. Biochem. 2002, 269:4297-4307.
25. Kovarik Z., Radić Z., Berman H., Simeon-Rudolf V., Reiner E., Taylor P. Acetylcholinesterase active centre and gorge conformations analysed by combinatorial mutations and enantiomeric phosphonates. Biochem. J. 2003, 373:33-40.
26. Till M.S., Ullmann G.M. McVol-a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J. Mol. Model. 2010, 16:419-429.