Blind conformational predictions were performed for 3 new peptoids using Replica Exchange Molecular Dynamics simulation and Quantum Mechanical refinement. Subsequent comparison with the 3D structure determined by X-ray crystallography showed these predictions to be accurate to within 1 Å, demonstrating that reliable de novo structural prediction for peptoids is possible.
Significance and Impact
The ability to correctly predict the 3-dimensional structure of peptoids, validates the effectiveness of current theoretical modeling techniques and demonstrates that de novo predictions of small peptoid structures is possible. This accomplishment helps pave the way for rational design of 3-dimensional structure, necessary to synthesize functional peptoid molecules.
- Using a blind prediction method, theoretical modelers predict the structures of three synthesized peptoids.
- Actual structure determined via X-ray crystallography was shown to match the predicted conformations with very high accuracy.
- This study led to characterization of the largest confirmed peptoid structure to date.