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dc.contributor.authorSerrano Aparicio, Natalia
dc.contributor.authorŚwiderek, Katarzyna
dc.contributor.authorTuñón, Iñaki
dc.contributor.authorMoliner, Vicent
dc.contributor.authorBertran, Joan
dc.date.accessioned2021-10-22T13:54:35Z
dc.date.available2021-10-22T13:54:35Z
dc.date.issued2021-08-25
dc.identifier.citationSerrano-Aparicio, N., Świderek, K., Tuñón, I. et al. Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism. Top Catal (2021). https://doi.org/10.1007/s11244-021-01494-1ca_CA
dc.identifier.issn1022-5528
dc.identifier.issn1572-9028
dc.identifier.urihttp://hdl.handle.net/10234/195133
dc.description.abstractRibozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries along independent MD simulations with different protonation states of the active site basic species reveals that only the canonical system, with no additional protonation changes, renders reactive conformations. A change in the coordination sphere of the Mg2+ ion has been observed during the simulations, which allows proposing a mechanism to explain the unique mode of action of the pistol ribozyme by comparison with other ribozymes. The present results are at the center of the debate originated from recent experimental and theoretical studies on pistol ribozyme.ca_CA
dc.description.sponsorShipFunding for open access charge: CRUE-Universitat Jaume I
dc.format.extent28 p.ca_CA
dc.format.mimetypeapplication/pdfca_CA
dc.language.isoengca_CA
dc.publisherSpringerca_CA
dc.relationUnravelling the reaction and inhibition mechanism of proteasome 205 and rhomboid protease by QM/MM theoretical methods: two bio-macromolecules involved in cancer proliferationca_CA
dc.relationTheoretical studies of peptide bond cleavage in cellular processes, from inhibition to design.ca_CA
dc.relationProyecto de tesis doctoral de Natalia Serrano Aparicio: modelización multiescala de reacciones químicas en entornos biológicosca_CA
dc.relationQmcube: una plataforma universal para simulaciones multiescala en sistemas biológicos. Interpretando y prediciendo la actividad enzimática (qmcube)ca_CA
dc.relationEstudios computacionales del mecanismo y la inhibición de la proteólisis enzimática como enfoque complementario del mundo del descubrimiento moderno de fármacosca_CA
dc.relationDiseño computacional de nuevos biocatalizadoresca_CA
dc.relationDiseño asistido por ordenador de nuevas enzimas basado en propiedades electrostáticasca_CA
dc.relation.isPartOfTopics in Catalysis, 2021ca_CA
dc.rights.urihttp://creativecommons.org/licenses/by-sa/4.0/ca_CA
dc.subjectPistol ribozymeca_CA
dc.subjectSelf-cleavage ribozymesca_CA
dc.subjectMolecular dynamicsca_CA
dc.subjectQM/MMca_CA
dc.subjectReaction mechanismsca_CA
dc.titleTheoretical Studies of the Self Cleavage Pistol Ribozyme Mechanismca_CA
dc.typeinfo:eu-repo/semantics/articleca_CA
dc.identifier.doi10.1007/s11244-021-01494-1
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessca_CA
dc.relation.publisherVersionhttps://link.springer.com/article/10.1007/s11244-021-01494-1ca_CA
dc.type.versioninfo:eu-repo/semantics/publishedVersionca_CA
oaire.awardNumberSEJI/2020/007ca_CA
oaire.awardNumberUJI-A2019-04ca_CA
oaire.awardNumberBES-2016-078029ca_CA
oaire.awardNumberPGC2018-094852-B-C21ca_CA
oaire.awardNumberPID2019-107098RJ-100ca_CA
oaire.awardNumberAICO/2019/195ca_CA
oaire.awardNumberUJI-2020-03ca_CA


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