Dataset Information

Tuning conformation and properties of peptidomimetic backbones through dual N/C?-substitution.

ABSTRACT: We demonstrate that changing the backbone between peptides, peptoids and the underexplored dual N/C?-substituted peptoids analogues allows for control over the preferred conformation of the intrinsically disordered biomimetic oligomers. The conformation tunability is directly probed using electron paramagnetic resonance (EPR), and is shown to manifest itself in differences in the nanoparticle-oligomer hybridization propensity.

SUBMITTER: Kaminker R

PROVIDER: S-EPMC6089238 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Tuning conformation and properties of peptidomimetic backbones through dual N/C<sub>α</sub>-substitution.

Kaminker R R Kaminker I I Gutekunst W R WR Luo Y Y Lee S S Niu J J Han S S Hawker C J CJ

Chemical communications (Cambridge, England) 20180501 41

We demonstrate that changing the backbone between peptides, peptoids and the underexplored dual N/Cα-substituted peptoids analogues allows for control over the preferred conformation of the intrinsically disordered biomimetic oligomers. The conformation tunability is directly probed using electron paramagnetic resonance (EPR), and is shown to manifest itself in differences in the nanoparticle-oligomer hybridization propensity. ...[more]

PMID: 29726557

Similar Datasets

Project description:Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones.

Dataset Information

Tuning conformation and properties of peptidomimetic backbones through dual N/C?-substitution.

Publications

Tuning conformation and properties of peptidomimetic backbones through dual N/C<sub>α</sub>-substitution.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure