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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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Energy Landscapes and Global Optimization of Self-Assembling Cyclic Peptides
Mark T Oakley1, Roy L Johnston1
1School of Chemistry, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
Journal of Chemical Theory and Computation
|November 19, 2015
Summary
Researchers explored cyclic peptide nanotube formation using computational methods. Group rotation moves efficiently mapped conformations, revealing distinct dimerization patterns for hexapeptides and octapeptides.
Area of Science:
- Biochemistry
- Computational Chemistry
- Materials Science
Background:
- Self-assembled cyclic peptide nanotubes show promise for antimicrobial applications.
- Understanding the conformational dynamics of cyclic peptides is crucial for designing functional nanotubes.
Purpose of the Study:
- To investigate the conformational space of cyclic peptides using computational modeling.
- To identify efficient algorithms for exploring cyclic peptide conformations.
- To analyze the dimerization behavior of cyclic peptide dimers.
Main Methods:
- Basin-hopping and discrete path sampling were employed for conformational analysis.
- Analysis of various basin-hopping move sets, including group rotation moves.
- Examination of intramolecular and intermolecular moves for cyclic peptide dimers.
Main Results:
- Group rotation moves are highly effective for exploring conformations of cyclic peptides up to 20 residues.
- A combination of intramolecular group rotation and intermolecular rigid body moves optimizes dimer exploration.
- Significant differences in dimerization were observed between hexapeptide and octapeptide dimers.
Conclusions:
- Computational methods, particularly optimized basin-hopping strategies, are effective for studying cyclic peptide self-assembly.
- The findings provide insights into the factors governing the formation and dimerization of cyclic peptide nanotubes.
- This work contributes to the rational design of peptide-based nanomaterials with potential antimicrobial activity.
