
doi: 10.1002/bip.21620
pmid: 22180911
AbstractPeptoids 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.
Peptoids, Molecular Structure, Computer Simulation, Molecular Dynamics Simulation, Peptides, Protein Structure, Secondary
Peptoids, Molecular Structure, Computer Simulation, Molecular Dynamics Simulation, Peptides, Protein Structure, Secondary
| selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 25 | |
| popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network. | Top 10% | |
| influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Average | |
| impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network. | Top 10% |
