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 R 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 F c 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. © 2009 American Chemical Society.

A statistical model for translocation of structured polypeptide chains through nanopores / Alessandro, Ammenti; Fabio, Cecconi; U. M. B., Marconi; Vulpiani, Angelo. - In: JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL. - ISSN 1520-6106. - 113:30(2009), pp. 10348-10356. [10.1021/jp900947f]

A statistical model for translocation of structured polypeptide chains through nanopores

VULPIANI, Angelo
2009

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 R 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 F c 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. © 2009 American Chemical Society.
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A statistical model for translocation of structured polypeptide chains through nanopores / Alessandro, Ammenti; Fabio, Cecconi; U. M. B., Marconi; Vulpiani, Angelo. - In: JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL. - ISSN 1520-6106. - 113:30(2009), pp. 10348-10356. [10.1021/jp900947f]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/85732
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