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Confinement-dependent friction in peptide bundles.

Aykut Erbaş1, Roland R Netz

  • 1Free University of Berlin, Fachbereich Physik, Berlin, Germany. aerbas@unc.edu

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|March 27, 2013
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Friction in protein systems dramatically increases with reduced water and increased chain interactions. This study quantifies friction enhancement in polyglycine peptide bundles, revealing a five-order-of-magnitude rise due to water depletion and cooperativity.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Materials Science

Background:

  • Friction in protein systems influences folding kinetics and self-assembly.
  • Understanding the role of the local environment, especially water, is crucial for friction analysis.

Purpose of the Study:

  • To investigate friction forces between polyglycine peptide chains.
  • To determine how friction depends on the aggregation number and water presence.

Main Methods:

  • Atomistic molecular dynamics (MD) simulations with explicit water.
  • Pulling a single polyglycine chain from bundles of varying sizes (k=2 to k=7).
  • Achieving stationary states at prescribed sliding velocities and extrapolating to zero velocity.

Main Results:

  • Friction coefficient per hydrogen bond increased by five orders of magnitude from k=2 to k=7.
  • Significant friction enhancement observed with increasing aggregation number and decreasing water content.
  • Water depletion and enhanced hydrogen-bond cooperativity identified as key factors.

Conclusions:

  • Confinement significantly enhances friction in proteinaceous systems.
  • Water plays a critical role in modulating friction at the molecular level.
  • Findings provide insights into self-assembly and protein dynamics in confined environments.