Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
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Títol
Theoretical Studies of the Self Cleavage Pistol Ribozyme MechanismAutoria
Data de publicació
2021-08-25Editor
SpringerISSN
1022-5528; 1572-9028Cita bibliogràfica
Serrano-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/s11244-021-01494-1Tipus de document
info:eu-repo/semantics/articleVersió de l'editorial
https://link.springer.com/article/10.1007/s11244-021-01494-1Versió
info:eu-repo/semantics/publishedVersionParaules clau / Matèries
Resum
Ribozymes 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, ... [+]
Ribozymes 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. [-]
Publicat a
Topics in Catalysis, 2021Codi del projecte o subvenció
SEJI/2020/007 | UJI-A2019-04 | BES-2016-078029 | PGC2018-094852-B-C21 | PID2019-107098RJ-100 | AICO/2019/195 | UJI-2020-03
Títol del projecte o subvenció
Unravelling the reaction and inhibition mechanism of proteasome 205 and rhomboid protease by QM/MM theoretical methods: two bio-macromolecules involved in cancer proliferation | Theoretical studies of peptide bond cleavage in cellular processes, from inhibition to design. | Proyecto de tesis doctoral de Natalia Serrano Aparicio: modelización multiescala de reacciones químicas en entornos biológicos | Qmcube: una plataforma universal para simulaciones multiescala en sistemas biológicos. Interpretando y prediciendo la actividad enzimática (qmcube) | Estudios computacionales del mecanismo y la inhibición de la proteólisis enzimática como enfoque complementario del mundo del descubrimiento moderno de fármacos | Diseño computacional de nuevos biocatalizadores | Diseño asistido por ordenador de nuevas enzimas basado en propiedades electrostáticas
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info:eu-repo/semantics/openAccess
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