Free-energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction (Articolo in rivista)

Type
Label
  • Free-energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction (Articolo in rivista) (literal)
Anno
  • 2008-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1103/PhysRevE.78.031907 (literal)
Alternative label
  • Luccioli S.; Imparato A.; Torcini A. (2008)
    Free-energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
    in Physical review. E, Statistical, nonlinear, and soft matter physics (Print)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Luccioli S.; Imparato A.; Torcini A. (literal)
Pagina inizio
  • 031907 (literal)
Pagina fine
  • [15] (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 78(3) (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#note
  • American Physical Society (APS). (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • 1) Istituto dei Sistemi Complessi, CNR, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy 2) INFN, Sezione Firenze, and CSDC, via Sansone, 1-I-50019 Sesto Fiorentino, Italy 3) ISI Foundation, Viale Settimio Severo 65, Villa Gualino, I-10133 Torino, Italy 4) Centre de Physique Théorique, Campus de Luminy, 13288 Marseille, France (literal)
Titolo
  • Free-energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction (literal)
Abstract
  • The equilibrium free-energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: By employing an extended version of the Jarzynski equality and the inherent structure formalism. A comparison of the free energies estimated with these two schemes with equilibrium results obtained via the umbrella sampling technique reveals a good quantitative agreement among all the approaches in a range of temperatures around the “folding transition” for the two examined sequences. In particular, for the sequence with good foldability properties, the mechanically induced structural transitions can be related to thermodynamical aspects of folding. Moreover, for the same sequence the knowledge of the landscape profile allows for a good estimation of the lifetimes of the native configuration for temperatures ranging from the folding to the collapse temperature. For the random sequence, mechanical and thermal unfolding appear to follow different paths along the landscape. (literal)
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