PmlBeta: A PyMOL extension for building β-amino acid insertions and β-peptide sequences

Abstract

β-peptides are peptide-mimetics with wide biomedical and biotechnological applications. Their most peculiar feature is their readiness to fold into various secondary structures not found in their natural counterparts. Furthermore, β-amino acid insertions to natural polypeptides were found to provide unique features and also increase enzymatic stability. This is due to the additional methylene group in their backbone, which on the other hand makes it impossible to use the established algorithms and computational tools developed for α-peptides and proteins. An extension to the PyMOL v2.x molecular graphics environment is presented for β-peptides, which allows rapid graphical visualization and greatly simplified model building for computational studies, with special emphasis also put on direct formation of diverse folding states.

Keywords

• PyMOL
• β-peptides
• Foldamers