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Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C(60). The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol(−1), while the contribution to the binding due to the amino acid side...

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Autores principales: Marforio, Tainah Dorina, Calza, Alessandro, Mattioli, Edoardo Jun, Zerbetto, Francesco, Calvaresi, Matteo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8583719/
https://www.ncbi.nlm.nih.gov/pubmed/34768997
http://dx.doi.org/10.3390/ijms222111567
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author Marforio, Tainah Dorina
Calza, Alessandro
Mattioli, Edoardo Jun
Zerbetto, Francesco
Calvaresi, Matteo
author_facet Marforio, Tainah Dorina
Calza, Alessandro
Mattioli, Edoardo Jun
Zerbetto, Francesco
Calvaresi, Matteo
author_sort Marforio, Tainah Dorina
collection PubMed
description Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C(60). The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol(−1), while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol(−1) for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C(60) was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C(60) binding.
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spelling pubmed-85837192021-11-12 Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60) Marforio, Tainah Dorina Calza, Alessandro Mattioli, Edoardo Jun Zerbetto, Francesco Calvaresi, Matteo Int J Mol Sci Article Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C(60). The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol(−1), while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol(−1) for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C(60) was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C(60) binding. MDPI 2021-10-26 /pmc/articles/PMC8583719/ /pubmed/34768997 http://dx.doi.org/10.3390/ijms222111567 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Marforio, Tainah Dorina
Calza, Alessandro
Mattioli, Edoardo Jun
Zerbetto, Francesco
Calvaresi, Matteo
Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title_full Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title_fullStr Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title_full_unstemmed Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title_short Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C(60)
title_sort dissecting the supramolecular dispersion of fullerenes by proteins/peptides: amino acid ranking and driving forces for binding to c(60)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8583719/
https://www.ncbi.nlm.nih.gov/pubmed/34768997
http://dx.doi.org/10.3390/ijms222111567
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