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Constructing Cyclic Peptides Using an On-Tether Sulfonium Center
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Insights into How Cyclic Peptides Switch Conformations.

Sean M McHugh1, Julia R Rogers1, Hongtao Yu1

  • 1Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States.

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|April 1, 2016
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Summary
This summary is machine-generated.

Predicting cyclic peptide structures is challenging due to complex conformational landscapes. This study reveals that conformational changes in small cyclic peptides involve local, coupled dihedral adjustments, enabling effective conformational sampling using specialized simulations.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Cyclic peptides are emerging as key modulators of protein-protein interactions.
  • Predicting cyclic peptide structures is difficult due to rugged conformational energy landscapes.

Purpose of the Study:

  • To investigate the conformational switching mechanisms of a flexible cyclic hexapeptide.
  • To develop enhanced simulation methods for effective conformational sampling of cyclic peptides.

Main Methods:

  • Analysis of conformational transitions in a cyclic hexapeptide.
  • Development and application of metadynamics simulations with targeted reaction coordinates.

Main Results:

  • Conformational changes in small cyclic peptides (6-8 residues) involve local, coupled dihedral angle modifications.
  • Simultaneous changes in adjacent dihedral angles (e.g., ϕi and ψi, or ψi and ϕi+1) facilitate transitions.
  • Metadynamics simulations utilizing these coupled dihedral changes effectively sample cyclic peptide conformational space.

Conclusions:

  • Understanding local dihedral dynamics is crucial for predicting cyclic peptide structures.
  • Targeted metadynamics simulations offer an effective strategy for exploring cyclic peptide conformational landscapes.
  • This work advances the computational prediction of cyclic peptide structures for drug discovery and design.