The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 779-785

  Petraglio, Gabriele ^a   Bartolini, Manuela ^b   Branduardi, Davide ^a   Andrisano, Vincenza ^b   Recanatini, Maurizio ^b   Gervasio, Francesco Luigi ^a   Cavalli, Andrea ^b   Parrinello, Michele ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Alkali cations; Alzheimer's disease, cation interactions; Catalytic efficiency; Enzymatic catalysis; Inhibition assays; Ligand penetration; Metadynamics; Molecular dynamics

Indexed keywords

ACETYLCHOLINE; ACETYLCHOLINESTERASE; ALKALI; CATION; LITHIUM; POTASSIUM; SODIUM; SOLVENT; TETRAMETHYLAMMONIUM;

ALZHEIMER DISEASE; ARTICLE; CATALYSIS; ENZYME INHIBITION; ENZYME SUBSTRATE; HUMAN; HYDROLYSIS; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SIMULATION;

ACETYLCHOLINESTERASE; BINDING SITES; CATIONS, MONOVALENT; COMPUTER SIMULATION; HUMANS; HYDROLYSIS; KINETICS; LIGANDS; LITHIUM; POTASSIUM; SODIUM;

EID: 38549176824     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21560     Document Type: Article

References (24)

1. Quinn DM. Acetylcholinesterase: enzyme structure, reaction dynamics, and virtual transition states. Chem Rev 1987;87:955-979.
2. Giacobini E. Cholinesterase inhibitors: from the Calabar bean to Alzheimer's disease. In: Giacobini E, editor. Cholinesterases and cholinesterase inhibitors. London: Martin Dunitz Ltd; 2000. pp 181-226.
3. Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P. Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J Biol Chem 1997;272:23265-23277.
4. Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers 1998;46:465-474.
5. Cavalli A, Bottegoni G, Raco C, De Vivo M, Recanatini M. A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase. J Med Chem 2004;47:3991-3999.
6. Branduardi D, Gervasio FL, Cavalli A, Recanatini M, Parrinello M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J Am Chem Soc 2005;127:9147-9155.
7. Savini L, Gaeta A, Fattorusso C, Catalanotti B, Campiani G, Chiasserini L, Pellerano C, Novellino E, McKissic D, Saxena A. Specific targeting of acetylcholinesterase and butyrylcholinesterase recognition sites. Rational design of novel, selective, and highly potent Cholinesterase inhibitors. J Med Chem 2003;46:1-4.
8. 2+) cations. Biochemistry 1984;23:2730-2734.
9. Kryger G, Hard M, Giles K, Toker L, Velan B, Lazar A, Kronman C, Barak D, Ariel N, Shafferman A, Silman I, Sussman JL. 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.
10. Bui JM, Henchman RH, McCammon JA. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys Js 2003;85:2267-2272.
11. Ellman GL, Courtney KD, Andres V, Featherstone RM. A new and rapid colorimetric determination of acetylcholinesterase activity. Biochem Pharmacol 1961;7:88-95.
12. Procacci P, Darden TA, Paci E, Marchi M. ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions. J Comput Chem 1997;18:1848-1862.
13. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
14. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-857.
15. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
16. Laio A, Parrinello M. Escaping free-energy minima. Proc Natl Acad Sci USA 2002;99:12562-12566.
17. Iannuzzi M, Laio A, Parrinello M. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys Rev Lett 2003;90:238302.
18. Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. Assessing the accuracy of metadynamics. J Phys Chem B 2005;109:6714-6721.
19. Gervasio FL, Laio A, Parrinello M. Flexible docking in solution using metadynamics. J Am Chem Soc 2005;127:2600-2607.
20. Dixon M, Webb EC. Enzymes, 2nd ed. London, UK: Longmans; 1964.
21. Bartolucci C, Perola E, Cellai L, Brufani M, Lamba D. "Back door" opening implied by the crystal structure of a carbamoylated acetylcholinesterase. Biochemistry 1999;38:5714-5719.
22. +-ion hydration. A molecular dynamics simulation study. J Phys Chem B 2003;107:3234-3242.
23. + by Monte Carlo simulations with refined ab initio based model potentials. Theor Chem Acc 2006;115:177-189.
24. Zhang Y, Kua J, McCammon JA. 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.