http://www.cnr.it/ontology/cnr/individuo/prodotto/ID57727

A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores (Articolo in rivista)

Type

Label

A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores (Articolo in rivista) (literal)

Anno

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

Alternative label

Ammenti A. (1), Cecconi F. (2), Marini Bettolo Marconi U. (3), Vulpiani A. (4) (2009)
A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores
in The journal of physical chemistry. B; ACS, American chemical society, Washington, DC (Stati Uniti d'America)
(literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

Ammenti A. (1), Cecconi F. (2), Marini Bettolo Marconi U. (3), Vulpiani A. (4) (literal)

Pagina inizio

Pagina fine

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#url

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume

Rivista

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#note

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo

Note

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni

1) Dipartimento di Fisica, Universita di Perugia, Via A. Pascoli, 06123 Perugia, Italy 2) INFM-CNR, Center for Statistical Mechanics and Complexity, Istituto dei Sistemi Complessi, Via dei Taurini 19, 00185 Rome, Italy 3) Dipartimento di Fisica, Università di Camerino, Via Madonna delle Carceri, 68032 Camerino (MC), Italy 4) Dipartimento di Fisica, Universita La Sapienza, INFN and INFM-CNR, P.le Aldo Moro 2, 00185 Rome (literal)

Titolo

A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores (literal)

Abstract

The translocation process of a globular protein (ubiquitin) across a cylindrical nanopore is studied via molecular dynamics simulations. The ubiquitin is described by a native-centric model on a C? carbon backbone to investigate the influence of protein-like structural properties on the translocation mechanism. A thermodynamical and kinetic characterization of the process is obtained by studying the statistics of blockage times, the mobility, and the translocation probability as a function of the pulling force F acting in the pore. The transport dynamics occurs when the force exceeds a threshold Fc depending on a free-energy barrier that ubiquitin has to overcome in order to slide along the channel. Such a barrier results from competition of the unfolding energy and the entropy associated with the confinement effects of the pore. We implement appropriate umbrella sampling simulations to compute the free-energy profile as a function of the position of the ubiquitin center of mass inside of the channel (reaction coordinate). This free energy is then used to construct a phenomenological drift-diffusion model in the reaction coordinate which explains and reproduces the behavior of the observables during the translocation. (literal)

Editore