Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field (Articolo in rivista)

Type
Label
  • Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field (Articolo in rivista) (literal)
Anno
  • 2013-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1371/journal.pcbi.1003002 (literal)
Alternative label
  • Beccara, Silvio A.; Skrbic, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro (2013)
    Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
    in PLOS computational biology (Online)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Beccara, Silvio A.; Skrbic, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 9 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali
  • 9 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 3 (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Bruno Kessler Fdn; Bruno Kessler Fdn; University of Trento; Istituto Nazionale di Fisica Nucleare; International School for Advanced Studies; CNR IOM Democritos (literal)
Titolo
  • Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field (literal)
Abstract
  • We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native beta-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. (literal)
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