Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

Enyedy, Istvan; Kovach, Ildiko M.; Bencsura, Ákos

doi:10.1042/bj3530645

Cited by 6 publications

(2 citation statements)

References 38 publications

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“…74 Enyedy et al studied continued reaction under organophosphorus inhibition with CHARMM. 75 In a series of articles from the same group, Henchman et al used MD to model water in and around AChE, 76,77 Kua et al employed a combined MD and multiple docking approach to study enzyme binding specificity with native and mutated AChE, 78,79 and Bui et al used MD to show ligand barrier crossing within the active-site gorge. 80 Zhang et al determined the structures and charges of the TS and the reactant with QM/ MM calculations.…”

Section: Carboxylic Ester Bond Hydrolysismentioning

confidence: 99%

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review

Reilly

Rovira

2015

Ind. Eng. Chem. Res.

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This article is a review of computational work over the last ∼15 years to elucidate the catalytic mechanisms of three major enzyme classes: glycoside hydrolases, carboxylic ester hydrolases, and thioesterases. The mechanisms of glycoside hydrolases that both invert and retain the configuration of the anomeric carbon atom of the labile glycosidic bond are covered, as is the twisting of the glycosidic bond exerted by members of different glycoside hydrolase families. The hydrolytic mechanisms and substrate binding of five different carboxylic ester hydrolase classesacetylcholinesterases, butyrylcholinesterases, cocaine esterases, carboxylesterases, and triacylglycerol lipasesare addressed. Finally, the mechanism of members of a thioesterase family with HotDog tertiary structures is covered.

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Section: Carboxylic Ester Bond Hydrolysismentioning

confidence: 99%

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review

Reilly

Rovira

2015

Ind. Eng. Chem. Res.

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“…Moreover, the residual catalytic activity seen for a complex of AChE with the gorge-capping mamba venom toxin, fasciculin − , can maybe be explained by molecular breathing. Later molecular dynamics studies have provided further evidence of loop movements creating doors for product exit − . In contrast, much evidence has suggested that conformational changes are not involved during substrate hydrolysis.…”

mentioning

confidence: 99%

Evidence for Subdomain Flexibility in Drosophila melanogaster Acetylcholinesterase

et al. 2008

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The catalytic domain of the acetylcholinesterases is composed of a single polypeptide chain, the folding of which determines two subdomains. We have linked these two subdomains by mutating two residues, I327 and D375, to cysteines, to form a disulfide bridge. As a consequence, the hydrodynamic radius of the protein was reduced, suggesting that there is some flexibility in the subdomain connection. In addition to the smaller size, the mutated protein is more stable than the wild-type protein. Therefore, the flexibility between the two domains is a weak point in terms of protein stability. As expected from the location of the disulfide bond at the rim of the active site, the kinetic studies show that it affects interactions with peripheral ligands and the entrance of some of the bulkier substrates, like o-nitrophenyl acetate. In addition, the mutations affect the catalytic step for o-nitrophenyl acetate and phosphorylation by organophosphates, suggesting that this movement between the two subdomains is connected with the cooperativity between the peripheral and catalytic sites.

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Inhibition studies on Rhodospirillum rubrum H+-pyrophosphatase expressed in Escherichia coli

Schultz

Baltscheffsky

2004

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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The membrane-bound proton-pumping inorganic pyrophosphatase from Rhodospirillum rubrum was heterologously expressed in Escherichia coli C43(DE3) cells and was inhibited by 4-bromophenacyl bromide (BPB), N,N'-dicyclohexylcarbodiimid (DCCD), diethyl pyrocarbonate (DEPC) and fluorescein 5'-isothiocyanate (FITC). In each case, the enzyme activity was rather well protected against inhibitory action by the substrate Mg(2)PPi. Site-directed mutagenesis was employed in attempts to identify target residues for these inhibitors. D217 and K469 appear to be the prime targets for DCCD and FITC, respectively, and may thus be involved in substrate binding. No major effect on enzyme activities was seen when any one of the four histidine residues present in the enzyme were substituted. Nevertheless, a mutant with all of the four charged histidine residues replaced retained only less than 10% of the hydrolysis and proton-pumping activities. Substitution of D217 with A or H yielded an enzyme with at least an order of magnitude lower hydrolysis activity. In contrast with the wild-type, these variants showed higher hydrolysis rates at lower concentrations of Mg(2+), possibly reflecting a change in substrate preference from Mg(2)PPi to MgPPi. BPB is a H(+)-pyrophosphatase inhibitor that apparently has not been used previously as an inhibitor of these enzymes.

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Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

Cited by 6 publications

References 38 publications

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review

Evidence for Subdomain Flexibility in Drosophila melanogaster Acetylcholinesterase

Inhibition studies on Rhodospirillum rubrum H+-pyrophosphatase expressed in Escherichia coli

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