Stereochemistry of polypeptoid chain configurations

Area of Science:

• Synthetic chemistry
• Biochemistry
• Structural biology

Background:

• Peptoids (N-substituted glycine oligomers) possess unique backbone structures distinct from polypeptides.
• Differences include tertiary amide bonds, lack of backbone hydrogen bond donors, and N-substituents, influencing conformational preferences.

Purpose of the Study:

• To analyze experimentally determined peptoid structures and identify their backbone conformational preferences.
• To compare observed conformations with calculated energy landscapes and protein structures.

Main Methods:

• Analysis of 46 high-quality, experimentally determined peptoid structures from the literature.
• Comparison of 132 monomer dihedral angle pairs (phi and psi) to calculated peptoid Ramachandran plots.

Main Results:

• Peptoid backbone dihedral angles populate two distinct, mirror-image regions on the Ramachandran plot.
• These two conformers exist in both cis and trans forms, resulting in four primary conformations.
• These four conformers describe nearly all observed peptoid backbone structures, irrespective of side chains or packing forces.

Conclusions:

• A set of four predominant conformers adequately describes peptoid backbone structures.
• These conformations differ significantly from those found in protein secondary structures.
• A new naming system is proposed to classify and describe peptoid structures based on these findings.