onr:"swepub:oai:lup.lub.lu.se:527ba0ee-7f0e-4c3e-b2aa-572b6b683431"
Search: onr:"swepub:oai:lup.lub.lu.se:527ba0ee-7f0e-4c3e-b2aa-572b6b683431" > QM/MM study of the ...
- 1 of 1
- Previous record
- Next record
- To hitlist
QM/MM study of the catalytic reaction of aphid myrosinase
-
- Jafari, Sonia (author)
- University of Kurdistan
-
- Ryde, Ulf (author)
- Lund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH
-
- Irani, Mehdi (author)
- University of Kurdistan
- (creator_code:org_t)
- 2024
- 2024
- English.
- In: International Journal of Biological Macromolecules. - 0141-8130. ; 262
- Journal article (peer-reviewed)
Abstract
Subject headings
Close
- 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.
Subject headings
- NATURVETENSKAP -- Kemi -- Teoretisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Theoretical Chemistry (hsv//eng)
Keyword
- MD simulations
- Mechanism
- Myrosinase
- QM/MM
Publication and Content Type
- art (subject category)
- ref (subject category)
Find in a library
- International Journal of Biological Macromolecules (Search for host publication in LIBRIS)
To the university's database
- 1 of 1
- Previous record
- Next record
- To hitlist
Find more in SwePub
- By the author/editor
- Jafari, Sonia
- Ryde, Ulf
- Irani, Mehdi
- About the subject
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Chemical Science ...
- and Theoretical Chem ...
- Articles in the publication
- International Jo ...
- By the university
- Lund University
Search outside SwePub
- Extend your search to:
- Google Book Search
- Google Scholar
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
- Copyright © LIBRIS - National Library Systems
- LIBRIS.kb.se
