Shah, NR, Wilkinson, C orcid.org/0000-0002-7469-7440, Harborne, SPD et al. (5 more authors) (2017) Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation. Structural Dynamics, 4 (3). 032105. 032105-032105.
Abstract
Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Naþ,Hþ, or both these ions across a membrane. Recently solved structures of the Naþ-pumping Thermotoga maritima mPPase (TmPPase) and Hþ-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5–6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures. Furthermore, creating an apo model of TmPPase by removing ligands from the TmPPase:IDP:Na structure in MD simulations resulted in increased dynamics in loop 5–6, which results in this loop moving to uncover the active site, suggesting that interactions between loop 5–6 and the imidodiphosphate and its associated Mg2þ are important for holding a loop-closed conformation. We also provide further evidence for the transport-before-hydrolysis mechanism by showing that the non-hydrolyzable substrate analogue, methylene diphosphonate, induces low levels of proton pumping by VrPPase.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2017 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license(http://creativecommons.org/licenses/by/4.0/). |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Biomedical Sciences (Leeds) The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Physics and Astronomy (Leeds) > Theoretical Physics (Leeds) |
Funding Information: | Funder Grant number BBSRC BB/M021610/1 |
Depositing User: | Symplectic Publications |
Date Deposited: | 27 Mar 2017 13:32 |
Last Modified: | 05 Oct 2017 16:18 |
Status: | Published |
Publisher: | AIP Publishing |
Identification Number: | 10.1063/1.4978038 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:114108 |