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image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Biopolymersarrow_drop_down
image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
Biopolymers
Article . 2011 . Peer-reviewed
License: Wiley Online Library User Agreement
Data sources: Crossref
Biopolymers
Article . 2012
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Systematic conformational investigations of peptoids and peptoid–peptide chimeras

Authors: Wolfgang, Brandt; Thomas, Herberg; Ludger, Wessjohann;

Systematic conformational investigations of peptoids and peptoid–peptide chimeras

Abstract

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.

Keywords

Peptoids, Molecular Structure, Computer Simulation, Molecular Dynamics Simulation, Peptides, Protein Structure, Secondary

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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).
BIP!Citations provided by BIP!
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.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
25
Top 10%
Average
Top 10%
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