Efficient perturbation analysis of elastic network models – Application to acetylcholinesterase of T. californica

Hamacher, Kay

doi:10.1016/j.jcp.2010.06.015

Cited by 2 publications

(1 citation statement)

References 38 publications

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“…Finally, Hamacher used the Gaussian Network Model to observe the breathing of the AChE active-site gorge as the substrate enters it. 96 3.2.2. Substrate Diffusion Rates.…”

Section: Industrial and Engineering Chemistry Researchmentioning

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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“…Finally, Hamacher used the Gaussian Network Model to observe the breathing of the AChE active-site gorge as the substrate enters it. 96 3.2.2. Substrate Diffusion Rates.…”

Section: Industrial and Engineering Chemistry Researchmentioning

confidence: 99%

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

Reilly

Rovira

2015

Ind. Eng. Chem. Res.

View full text Add to dashboard Cite

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Biological Implications of the Intrinsic Deformability of Human Acetylcholinesterase Induced by Diverse Compounds: A Computational Study

Alvarado,

González-Paz,

Paz

et al. 2024

Biology

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The enzyme acetylcholinesterase (AChE) plays a crucial role in the termination of nerve impulses by hydrolyzing the neurotransmitter acetylcholine (ACh). The inhibition of AChE has emerged as a promising therapeutic approach for the management of neurological disorders such as Lewy body dementia and Alzheimer’s disease. The potential of various compounds as AChE inhibitors was investigated. In this study, we evaluated the impact of natural compounds of interest on the intrinsic deformability of human AChE using computational biophysical analysis. Our approach incorporates classical dynamics, elastic networks (ENM and NMA), statistical potentials (CUPSAT and SWOTein), energy frustration (Frustratometer), and volumetric cavity analyses (MOLE and PockDrug). The results revealed that cyanidin induced significant changes in the flexibility and rigidity of AChE, especially in the distribution and volume of internal cavities, compared to model inhibitors such as TZ2PA6, and through a distinct biophysical-molecular mechanism from the other inhibitors considered. These findings suggest that cyanidin could offer potential mechanistic pathways for future research and applications in the development of new treatments for neurodegenerative diseases.

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Efficient perturbation analysis of elastic network models – Application to acetylcholinesterase of T. californica

Cited by 2 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

Biological Implications of the Intrinsic Deformability of Human Acetylcholinesterase Induced by Diverse Compounds: A Computational Study

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