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Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
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Probing the Conformational Preference to β-Strand during Peptide Self-Assembly.

Vidhya Ganesan1, M Hamsa Priya1

  • 1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India.

The Journal of Physical Chemistry. B
|June 26, 2023
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Summary
This summary is machine-generated.

Alanine-rich tetrapeptides transition from polyproline II helices to beta-strands during self-assembly. This conformational change, driven by energy minimization, is crucial for forming structures like amyloid fibrils.

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Area of Science:

  • Biophysics
  • Materials Science
  • Computational Chemistry

Background:

  • Alanine-rich tetrapeptides, such as A3K, predominantly adopt polyproline II helices in dilute solutions.
  • Peptide self-assembly into ordered structures, like amyloid fibrils, often involves conformational changes.

Purpose of the Study:

  • To investigate the conformational transitions of alanine-rich tetrapeptides during self-assembly.
  • To understand the energetic landscape governing peptide self-assembly and fibril formation.

Main Methods:

  • Free energy calculations in implicit solvent to screen peptide conformations.
  • Umbrella sampling simulations in explicit solvent to validate findings and study dynamic processes.
  • Analysis of interpeptide distances and comparison with experimental data (X-ray diffraction).

Main Results:

  • Only beta-strand conformations allow for close packing necessary for self-assembly.
  • Implicit solvent calculations accurately predict free energy minima corresponding to self-assembly.
  • A significant energy barrier exists due to water molecule interactions, suggesting initial assembly in polyproline II before transitioning to beta-strands.

Conclusions:

  • Peptide self-assembly involves a dynamic conformational transition from polyproline II to beta-strands.
  • Implicit solvent methods are effective for rapid screening of favorable peptide configurations.
  • The findings support a 'dock and lock' mechanism for amyloid fibril growth.