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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Hydrodynamic effects on β-amyloid (16-22) peptide aggregation.

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  • 1Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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Hydrodynamic interactions (HIs) significantly impact amyloid Aβ16-22 peptide aggregation. This study uses Lattice Boltzmann Molecular Dynamics (LBMD) to reveal how HIs influence aggregation kinetics and fibril structures.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Materials Science

Background:

  • Computer simulations are crucial for studying amyloid aggregation.
  • Implicit solvent models neglect solvent-induced correlations, affecting aggregation kinetics.
  • Amyloid peptides like Aβ16-22 are implicated in neurodegenerative diseases.

Purpose of the Study:

  • To investigate the effect of hydrodynamic interactions (HIs) on amyloid Aβ16-22 peptide aggregation.
  • To explore the aggregation pathways and resulting structures using a multi-scale simulation technique.
  • To bridge the gap between simplified simulations and experimental observations.

Main Methods:

  • Application of the multi-scale Lattice Boltzmann Molecular Dynamics (LBMD) technique.
  • Utilizing the OPEP coarse-grained force field for peptide representation.
  • Parameter tuning to match experimental diffusivity of species.

Main Results:

  • Hydrodynamic interactions (HIs) were shown to impact aggregation kinetics and oligomer size fluctuations.
  • HIs favor fusion and exchange dynamics between aggregates, guiding the growth of the largest cluster.
  • Simulations revealed the transition from ellipsoidal assemblies to elongated, twisted aggregates (100 peptides) and novel branched fibril-like structures (1000 peptides).

Conclusions:

  • LBMD simulations including HIs provide a more accurate representation of amyloid aggregation.
  • The study demonstrates the critical role of solvent effects in determining fibril morphology and aggregation dynamics.
  • The findings offer insights into the formation of experimentally observed amyloid structures, including disordered fibril-like forms.