A Peptoid Ribbon Secondary Structure

Crapster, J. Aaron; Guzei, Ilia A.; Blackwell, Helen E.

doi:10.1002/anie.201208630

Cited by 109 publications

(130 citation statements)

References 54 publications

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“…In the threaded loop peptoid, the amide backbone alternates between Z S c and Z S t with a Z R t break midway along the backbone . The peptoid ribbon also shows a repeating pattern, alternating between Z R t and Z S c. Finally, the peptoid square helix also shows an interesting pattern with a 4‐fold repeat of Z R t to Z R c to Z S t to Z S c. These structures share similar motifs in which the trans and cis backbones or Z S and Z R alternate in a periodic fashion, giving rise to these unique peptoid structures. Different periodic combinations of Z S and Z R may lead to yet undiscovered peptoid structures.…”

Section: Applying Nomenclature To Peptoid Structuresmentioning

confidence: 96%

“…An analysis of the ϕ and ψ angles present in published peptoid structures (41 crystal structures, 5 NMR structures, 132 total dihedral combinations, Supporting Information Table S1) reveal that trans‐ and cis ‐amides show similar preferences for ϕ and ψ combinations, with trans ‐amide and cis ‐amide residues primarily occupying two main regions that span across the bottom and top edges of the Ramachandran plot (ϕ ≈ 70° and −70° and ψ ≈ 180° and −180°, Figure ). Replotting these data to represent ϕ and ψ from 0° to 360° (adding 360° to ϕ and ψ values below 0°, Figure C,F) shows that the preferred dihedrals lay in the same low‐energy regions for trans and cis disarcosine calculatations, with regions centered around (70°, 180°) and (290°,180°) (Figure C,F).…”

Section: The Ramachandran Plotmentioning

confidence: 99%

“…The number of peptoid structures and peptoid nanostructures is growing rapidly. The peptoid specific nomenclature described above can easily be applied to repeating structures, such as peptoid helices and peptoid sheets, but can also be applied to other peptoid structures such as a threaded loop, a peptoid ribbon, and a square peptoid helix . Each of these structures can be generated almost entirely by different combinations of Z S c , Z S t , Z R c , and Z R t (Table ).…”

Section: Applying Nomenclature To Peptoid Structuresmentioning

confidence: 99%

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Stereochemistry of polypeptoid chain configurations

et al. 2019

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Like polypeptides, peptoids, or N‐substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N‐substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty‐two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.

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Section: Applying Nomenclature To Peptoid Structuresmentioning

confidence: 96%

Section: The Ramachandran Plotmentioning

confidence: 99%

Section: Applying Nomenclature To Peptoid Structuresmentioning

confidence: 99%

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Stereochemistry of polypeptoid chain configurations

et al. 2019

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“…Peptoid chemists have developed specific side chains capable of controlling the amide conformation by forming local interactions with the backbone. This has enabled the design of peptoid oligomers exhibiting various privileged secondary structures, such as helices (polyproline type I [PPI], polyproline type II, and η‐helix), ribbons, loops, and Σ‐strands . Despite a modest cis ‐directing control on the tertiary amide bond isomerism, the chiral aromatic phenylethyl side chain (spe) has been used extensively to promote the PPI peptoid helical conformation.…”

Section: Introductionmentioning

confidence: 99%

NCα‐gem‐dimethylated peptoid side chains: A novel approach for structural control and peptide sequence mimetics

et al. 2019

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The design of linear peptoid oligomers adopting well‐defined secondary structures while mimicking defined peptide primary sequences is a major challenge in the context of drug discovery. To this end, chemists have developed cis‐inducing peptoid side chains to build robust polyproline type I helices. However, the number of efficient examples remains scarce and chemical diversity accessible through the use of these side chains is limited. Herein, we introduce an array of NCα‐gem‐dimethylated peptoid residues mimicking proteinogenic amino acids. Submonomer synthesis and block‐coupling approaches were explored to access heterooligomers incorporating these novel types of side chains. NMR studies of monomer and trimer models showed that the NCα‐gem‐dimethylated groups exert complete cis control on the backbone amide conformation. Lastly, a preliminary molecular modeling study gave an insight into the preferred orientation of the substituents of the NCα‐gem‐dimethyl side chains relative to the peptoid backbone.

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“…1,2 Peptoids are a class of robust, informationrich, chemically-diverse peptidomimetic polymers composed of N-substituted glycine monomers. 3 Like peptides, they have the ability to adopt distinct secondary structures such as ribbons, 4 helices, 5,6 sheets, 7 turns, 8 and cyclic structures; 9,10 however, the lack of a backbone hydrogen bond donor (NH) and chirality forces peptoid oligomers to conform to different folding rules as compared to their peptide counterparts. 11 Peptoids can be engineered to adopt multiple two and three-dimensional supramolecular assemblies including superhelices, 12 multi-helical bundles 13,14 and two-dimensional nanosheets.…”

mentioning

confidence: 99%