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Updated: Jun 22, 2026
11:55
Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
Published on: August 16, 2016
A statistical model for translocation of structured polypeptide chains through nanopores
Alessandro Ammenti1, Fabio Cecconi, Umberto Marini Bettolo Marconi
1Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, 06123 Perugia, Italy.
The Journal of Physical Chemistry. B
|July 4, 2009
Summary
Protein translocation through nanopores is force-dependent. A critical force is needed to overcome an energy barrier, influenced by unfolding and confinement effects, enabling efficient protein transport.
Area of Science:
- Biophysics
- Computational Biology
- Nanotechnology
Background:
- Understanding protein translocation across nanopores is crucial for biosensing and drug delivery.
- The influence of protein structure on translocation dynamics remains an active research area.
Purpose of the Study:
- To investigate the translocation mechanism of ubiquitin across a cylindrical nanopore using molecular dynamics simulations.
- To characterize the thermodynamics and kinetics of protein transport under varying forces.
Main Methods:
- Molecular dynamics simulations using a native-centric model of ubiquitin.
- Analysis of blockage times, mobility, and translocation probability.
- Umbrella sampling simulations to compute the free-energy profile.
- Development of a phenomenological drift-diffusion model.
Main Results:
- Protein translocation occurs above a critical force (Fc).
- The translocation barrier arises from a balance between unfolding energy and entropic confinement effects.
- A drift-diffusion model accurately reproduces observed translocation dynamics.
Conclusions:
- Protein structural properties significantly impact nanopore translocation.
- The free-energy landscape governs the force-dependent transport dynamics.
- Computational models can effectively predict and explain protein translocation mechanisms.
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