Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
- PMID: 20550161
- PMCID: PMC2919153
- DOI: 10.1021/jp104258d
Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
Abstract
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.
Figures
Similar articles
-
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.J Am Chem Soc. 2002 Sep 4;124(35):10572-7. doi: 10.1021/ja020243m. J Am Chem Soc. 2002. PMID: 12197759
-
Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.J Phys Chem B. 2009 Dec 31;113(52):16705-10. doi: 10.1021/jp9080614. J Phys Chem B. 2009. PMID: 20028143 Free PMC article.
-
Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.J Phys Chem B. 2009 Sep 24;113(38):12750-8. doi: 10.1021/jp903173c. J Phys Chem B. 2009. PMID: 19507815 Free PMC article.
-
Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms.Chemistry. 2024 Oct 28;30(60):e202402468. doi: 10.1002/chem.202402468. Epub 2024 Oct 7. Chemistry. 2024. PMID: 39109881 Review.
-
Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.J Mol Model. 2024 May 23;30(6):180. doi: 10.1007/s00894-024-05963-8. J Mol Model. 2024. PMID: 38780881 Review.
Cited by
-
Why does the G117H mutation considerably improve the activity of human butyrylcholinesterase against sarin? Insights from quantum mechanical/molecular mechanical free energy calculations.Biochemistry. 2012 Nov 6;51(44):8980-92. doi: 10.1021/bi3009246. Epub 2012 Oct 23. Biochemistry. 2012. PMID: 23092211 Free PMC article.
-
Fundamental reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of heroin.Biochemistry. 2013 Sep 17;52(37):6467-79. doi: 10.1021/bi400709v. Epub 2013 Aug 30. Biochemistry. 2013. PMID: 23992153 Free PMC article.
-
Reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of acetylcholine.J Phys Chem B. 2011 Feb 10;115(5):1315-22. doi: 10.1021/jp110709a. Epub 2010 Dec 22. J Phys Chem B. 2011. PMID: 21175195 Free PMC article.
-
Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.J Phys Chem B. 2011 Nov 24;115(46):13713-22. doi: 10.1021/jp207532s. Epub 2011 Nov 3. J Phys Chem B. 2011. PMID: 21999515 Free PMC article.
-
Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate.Chem Commun (Camb). 2011 Feb 7;47(5):1577-9. doi: 10.1039/c0cc04112b. Epub 2010 Nov 29. Chem Commun (Camb). 2011. PMID: 21116528 Free PMC article.
References
-
- Frey PA, Hegeman AD. Enzymatic Reaction Mechanisms. Oxford University Press; Oxford: 2007.
-
- Kraut DA, Carroll KS, Herschlag D. Annu Rev Biochem. 2003;72:517–571. - PubMed
-
- Potashman MH, Duggan ME. J Med Chem. 2009;52:1231–1246. - PubMed
-
- Robertson JG. Biochemistry. 2005;44:5561–5571. - PubMed
-
- Schramm VL. Accounts Chem Res. 2003;36:588–596. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources