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Systematic conformational investigations of peptoids and peptoid–peptide chimeras
Author(s) -
Brandt Wolfgang,
Herberg Thomas,
Wessjohann Ludger
Publication year - 2011
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21620
Subject(s) - ramachandran plot , polyproline helix , peptoid , chemistry , dihedral angle , steric effects , force field (fiction) , peptide , molecular dynamics , crystallography , computational chemistry , stereochemistry , protein structure , molecule , hydrogen bond , organic chemistry , biochemistry , artificial intelligence , computer science
Abstract Peptoids are originally defined as N‐substituted oligoglycine derivatives, and in a broader definition as N‐substituted peptides (peptoid–peptide chimeras). Both types were systematically investigated by force field calculations. The Merck MMFF and YASARA2 force fields were shown to be, among others, the most suitable ones for conformational investigations of peptoids with no missing parameterizations, in contrast to AMBER or CHARMM. Ramachandran‐like plots were calculated for dipeptoids and chimeras using energy calculations and grid searches by varying the dihedral angels Φ and Ψ in steps of 10° for s‐ cis ‐ and s‐ trans amide bonds. Barriers as well as low energy conformations are compared to peptide Ramachandran plots, showing that peptoids have both, more barriers due to additional steric interactions as well as access to minimum conformations not accessible by peptides. Low energy conformations of dimers were used as starting conformations of higher oligomers of the peptoids for extensive molecular dynamics simulations over 10 or 20 ns with the YASARA2 force field and an explicit water solvent box to evaluate their potential to form secondary structural elements. Especially peptoids with aminoisobutyric acid‐like monomer units were found to form left‐handed or polyproline‐like helices also known from less common natural peptides. Furthermore, new secondary structures appear feasible based on stable conformations outside the allowed areas of the Ramachandran plot for peptides, but allowed for peptoids. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 651–668, 2011.