Analysis of a 10-ns Molecular Dynamics Simulation of Mouse Acetylcholinesterase

Tai, Kaihsu; Shen, Tongye; Börjesson, Ulf; Philippopoulos, Marios; McCammon, J. Andrew

doi:10.1016/s0006-3495(01)75736-0

Cited by 164 publications

(210 citation statements)

References 24 publications

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“…Tai et al 32 report an opening and closing movement of the gorge in studies of MD simulations with mouse AChE. Bui et al 33 have shown that this local conformational fluctuations of the gorge residues and large scale collective motions of the protein correlate highly with the crossing of tetramethylammonium by the AChE gorge. Those fluctuations could also be involved in the retention of DZP inside the gorge.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics of the interaction of pralidoxime and deazapralidoxime with acetylcholinesterase inhibited by the neurotoxic agent tabun

Gonçalves¹,

França²,

Wilter³

et al. 2006

J. Braz. Chem. Soc.

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Reativadores eficientes de Aceticolinesterase são fundamentais para o desenvolvimento de antídotos contra o envenenamento por pesticidas neurotóxicos e agentes de guerra química. Todavia, o mecanismo da reação de reativação e as características estruturais dos reativadores conhecidos são pouco compreendidos. Com o objetivo de estudar o comportamento dinâmico e o efeito da carga líquida do antídoto na reativação desta enzima, foi conduzido um estudo por dinâmica molecular da acetilcolinesterase humana inibida por tabun em complexo com o antídoto pralidoxima e com seu análogo deazapralidoxima nas formas neutra e aniônica. Os resultados mostraram que a carga positiva da pralidoxima é importrante para sua admissão e permanência dentro do sítio ativo. Além disso, os análogos, diferente da pralidoxima, quando colocados dentro do sítio ativo, se distanciam do resíduo serina fosforilado da enzima e são repelidos pelo potencial eletrostático na entrada do canal que conduz ao sítio ativo.Efficient acetylcholinesterase reactivators are fundamental for the development of antidotes against poisoning by neurotoxic pesticides and chemical warfare agents. However, the mechanism of the reactivation reaction and the structural characteristics of the known reactivators are poorly understood. In order to study the dynamic behavior and the effect of the antidote net charge in the reactivation of this enzyme, we carried out a molecular dynamics study of human acetylcholinesterase inhibited by tabun in complex with the antidote pralidoxime and with its deaza analogues in the neutral and anionic forms. Results show that the positive charge of pralidoxime is important for its admission and permanence inside the active site. Also, the analogues, unlike pralidoxime, when forced inside the active site, move away from the phosphorilated serine residue of the enzyme and are repelled by the electrostatic potential at the entrance of the channel that conducts to the active site. Keywords: acetylcholinesterase, molecular dynamics, tabun, antidotes, neurotoxic agents IntroductionThe intensive use of neurotoxic organophosphorous compounds as pesticides in agriculture, as well as their potential use as mass destruction agents in chemical warfare, has attracted attention to the development of efficient antidotes for this type of poisoning.1,2 However, the knowledge on the appropriate treatment for patients exposed to this kind of compounds is limited to few groups of physicians around the world. 1,2One particularly important family of lethal tactical warfare chemicals is the group known as the nerve agents, which are closely related in chemical structure and biological action to many commonly used organophosphorous insecticides, but which are much more lethal. 1,2The nerve agents are esters of phosphoric acid and are potent inhibitors of acetylcholinesterase, a fundamental enzyme for ending nervous impulses. These compounds inhibit all acetylcholinesterases, including the human enzyme (HuAChE), by phosphorylating a serine hydroxyl group (Ser203 in ...

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Section: Discussionmentioning

confidence: 99%

Molecular dynamics of the interaction of pralidoxime and deazapralidoxime with acetylcholinesterase inhibited by the neurotoxic agent tabun

Gonçalves¹,

França²,

Wilter³

et al. 2006

J. Braz. Chem. Soc.

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“…These findings raise an interesting possibility that the unliganded enzyme exists in a rapidly converting conformational equilibrium between open and closed states, and both ligand binding and conditions of crystallization favor formation of a closed gorge state. In fact, analysis of the molecular dynamics of a solvated mouse AChE shows fluctuations yielding an average widening of the gorge over a 10-ns interval (46). Such opening and closing motions of the gorge may also be integral to the catalytic cycle of transacylation and deacylation during ester hydrolysis.…”

Section: Influence Of Residue Modification On Ligand Binding-mentioning

confidence: 99%

Reversibly Bound and Covalently Attached Ligands Induce Conformational Changes in the Omega Loop, Cys69–Cys96, of Mouse Acetylcholinesterase

Shi

Boyd²,

Radić

et al. 2001

Journal of Biological Chemistry

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We have used a combination of cysteine substitution mutagenesis and site-specific labeling to characterize the structural dynamics of mouse acetylcholinesterase (mAChE). Six cysteine-substituted sites of mAChE (Leu 76 , Glu 81 , Glu 84 , Tyr 124 , Ala 262 , and His 287 ) were labeled with the environmentally sensitive fluorophore, acrylodan, and the kinetics of substrate hydrolysis and inhibitor association were examined along with spectroscopic characteristics of the acrylodan-conjugated, cysteine-substituted enzymes. Residue 262, being well removed from the active center, appears unaffected by inhibitor binding. Following the binding of ligand, hypsochromic shifts in emission of acrylodan at residues 124 and 287, located near the perimeter of the gorge, reflect the exclusion of solvent and a hydrophobic environment created by the associated ligand. By contrast, the bathochromic shifts upon inhibitor binding seen for acrylodan conjugated to three omega loop (⍀ loop) residues 76, 81, and 84 reveal that the acrylodan side chains at these positions are displaced from a hydrophobic environment and become exposed to solvent. The magnitude of fluorescence emission shift is largest at position 84 and smallest at position 76, indicating that a concerted movement of residues on the ⍀ loop accompanies gorge closure upon ligand binding. Acrylodan modification of substituted cysteine at position 84 reduces ligand binding and steady-state kinetic parameters between 1 and 2 orders of magnitude, but a similar substitution at position 81 only minimally alters the kinetics. Thus, combined kinetic and spectroscopic analyses provide strong evidence that conformational changes of the ⍀ loop accompany ligand binding.Acetylcholinesterase (AChE), 1 a serine hydrolase in the ␣/␤-fold hydrolase protein superfamily (1), terminates nerve signals by catalyzing hydrolysis of the neurotransmitter acetylcholine at a diffusion limited rate (2, 3). The crystallographic structure of mouse AChE reveals a catalytic triad (Ser 203 , Glu 334 , and His 447 ) located at the bottom of a narrow active site gorge 20 Å in depth (4 -6). Because the cross-section of the physiological substrate acetylcholine is larger than the narrowest part of the gorge, the remarkably high turnover rate of AChE raises questions regarding substrate access to the catalytic site.Molecular dynamic simulations suggest that rapid fluctuations of gorge width combined with diffusion facilitated by electrostatic forces could enhance substrate accessibility (7-10). In addition, the high affinity and slowly dissociating complex of fasciculin and AChE retains slight residual catalytic activity (11, 12), despite the occlusion of the active site gorge by fasciculin as shown in the crystal structures (5, 13, 14). Rapid fluctuations in residues lining the gorge walls may leave transient gaps at the fasciculin-AChE interface and may account for residual activity.The large omega loop (⍀ loop), Cys 69 -Cys 96 , flanking the active site gorge in mouse AChE corresponds to the activation loop ...

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“…the Catalytic Sites Atlas Crystallographic structures show that these enzymes do not have related folds, but have similar active sites, a catalytic triad of amino acid residues (Figures 1 and 2). In mouse (Mus musculus) AChE, the active site (Ser203, His447, Glu334) has the favorable arrangement conducive to proton transfer where the imidazole ring of His447 is placed between the carboxyl group of Glu334 and the hydroxyl group of Ser203 (16,21,22). In Escherichia coli OMPLA, the active site consists of the analogous Ser144, His142, and Asn156.…”

Section: Introductionmentioning

confidence: 99%

Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database

Tai

Baaden

Murdock

et al. 2007

Journal of Molecular Graphics and Modelling

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Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid (http://www.biosimgrid.org) database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely acetylcholinesterase, outer-membrane phospholipase A, outer-membrane protease T, and PagP (an outer membrane enzyme which transfers a palmitate chain from a phospholipid to lipid A). A set of 17 simulations were analyzed corresponding to a total of ~0.1 μs simulation time. A simple metric for active site integrity was used to demonstrate the existence of clusters of dynamic conformational behaviour of the active sites. Small (i.e. within a cluster) fluctuations appear to be related to the function of an enzymatically active site. Larger fluctuations (i.e. between clusters) correlate with transitions between catalytically active and inactive states. Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods.

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Analysis of a 10-ns Molecular Dynamics Simulation of Mouse Acetylcholinesterase

Cited by 164 publications

References 24 publications

Molecular dynamics of the interaction of pralidoxime and deazapralidoxime with acetylcholinesterase inhibited by the neurotoxic agent tabun

Molecular dynamics of the interaction of pralidoxime and deazapralidoxime with acetylcholinesterase inhibited by the neurotoxic agent tabun

Reversibly Bound and Covalently Attached Ligands Induce Conformational Changes in the Omega Loop, Cys69–Cys96, of Mouse Acetylcholinesterase

Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database

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