Development of a Systematic and Extensible Force Field for Peptoids (STEPs)
Bradley S Harris1, Karteek K Bejagam1, Marcel D Baer1
1Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States.
The Journal of Physical Chemistry. B
|July 18, 2023
Summary
Researchers developed a new computational force field for peptoids (N-substituted glycines), enhancing the accuracy of predicting these biomimetic polymer structures for advanced material design.
Area of Science:
- Biomimetic Polymers
- Computational Chemistry
- Materials Science
Background:
- Peptoids offer enhanced stability over polypeptides but pose challenges for computational structure prediction.
- Existing computational models for proteins are not directly applicable to peptoids.
- Fragmented efforts in developing peptoid-specific force fields hinder progress.
Purpose of the Study:
- To develop and validate a comprehensive peptoid-specific force field.
- To improve the accuracy of computational modeling for peptoid-based materials.
- To facilitate de novo design and structure prediction of peptoid sequences.
Main Methods:
- Developed a peptoid-specific force field using GAFF2 as a base, parameterizing 70 side chains.
- Validated the force field using DFT optimization for Ramachandran-like plots.
- Compared force field-generated potential and free energy surfaces with DFT results.
- Assessed the reproduction of experimental cis/trans equilibrium values for helical residues.
Main Results:
- A validated peptoid-specific force field with 70 parameterized side chains was created.
- The force field accurately reproduces potential and free energy surfaces.
- Equilibrium cis/trans distributions were estimated for all residues, identifying propensities for specific states.
Conclusions:
- The developed force field significantly advances computational structure prediction for peptoids.
- This work provides a foundation for more robust peptoid-based material design.
- Accurate force fields are crucial for realizing the potential of peptoid polymers.
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