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Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and molecular docking calculations
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- Saenz Mendez, Patricia (author)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,Universidad de la Republica, URY; Göteborgs Universitet
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- Katz, A. (author)
- Göteborgs Universitet
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- Perez-Kempner, M. L. (author)
- Göteborgs Universitet
- show more...
- Vazquez, M. (author)
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- (creator_code:org_t)
- 2017-02-09
- 2017
- English.
- In: Proteins-Structure Function and Bioinformatics. - : Wiley. - 0887-3585 .- 1097-0134. ; 85:4, s. 720-730
- Journal article (peer-reviewed)
Abstract
Subject headings
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- A new homology model of human microsomal epoxide hydrolase was derived based on multiple templates. The model obtained was fully evaluated, including MD simulations and ensemble-based docking, showing that the quality of the structure is better than that of only previously known model. Particularly, a catalytic triad was clearly identified, in agreement with the experimental information available. Analysis of intermediates in the enzymatic mechanism led to the identification of key residues for substrate binding, stereoselectivity, and intermediate stabilization during the reaction. In particular, we have confirmed the role of the oxyanion hole and the conserved motif (HGXP) in epoxide hydrolases, in excellent agreement with known experimental and computational data on similar systems. The model obtained is the first one that fully agrees with all the experimental observations on the system. (C) 2017 Wiley Periodicals, Inc.
Subject headings
- NATURVETENSKAP -- Kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Keyword
- microsomal epoxide hydrolase
- homology models
- clustering
- ensemble-based docking
- epilepsy
- agrobacterium-radiobacter ad1
- particle mesh ewald
- aspergillus-niger
- catalyzed-hydrolysis
- reaction-mechanism
- hypersensitivity reactions
- force-field
- enantioselectivity
- carbamazepine
- quality
- Biochemistry & Molecular Biology
- Biophysics
- clustering
- Biology
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- ref (subject category)
- art (subject category)
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- NATURAL SCIENCES
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- University of Gothenburg
- Karlstad University
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