dc.contributor.author	Dragelj, Jovan
dc.contributor.author	Karafoulidi-Retsou, Chara
dc.contributor.author	Katz, Sagie
dc.contributor.author	Lenz, Oliver
dc.contributor.author	Zebger, Ingo
dc.contributor.author	Caserta, Giorgio
dc.contributor.author	Sacquin-Mora, Sophie
dc.contributor.author	Mroginski, Maria Andrea
dc.date.accessioned	2023-02-06T10:56:29Z
dc.date.available	2023-02-06T10:56:29Z
dc.date.issued	2023-01-17
dc.date.updated	2023-01-31T06:42:26Z
dc.description.abstract	Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel–iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.
dc.description.sponsorship	DFG, 390540038, EXC 2008: Unifying Systems in Catalysis "UniSysCat"
dc.description.sponsorship	TU Berlin, Open-Access-Mittel - 2023
dc.identifier.eissn	1664-302X
dc.identifier.uri	https://depositonce.tu-berlin.de/handle/11303/18142
dc.identifier.uri	https://doi.org/10.14279/depositonce-16935
dc.language.iso	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/
dc.subject.ddc	570 Biowissenschaften; Biologie	de
dc.subject.other	hydrogenase
dc.subject.other	molecular modelling
dc.subject.other	Gaussian accelerated molecular dynamics
dc.subject.other	rigidity profile
dc.subject.other	electrostatic potential
dc.subject.other	dipole moment
dc.subject.other	IR spectroscopy
dc.subject.other	size exclusion chromatography
dc.title	Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator
dc.type	Article
dc.type.version	publishedVersion
dcterms.bibliographicCitation.articlenumber	1073315
dcterms.bibliographicCitation.doi	10.3389/fmicb.2022.1073315
dcterms.bibliographicCitation.journaltitle	Frontiers in Microbiology
dcterms.bibliographicCitation.originalpublishername	Frontiers
dcterms.bibliographicCitation.originalpublisherplace	Lausanne
dcterms.bibliographicCitation.volume	13
dcterms.rightsHolder.reference	Creative-Commons-Lizenz
tub.accessrights.dnb	free
tub.affiliation	Fak. 2 Mathematik und Naturwissenschaften::Inst. Chemie::FG Modellierung biomolekularer Systeme
tub.publisher.universityorinstitution	Technische Universität Berlin

Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator

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