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Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions

by Avneet Saini
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 143 - Number 7
Year of Publication: 2016
Authors: Avneet Saini
10.5120/ijca2016910265

Avneet Saini . Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions. International Journal of Computer Applications. 143, 7 ( Jun 2016), 46-56. DOI=10.5120/ijca2016910265

@article{ 10.5120/ijca2016910265,
author = { Avneet Saini },
title = { Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions },
journal = { International Journal of Computer Applications },
issue_date = { Jun 2016 },
volume = { 143 },
number = { 7 },
month = { Jun },
year = { 2016 },
issn = { 0975-8887 },
pages = { 46-56 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume143/number7/25093-2016910265/ },
doi = { 10.5120/ijca2016910265 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T23:45:45.914001+05:30
%A Avneet Saini
%T Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions
%J International Journal of Computer Applications
%@ 0975-8887
%V 143
%N 7
%P 46-56
%D 2016
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Conformations of achiral and chiral aromatic homo-polypeptoids of Nphe, Nspe and Nrpe were studied by quantum mechanics and molecular dynamics approaches. The amide bond geometry in model peptoids Ac-X-NMe2 could be both cis and trans and the Nphe peptoids adopted degenerate conformations of opposite handedness with Φ, Ψ values of ~ ± 120º, ± 150º with trans amide bond geometry. This degeneracy was lifted with increase in chain length; in favor of the structure with Φ = -120º, Ψ = -150º. Polypeptoids of Nspe and Nrpe with and without protecting groups populated states with Φ, Ψ values of ~ 110º, 155º & -110º, -165º respectively with trans amide bond geometry. Simulation studies in water revealed that with protecting groups peptoid Ac-(Nspe/Nrpe)5-NMe2 populated with cis amide bond geometry in PP type I and inverse PP type I helices respectively due to interactions between the solvent molecules and carbonyl oxygens of the backbone. Without protecting groups these polypeptoids populated poly-L-proline type II conformations. In DMSO these peptoids were shown to populate in PP type-I and inverse PP type-I helices and without protecting groups they could be realized in PP type-I as well as inverse PP type-I conformation whereas the peptoid -Nrpe6-NH2 could be realized in inverse PP type-I conformation. Analysis of simulation results as a function of time ruled out amide bond inter-conversions between cis and trans geometry. Hence, like polyproline peptoids can also be exploited as molecular spacers.

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Index Terms

Computer Science
Information Sciences

Keywords

biomimetic Nphe/Nrpe/Nspe peptoids simulations conformational analysis PP and inverse PP structures.

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