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Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
Published on: August 16, 2016
Translocation of a knotted polypeptide through a pore
1Department of Chemistry and Biochemistry and Institute for Theoretical Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
The Journal of Chemical Physics
|December 3, 2008
Summary
Deep knots significantly impede polypeptide chain translocation through pores. Complex knots, like the 5(2) type, can increase translocation time by 100-fold, revealing complex energy landscapes.
Area of Science:
- Biophysics
- Computational Biology
- Polymer Physics
Background:
- Understanding protein folding and translocation is crucial for molecular biology.
- Knots in polypeptide chains can affect their stability and function.
- Previous studies have explored translocation of unknotted chains through nanopores.
Purpose of the Study:
- To investigate the impact of deep knots on the time required for polypeptide chain translocation through a narrow pore.
- To quantify the effect of knot complexity on translocation dynamics.
- To elucidate the translocation mechanism for knotted polypeptide chains.
Main Methods:
- Langevin dynamics simulations were employed to model the system.
- A polypeptide chain with a knotted segment between beta-hairpins was designed to prevent knot slippage.
- Mechanical pulling at the chain end was simulated across a range of forces (40-200 pN).
Main Results:
- Translocation time increased with increasing knot complexity.
- The type 5(2) knot, the most complex found in proteins, slowed translocation by approximately two orders of magnitude compared to unknotted chains.
- Knotted chain translocation involved multiple slippage events, unlike unknotted chains.
Conclusions:
- The presence of deep knots significantly hinders polypeptide translocation through narrow pores.
- Knot complexity is a critical factor determining translocation time.
- The translocation mechanism for knotted chains is characterized by a rugged free energy landscape with multiple metastable states.
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