Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Tainah Dorina Marforio, Alessandro Calza, Edoardo Jun Mattioli, Francesco Zerbetto, Matteo Calvaresi
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	fullerene amino acids proteins peptides molecular dynamics simulations nanobiotechnology Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/71321e2ce50e4d01ac38aa3495d3a731
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:71321e2ce50e4d01ac38aa3495d3a731
record_format	dspace
spelling	oai:doaj.org-article:71321e2ce50e4d01ac38aa3495d3a7312021-11-11T17:02:58ZDissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>10.3390/ijms2221115671422-00671661-6596https://doaj.org/article/71321e2ce50e4d01ac38aa3495d3a7312021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11567https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C<sub>60</sub>. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol<sup>−1</sup>, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol<sup>−1</sup> 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<sub>60</sub> 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<sub>60</sub> binding.Tainah Dorina MarforioAlessandro CalzaEdoardo Jun MattioliFrancesco ZerbettoMatteo CalvaresiMDPI AGarticlefullereneamino acidsproteinspeptidesmolecular dynamics simulationsnanobiotechnologyBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11567, p 11567 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	fullerene amino acids proteins peptides molecular dynamics simulations nanobiotechnology Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	fullerene amino acids proteins peptides molecular dynamics simulations nanobiotechnology Biology (General) QH301-705.5 Chemistry QD1-999 Tainah Dorina Marforio Alessandro Calza Edoardo Jun Mattioli Francesco Zerbetto Matteo Calvaresi Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
description	Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C<sub>60</sub>. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol<sup>−1</sup>, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol<sup>−1</sup> 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<sub>60</sub> 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<sub>60</sub> binding.
format	article
author	Tainah Dorina Marforio Alessandro Calza Edoardo Jun Mattioli Francesco Zerbetto Matteo Calvaresi
author_facet	Tainah Dorina Marforio Alessandro Calza Edoardo Jun Mattioli Francesco Zerbetto Matteo Calvaresi
author_sort	Tainah Dorina Marforio
title	Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
title_short	Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
title_full	Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
title_fullStr	Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
title_full_unstemmed	Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C<sub>60</sub>
title_sort	dissecting the supramolecular dispersion of fullerenes by proteins/peptides: amino acid ranking and driving forces for binding to c<sub>60</sub>
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/71321e2ce50e4d01ac38aa3495d3a731
work_keys_str_mv	AT tainahdorinamarforio dissectingthesupramoleculardispersionoffullerenesbyproteinspeptidesaminoacidrankinganddrivingforcesforbindingtocsub60sub AT alessandrocalza dissectingthesupramoleculardispersionoffullerenesbyproteinspeptidesaminoacidrankinganddrivingforcesforbindingtocsub60sub AT edoardojunmattioli dissectingthesupramoleculardispersionoffullerenesbyproteinspeptidesaminoacidrankinganddrivingforcesforbindingtocsub60sub AT francescozerbetto dissectingthesupramoleculardispersionoffullerenesbyproteinspeptidesaminoacidrankinganddrivingforcesforbindingtocsub60sub AT matteocalvaresi dissectingthesupramoleculardispersionoffullerenesbyproteinspeptidesaminoacidrankinganddrivingforcesforbindingtocsub60sub
_version_	1718432183806328832

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

Ejemplares similares