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 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 configura-tions (i.e., regions of the Ramachandran plot) that were absent when C60 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 C60 binding.

Dissecting the supramolecular dispersion of fullerenes by proteins/peptides: Amino acid ranking and driving forces for binding to c60

Marforio T. D.
;
Mattioli E. J.;Zerbetto F.;Calvaresi M.
2021

Abstract

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 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 configura-tions (i.e., regions of the Ramachandran plot) that were absent when C60 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 C60 binding.
Marforio T.D.; Calza A.; Mattioli E.J.; Zerbetto F.; Calvaresi M.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/849600
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