article · 04/01/2021
Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects
Résumé
During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH3+, N–H, Cdouble bondO and NH2) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.
Citer cet article
Hernández, B., Pflüger, F., Kruglik, S.-G., & Ghomi, M. (2021). Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects. Journal of Molecular Graphics and Modelling, 102, article No. 107790. https://doi.org/10.1016/j.jmgm.2020.107790@article{Hernandez2021_316,
author = {Hernández, Belén and Pflüger, Fernando and Kruglik, Sergei G. and Ghomi, Mahmoud},
year = {2021},
month = {1},
title = {Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects},
journal = {Journal of Molecular Graphics and Modelling},
volume = {102},
pages = {article No. 107790},
abstract = {During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH3+, N–H, Cdouble bondO and NH2) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.},
url = {https://www.sciencedirect.com/science/article/abs/pii/S1093326320305799},
doi = {10.1016/j.jmgm.2020.107790},
}TY - JOUR
AU - Hernández, Belén
AU - Pflüger, Fernando
AU - Kruglik, Sergei G.
AU - Ghomi, Mahmoud
PY - 2021
DA - 2021/01/04
TI - Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects
JO - Journal of Molecular Graphics and Modelling
VL - 102
AB - During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH3+, N–H, Cdouble bondO and NH2) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.
SP - article No. 107790
DO - 10.1016/j.jmgm.2020.107790
UR - https://www.sciencedirect.com/science/article/abs/pii/S1093326320305799
ER -