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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

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cris.lastimport.scopus2024-02-12T19:56:27Z
dc.abstract.enFluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKouza, Maksim
dc.contributor.authorKmiecik, Sebastian
dc.contributor.authorKloczkowski, Andrzej
dc.contributor.authorBadaczewska-Dawid, Aleksandra Elżbieta
dc.contributor.authorKoliński, Andrzej
dc.date.accessioned2024-01-25T12:49:50Z
dc.date.available2024-01-25T12:49:50Z
dc.date.copyright2018-11-06
dc.date.issued2018
dc.description.accesstimeAT_PUBLICATION
dc.description.financeNie dotyczy
dc.description.number11
dc.description.versionFINAL_PUBLISHED
dc.description.volume19
dc.identifier.doi10.3390/IJMS19113496
dc.identifier.issn1422-0067
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/112760
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.relation.pages3496
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.enprotein dynamics
dc.subject.encoarse-grained simulation
dc.subject.enMonte Carlo dynamics
dc.subject.enstructural flexibility
dc.subject.enlarge-scale dynamics
dc.subject.enelastic network model
dc.titleModeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models
dc.typeJournalArticle
dspace.entity.typePublication