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QM/MM study of the catalytic reaction of aphid myrosinase

Jafari, Sonia ; Ryde, Ulf LU orcid and Irani, Mehdi LU (2024) In International Journal of Biological Macromolecules 262.
Abstract

Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122... (More)

Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.

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Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
MD simulations, Mechanism, Myrosinase, QM/MM
in
International Journal of Biological Macromolecules
volume
262
article number
130089
publisher
Elsevier
external identifiers
  • pmid:38360236
  • scopus:85185531221
ISSN
0141-8130
DOI
10.1016/j.ijbiomac.2024.130089
language
English
LU publication?
yes
id
527ba0ee-7f0e-4c3e-b2aa-572b6b683431
date added to LUP
2024-03-27 15:52:38
date last changed
2024-04-24 19:52:30
@article{527ba0ee-7f0e-4c3e-b2aa-572b6b683431,
  abstract     = {{<p>Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.</p>}},
  author       = {{Jafari, Sonia and Ryde, Ulf and Irani, Mehdi}},
  issn         = {{0141-8130}},
  keywords     = {{MD simulations; Mechanism; Myrosinase; QM/MM}},
  language     = {{eng}},
  publisher    = {{Elsevier}},
  series       = {{International Journal of Biological Macromolecules}},
  title        = {{QM/MM study of the catalytic reaction of aphid myrosinase}},
  url          = {{http://dx.doi.org/10.1016/j.ijbiomac.2024.130089}},
  doi          = {{10.1016/j.ijbiomac.2024.130089}},
  volume       = {{262}},
  year         = {{2024}},
}