Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Show others and affiliations
2016 (English)In: Philosophical Transactions of the Royal Society of London A, Mathematical, Physical and Engineering Sciences, Vol. 374, p. 20160150-Article in journal (Refereed) Published
Abstract [en]

Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal–metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.

This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

Place, publisher, year, edition, pages
2016. Vol. 374, p. 20160150-
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:uu:diva-314104DOI: 10.1098/rsta.2016.0150ISI: 000391139300011OAI: oai:DiVA.org:uu-314104DiVA, id: diva2:1069218
Funder
Knut and Alice Wallenberg FoundationWenner-Gren FoundationsSwedish National Infrastructure for Computing (SNIC), 2014/11-2Available from: 2017-01-27 Created: 2017-01-27 Last updated: 2018-09-14Bibliographically approved
In thesis
1. Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases
Open this publication in new window or tab >>Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Computational modeling is becoming an increasingly integral part of (bio)chemistry, providing a powerful complementary view into the dynamics, binding, and reactivity of biochemical systems. In particular, molecular simulations based on multiscale models are now regularly employed in studies of enzymatic reactions, offering invaluable mechanistic insight through the lens of molecular energy landscapes. In this thesis, I used the empirical valence bond (EVB) and related methods to study the mechanisms and selectivity of organophosphate hydrolases.

Organophosphate hydrolases are a diverse class of enzymes capable of degrading some of the most toxic compounds known to mankind, including pesticides and chemical warfare agents. They are particularly interesting from a mechanistic and evolutionary point of view, having evolved the ability to catalyze the hydrolysis of compounds which were introduced to nature less than a century ago. Moreover, they show promise as effective organophosphate decontamination agents and a thorough understanding of their function is fundamental to the future design of efficient and selective biocatalysts. 

As organophosphate hydrolases are metal-dependent enzymes, a reliable metal model was a prerequisite to our simulations. First, I present the development of force-field independent parameters for several alkaline-earth and transition-metal ions described using the nonbonded cationic dummy model. The model was subsequently employed in EVB simulations to probe the origin of metal-ion activity and selectivity patterns observed in methyl parathion hydrolase (MPH) and to provide mechanistic insight into its paraoxonase and promiscuous arylesterase activities. I further set out to resolve open mechanistic questions surrounding diisopropyl fluorophosphatase (DFPase) by performing extensive simulations of two mechanistic pathways proposed in literature, including calculating the effects of mutations, temperature, and protonation states on the rate of hydrolysis. Using this knowledge, I address the origin of cross-selectivity between DFPase and a structurally similar enzyme serum paraoxonase 1 (PON1). Finally, I present the latest developments in the software used to perform the simulations.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 92
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1722
Keywords
Organophosphate Hydrolase, Computational enzymology, MPH, DFPase, PON1, Empirical Valence Bond, EVB
National Category
Biochemistry and Molecular Biology Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-360518 (URN)978-91-513-0444-1 (ISBN)
Public defence
2018-11-02, BMC:B22, Husargatan 3, Uppsala, 09:00 (English)
Opponent
Supervisors
Available from: 2018-10-08 Created: 2018-09-14 Last updated: 2018-10-16

Open Access in DiVA

fulltext(838 kB)29 downloads
File information
File name FULLTEXT01.pdfFile size 838 kBChecksum SHA-512
1492bac9cad43e99899f4a3f46847e51a5593a1c12dbceb2c9d185a29c630d6cace752afe19b4d026ea89c4509f7bed72d6e0f54c4386be597772281ee3cf048
Type fulltextMimetype application/pdf

Other links

Publisher's full textPublisher's PDF

Search in DiVA

By author/editor
Purg, MihaPabis, AnnaKamerlin, Shina Caroline Lynn
By organisation
Structure and Molecular BiologyScience for Life Laboratory, SciLifeLab
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 29 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 302 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf