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Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution

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cris.lastimport.scopus2024-02-12T19:45:10Z
dc.abstract.enStructure determination using cryo-electron microscopy (cryo-EM) medium-resolution density maps is often facilitated by flexible fitting. Avoiding overfitting, adjusting force constants driving the structure to the density map, and emulating complex conformational transitions are major concerns in the fitting. To address them, we develop a new method based on a three-step multi-scale protocol. First, flexible fitting molecular dynamics (MD) simulations with coarse-grained structure-based force field and replica-exchange scheme between different force constants replicas are performed. Second, fitted Cα atom positions guide the all-atom structure in targeted MD. Finally, the all-atom flexible fitting refinement in implicit solvent adjusts the positions of the side chains in the density map. Final models obtained via the multi-scale protocol are significantly better resolved and more reliable in comparison with long all-atom flexible fitting simulations. The protocol is useful for multi-domain systems with intricate structural transitions as it preserves the secondary structure of single domains.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKulik, Marta
dc.contributor.authorSugita, Yuji
dc.contributor.authorMori, Takaharu
dc.date.accessioned2024-01-25T13:17:26Z
dc.date.available2024-01-25T13:17:26Z
dc.date.copyright2021-03-19
dc.date.issued2021
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.versionFINAL_PUBLISHED
dc.description.volume8
dc.identifier.doi10.3389/FMOLB.2021.631854
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/113132
dc.identifier.weblinkhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.631854/full
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofFrontiers in Molecular Biosciences
dc.relation.pagesart.no. 631854
dc.rightsOther
dc.sciencecloudnosend
dc.subject.enall-atom force field
dc.subject.encoarse-grained force field
dc.subject.encryo-EM density map
dc.subject.enflexible fitting
dc.subject.enmolecular dynamics simulation
dc.subject.enmulti-scale methods
dc.subject.enreplica exchange
dc.subject.entargeted molecular dynamics
dc.titleMulti-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution
dc.typeJournalArticle
dspace.entity.typePublication