Molecular modeling studies of peptoid polymers

Weiser, Laura J.; Santiso, Erik E.

doi:10.3934/matersci.2017.5.1029

Cited by 20 publications

(30 citation statements)

References 67 publications

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“…This is further corroborated by molecular simulations . These studies, which were validated by NMR experiments, show that peptoid helix formation is a function of temperature and chain length ultimately proving that as chain length increases helicity increases and peptoid helix formation is thermodynamically favorable …”

Section: Resultssupporting

confidence: 59%

Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength

et al. 2019

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Peptoids are peptidomimetic oligomers that predominantly harness similarities to peptides for biomimetic functionality. They have potential for use in biomedical applications and biosensors due to resistance to proteolytic degradation and low immunogenicity. The incorporation of chiral, aromatic side chains in the peptoid sequence allows for the formation of distinct secondary structures and self‐assembly into supramolecular assemblies, including microspheres. Peptoid microspheres can be coated onto substrates for potential use in biosensor technologies, tissue engineering platforms, and drug‐delivery systems. In order to be useful for these applications, the peptoid coatings must be robust under physiological conditions. In this study, we report the effects of various conditions on the peptoid microsphere coatings, including (i) helicity, (ii) temperature, (iii) pH, and (iv) ionic strength. These studies show that microsphere size decreases with increasing peptoid helicity and the positively charged side chains are positioned on the outside of the microspheres. The peptoid microsphere coatings are robust under physiological conditions but degrade in acidic conditions (pH < 7) and at low ionic strengths (<150 μM).

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Section: Resultssupporting

confidence: 59%

Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength

et al. 2019

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“…Computational studies have played an important role in defining how certain side chains can induce peptoid backbone folding. In 1997, Armand used molecular mechanics calculations to show that peptoids with repeating chiral N‐(S)‐1‐phenylethylglycine (NSPE) side chains form stable poly‐proline type I (PPI) helices .…”

Section: Introductionmentioning

confidence: 99%

A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds

Weiser

Santiso

2019

J Comput Chem

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Peptoids, or poly-n-substituted glycines, are peptide-like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of selfassembling structures based on the type and sequence of the side chains attached to their backbones. All-atom molecular dynamics simulations have been useful in predicting the conformational structures of proteins and will be valuable tools for identifying combinations of peptoid side chains that may form interesting folded structures. However, peptoid models must address a major degree of freedom not common in proteins -the cis/trans isomerization of the peptide bond. This work presents CHARMM general force field (CGenFF) parameters developed to accurately represent peptoid conformational behavior, with an emphasis on a correct representation of both the cis and trans isomers of the peptoid backbone. These parameters are validated against experimental and quantum mechanics data and used to simulate three peptoid side chains in explicitly solvated systems.

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“…3,4,6,9,58 Based on various sequence-structure analyses, nowadays, both the rational design and the computer-aided structure prediction of peptoid foldamers is possible. 1,5,115,[130][131][132][133][134]…”

Section: Combinatorial Libraries For the Discovery Of Peptoid Foldamersmentioning

confidence: 99%

Bio-instructive materials on-demand – combinatorial chemistry of peptoids, foldamers, and beyond

et al. 2021

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Molecular modeling studies of peptoid polymers

Cited by 20 publications

References 67 publications

Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength

Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength

A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds

Bio-instructive materials on-demand – combinatorial chemistry of peptoids, foldamers, and beyond

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