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Long-lived metastable knots in polyampholyte chains.

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Protein and DNA knot dynamics are significantly influenced by charge distribution. Varied charges on polyampholyte chains create long-lived knots, unlike neutral chains, impacting their escape dynamics.

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Area of Science:

  • Polymer Physics
  • Biophysics
  • Computational Biology

Background:

  • Knots in biological polymers like proteins and DNA affect their properties and function.
  • Knot dynamics in neutral or uniformly charged chains are understood, but proteins are polyampholytes with complex charge distributions.
  • The influence of varied charge distributions on polyampholyte knot dynamics remains less explored.

Purpose of the Study:

  • To investigate how charge distribution variations in zero net charge polyampholyte chains affect knot dynamics.
  • To understand the mechanisms behind long-lived metastable knots in such systems.
  • To develop a predictive model for knot lifetimes in polyampholyte chains.

Main Methods:

  • Simulations of knotted polymer chains with varying charge distributions.
  • Analysis of knot escape timescales and dynamics.
  • Development and application of a one-dimensional biased Brownian motion model.

Main Results:

  • Charge distribution variations significantly alter knot dynamics in polyampholyte chains.
  • Certain charge distributions lead to long-lived metastable knots with much longer escape times than neutral chains.
  • Knot dynamics can be quantitatively described by a model of biased Brownian motion influenced by a potential of mean force.

Conclusions:

  • Electrostatic interactions arising from charge distribution are critical in determining polyampholyte knot stability and dynamics.
  • Large electrostatic barriers to knot escape, caused by specific charge sequences, result in long-lived knots.
  • The developed model accurately predicts knot lifetimes, even for timescales inaccessible to direct simulation.