Adsorption of amino acids on graphene: assessment of current force fields

Dasetty, Siva; Barrows, John K.; Sarupria, Sapna

doi:10.1039/c8sm02621a

Cited by 25 publications

(39 citation statements)

References 108 publications

(115 reference statements)

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“…In particular, Trp exhibited the largest value of binding energy among the twenty proteinogenic amino acids. Trp is commonly recognized as the amino acid that most interacts with carbon nanoparticles, such as carbon nanotubes [ 55 ] or graphene [ 56 ]. The large indole group of tryptophan also demonstrated the largest interaction with the C 60 (

−5.0 kcal mol −1 ), followed by tyrosine (

−2.5 kcal mol −1 ), histidine (

−2.5 kcal mol −1 ), and phenylalanine (

−2.4 kcal mol −1 ).…”

Section: Resultsmentioning

confidence: 99%

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

Marforio

Calza

Mattioli

et al. 2021

IJMS

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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 configurations (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.

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−5.0 kcal mol −1 ), followed by tyrosine (

−2.5 kcal mol −1 ), histidine (

−2.5 kcal mol −1 ), and phenylalanine (

−2.4 kcal mol −1 ).…”

Section: Resultsmentioning

confidence: 99%

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

Marforio

Calza

Mattioli

et al. 2021

IJMS

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“…As mentioned above, a number of models can be used to represent the thermodynamic properties of amino acids in aqueous solutions, ranging from those with atomic details to coarse-grained approaches with the solvent treated implicitly as a dielectric continuum. ,,, Nonetheless, understanding the charge regulation of amino acids remains a challenge because it requires quantitative predictions of both equilibrium constants and activity coefficients over a broad range of conditions. In this work, we propose an augmented primitive model (APM) to represent amino acids in aqueous systems.…”

Section: Thermodynamic Model and Methodsmentioning

confidence: 99%

Charge Regulation of Natural Amino Acids in Aqueous Solutions

Gallegos

2020

J. Chem. Eng. Data

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The aim of this work is to develop a predictive model to describe the electrostatic behavior of 20 natural amino acids under diverse solution conditions. A coarse-grained model is proposed to account for the key ingredients of thermodynamic nonideality arising from the interaction of amino acids with various solvated ions in an aqueous solution including the molecular volume excluded effects, solvent-mediated electrostatic interactions, van der Waals attraction, and hydrophobic and hydration forces. With a small set of parameters characterizing the intermolecular interactions and dissociation equilibrium, the thermodynamic model is able to correlate extensive experimental data for the activity coefficients and solubility of amino acids in pure water and in aqueous sodium chloride solutions. Moreover, it predicts apparent equilibrium constants for the charge regulation of all amino acids in excellent agreement with experimental data. Importantly, the thermodynamic model allows for the extrapolation of the intrinsic equilibrium constants for amino-acids conversion among different charge states (viz., negative, neutral, and positive charges) thereby enabling the prediction of the charge behavior for all natural amino acids under arbitrary solution conditions.

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“…The molecular contacts of SS-GrBP5 with graphene were analogous to those of GrBP5-WT, save the Met-graphene interaction. Using these potential molecular contacts, a ballpark energetic estimate of the binding energy of the peptides was calculated based on MD determined free energies of adsorption available in the literature, provided in Table . As the IFA energies were determined on dried peptide monolayers, there may be some inherent error in the binding energy estimates as they are based on aqueous MD.…”

Section: Resultsmentioning

confidence: 99%

Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces

et al. 2019

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Key to the development of functional bioinorganic soft interfaces is the predictive control over the micron-scale assembly structure and energetics of biomolecules at solid interfaces. While assembly of labile biomolecules, such as short peptides, at interfaces is a great deal affected by the shape of the molecule, biomolecular conformations are prompted by external solution conditions, involving temperature, pH, and salt concentration. In this light, one can expect that the environmental conformational selection of aqueous biomolecules could potentially allow for fine-tuning of the equilibrium assembly structure at interfaces, as well as, the binding strength and molecular mobility within these assemblies. Here, we demonstrate the energetic and structural tailoring of two-dimensional surface assemblies of graphite-binding dodecapeptides, through the thermal selection of aqueous peptide conformations. Our findings based on a scanning probe energetic analysis, supplemented by molecular dynamics modeling, show that peptide-graphite and peptide−peptide intermolecular interactions strongly depend on the thermally selected molecular conformation and that the extent of the conformational change is directly related to the observed assembled structure. Enabled by these results was the design of a peptide with predictable binding and assembled structure, thus, suggesting environmental preconditioning of peptides as a means for controlling self-assembling active bioinorganic interfaces for bioelectronic implementations such as biomolecular fuel cells and biosensors.

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Adsorption of amino acids on graphene: assessment of current force fields

Abstract: We thoroughly investigate the differences in free energy of adsorption and the structures of the amino acids adsorbed on graphene with force fields.

Cited by 25 publications

References 108 publications

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

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

Charge Regulation of Natural Amino Acids in Aqueous Solutions

Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces

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