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dc.contributor.authorHassan, Sameer
dc.contributor.authorGuallar, Victor
dc.contributor.authorSolymosi, Katalin
dc.contributor.authorAronsson, Henrik
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2021-09-01T14:32:42Z
dc.date.available2021-09-01T14:32:42Z
dc.date.issued2021-05
dc.identifier.citationHassan, S. [et al.]. Elucidation of ligand binding and dimerization of NADPH: protochlorophyllide (Pchlide) oxidoreductase from pea (Pisum sativum L.) by structural analysis and simulations. "Proteins: Structure, Function, and Bioinformatics", Maig 2021,
dc.identifier.issn0887-3585
dc.identifier.urihttp://hdl.handle.net/2117/350615
dc.description.abstractNADPH:protochlorophyllide (Pchlide) oxidoreductase (POR) is a key enzyme of chlorophyll biosynthesis in angiosperms. It is one of few known photoenzymes, which catalyzes the light-activated trans-reduction of the C17-C18 double bond of Pchlide's porphyrin ring. Due to the light requirement, dark-grown angiosperms cannot synthesize chlorophyll. No crystal structure of POR is available, so to improve understanding of the protein's three-dimensional structure, its dimerization, and binding of ligands (both the cofactor NADPH and substrate Pchlide), we computationally investigated the sequence and structural relationships among homologous proteins identified through database searches. The results indicate that α4 and α7 helices of monomers form the interface of POR dimers. On the basis of conserved residues, we predicted 11 functionally important amino acids that play important roles in POR binding to NADPH. Structural comparison of available crystal structures revealed that they participate in formation of binding pockets that accommodate the Pchlide ligand, and that five atoms of the closed tetrapyrrole are involved in non-bonding interactions. However, we detected no clear pattern in the physico-chemical characteristics of the amino acids they interact with. Thus, we hypothesize that interactions of these atoms in the Pchlide porphyrin ring are important to hold the ligand within the POR binding site. Analysis of Pchlide binding in POR by molecular docking and PELE simulations revealed that the orientation of the nicotinamide group is important for Pchlide binding. These findings highlight the complexity of interactions of porphyrin-containing ligands with proteins, and we suggest that fit-inducing processes play important roles in POR-Pchlide interactions.
dc.description.sponsorshipThe authors are grateful for the following providers of financial support: the Carl Tryggers Foundation (grants CTS 15:34, CTS 17:32 for Hassan Sameer, Aronsson Henrik), the Hungarian Academy of Sciences (a Bolyai János Research Scholarship for Solymosi Katalin), Hungarian Scientific Research Fund (grant OTKA FK 124748 for Solymosi Katalin), and the Spanish Ministry of Science and Innovation (grant PID2019-106370RB-I00 for Guallar Victor). The authors declare that there is no conflict of interest regarding the publication of this article.
dc.format.extent15 p.
dc.language.isoeng
dc.publisherWiley
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Spain
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subject.lcshPorphyrins
dc.subject.lcshChlorophyll
dc.subject.otherBinding
dc.subject.otherComputational
dc.subject.otherLigand
dc.subject.otherPELE
dc.subject.otherPorphyrin
dc.subject.otherStructural
dc.titleElucidation of ligand binding and dimerization of NADPH: protochlorophyllide (Pchlide) oxidoreductase from pea (Pisum sativum L.) by structural analysis and simulations
dc.typeArticle
dc.subject.lemacProteïnes -- Anàlisi -- Informàtica
dc.identifier.doi10.1002/prot.26151
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://onlinelibrary.wiley.com/doi/10.1002/prot.26151
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
local.citation.publicationNameProteins: Structure, Function, and Bioinformatics


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