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Updated: Apr 11, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
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Peptide folding driven by Van der Waals interactions.

Shen-Shu Sung1

  • 1Department of Pharmacology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033.

Protein Science : a Publication of the Protein Society
|May 28, 2015
PubMed
Summary

Protein folding into helical structures can occur without hydrogen bonding, driven by van der Waals interactions. These findings challenge conventional views on protein folding mechanisms.

Keywords:
compact structurecovalent bonding constraintfolding mechanismhydrogen bondingintramolecular interactionsecondary structure

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Science

Background:

  • The dominant role of hydrogen bonding in protein folding is widely accepted.
  • Molecular dynamics (MD) simulations typically model hydrogen bonding via atomic partial charges.

Purpose of the Study:

  • To investigate protein folding mechanisms in the absence of hydrogen bonding.
  • To explore the influence of van der Waals interactions on protein secondary structure formation.

Main Methods:

  • Utilized MD simulations with atomic charges of peptide and solvent set to zero, effectively removing hydrogen bonding.
  • Focused on van der Waals (VDW) interactions and covalent bonding constraints.

Main Results:

  • Observed spontaneous folding into helical and hairpin-like structures without hydrogen bonding.
  • VDW interactions favored intramolecular peptide interactions, leading to structural compactness.
  • Compact structures were sequence-dependent and resembled standard secondary structures.

Conclusions:

  • Van der Waals interactions are a significant factor in protein folding and secondary structure formation.
  • Protein folding can proceed via mechanisms not solely reliant on hydrogen bonding.
  • These findings offer a new perspective on protein folding dynamics.