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Updated: Sep 5, 2025
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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
Published on: February 6, 2020
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Evaluating the Conformations and Dynamics of Peptoid Macrocycles
James R B Eastwood1, Linhai Jiang1, Richard Bonneau2,3
1Department of Chemistry, New York University, New York, New York 10003, United States.
The Journal of Physical Chemistry. B
|July 12, 2022
Summary
Peptoid macrocycles exhibit limited, predictable conformations and dynamics. Molecular dynamics simulations revealed correlated "crankshaft flip" motions, mapping their energy landscape for up to eight residues.
Area of Science:
- Chemical Biology
- Computational Chemistry
- Polymer Science
Background:
- Peptoid macrocycles are versatile peptidomimetics.
- Conformational analysis of peptoid macrocycles is incomplete.
- Two degrees of freedom and four conformations describe monomer behavior.
Purpose of the Study:
- To comprehensively evaluate peptoid macrocycle conformations and dynamics.
- To map the conformational energy landscape of peptoid macrocycles.
- To investigate the relationship between structure and dynamics.
Main Methods:
- Molecular dynamics simulations of model peptoid macrocycles.
- Exhaustive set of idealized starting conformations.
- Analysis of dihedral angles and correlated motions.
Main Results:
- Simulations identified a limited set of populated conformations.
- Reproduced experimentally observed conformations.
- Predicted and experimentally observed a cyclo-octamer conformation.
- Identified correlated crankshaft motions in macrocycles (≥6 residues).
Conclusions:
- Peptoid macrocycle energy landscapes are networks of conformations linked by crankshaft flips.
- The conformational landscape is well-mapped for macrocycles up to eight residues.
- Cranshaft flip motions are key to understanding peptoid macrocycle dynamics.
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