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Viral replication modulated by hallmark conformational ensembles: how AlphaFold-predicted features of RdRp folding dynamics combined with intrinsic disorder-mediated function enable RNA virus discovery

hal.structure.identifierGembloux Agro-Bio Tech [Faculté universitaire des sciences agronomiques de Gembloux] [[FUSAGx]]
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorTAHZIMA, Rachid
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCHARON, Justine
hal.structure.identifierInteruniversity Institute of Bioinformatics in Brussels [IB2]
dc.contributor.authorDIAZ, Adrian
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorDE JONGHE, Kris
hal.structure.identifierUniversité de Liège = University of Liège = Universiteit van Luik = Universität Lüttich [ULiège]
dc.contributor.authorMASSART, Sebastien
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMICHON, Thierry
hal.structure.identifierVrije Universiteit Brussel [Bruxelles] [VUB]
dc.contributor.authorVRANKEN, Wim
dc.date.accessioned2025-09-19T02:08:00Z
dc.date.available2025-09-19T02:08:00Z
dc.date.issued2025-08-22
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/207647
dc.description.abstractEn<div><p>The functions of RNA-dependent RNA polymerases (RdRps) in RNA viruses are demonstrably modulated by native substrates of dynamic and interconvertible conformational ensembles. Many of these are populated by essential flexible or intrinsically disordered regions (IDRs) that lack a stable three-dimensional (3D) structure and that make up nearly 16% of the conserved RdRp domains across Riboviria lineages. Typical structural models of RdRps are conversely generally agnostic of multiple conformations and their fluctuations, whether derived from protein structure predictors or from experimentally resolved structures from crystal states or dynamic conformer sets. In this review, we highlight how biophysics-inspired prediction tools combined with advanced deep learning algorithms, such as AlphaFold2 (AF2), can help efficiently infer the conformational heterogeneity and dynamics of RdRps. We discuss the use of AF2 for protein structure prediction, together with its limitations and impacts on RNA virus protein characterization, and specifically address its low-confidence prediction scores, which largely capture IDRs. Key examples illustrate how biophysical-encoded preferences of generic sequence-ensemble relationships can help estimate the global RdRp structural diversity and RNA virus discovery. The quantitative perception we present also highlights the challenging magnitude of the emergent sequence-to-conformations relationships of proteins and illustrates more robust and accurate annotations of novel or divergent RdRps. Finally, the coarse-grained IDR-based structural depiction of RdRp conformations offers concrete perspectives on an integrative framework to Frontiers in Virology frontiersin.org 01</p></div>
dc.description.sponsorshipRôle du désordre intrinsèque des protéines dans l'adaptation du potyvirus à ses hôtes - ANR-21-CE35-0009
dc.language.isoen
dc.publisherFrontiers Media
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enRNA virus discovery
dc.subject.enconformational ensembles
dc.subject.enintrinsic disorder (IDP/IDR)
dc.subject.enstructural biology
dc.subject.enAlphaFold2 (AF2)
dc.subject.enfolding dynamics
dc.subject.enmodulome and artificial intelligence
dc.subject.enRNA-dependent RNA polymerase
dc.title.enViral replication modulated by hallmark conformational ensembles: how AlphaFold-predicted features of RdRp folding dynamics combined with intrinsic disorder-mediated function enable RNA virus discovery
dc.typeArticle de revue
dc.identifier.doi10.3389/fviro.2025.1501616
dc.subject.halSciences de l'environnement
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalFrontiers in Virology
bordeaux.page1501616
bordeaux.volume5
bordeaux.hal.laboratoriesBiologie du Fruit & Pathologie (BFP) - UMR 1332*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-05267402
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05267402v1
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.jtitle=Frontiers%20in%20Virology&amp;rft.date=2025-08-22&amp;rft.volume=5&amp;rft.spage=1501616&amp;rft.epage=1501616&amp;rft.au=TAHZIMA,%20Rachid&amp;CHARON,%20Justine&amp;DIAZ,%20Adrian&amp;DE%20JONGHE,%20Kris&amp;MASSART,%20Sebastien&amp;rft.genre=article


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