Classical atomistic simulations of protein adsorption on carbon nanomaterials

Abstract

Carbon nanomaterials are receiving an increasingly large interest in a variety of fields, including also nanomedicine. In this area, much attention is devoted to investigating and modeling the behavior of these nanomaterials when they interact with biological fluids and with biological macromolecules, in particular proteins and oligopeptides. The interaction with these molecules is in fact crucial to understand and predict the efficacy of nanomaterials as drug carriers or therapeutic agents as well as their potential toxicity when they occupy the active site of a protein or severely affect the secondary and tertiary structure, or even the local dynamics, thus inhibiting their biological function. In this review, therefore, we describe the most recent work carried out in the last few years to model the interaction between carbon nanomaterials, either pristine or functionalized, and proteins or oligopeptides using classical atomistic methods, mainly molecular dynamics simulations. The attention is focused on 0dimensional fullerenes, mainly C 60 , on 1-dimensional carbon nanotubes, mostly the single-walled armchair and some chiral ones, and on 2-dimensional graphene and graphyne, the latter containing also sp hybridized atoms in addition to the sp 2 ones common to the other carbon nanomaterials.

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

“…The atomistic details of the interaction between amino acids and fullerene were obtained using molecular dynamics (MD) simulations. MD simulations are a powerful tool to unravel the mechanisms of interaction of proteins with carbon nanomaterials, providing detailed structural information [ 43 ]. An analysis of the binding components of the energy was performed by using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) methodologies [ 44 ].…”

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease

“…The atomistic understanding of the interactions of C 60 with SARS-CoV-2 M pro is crucial for real applications of nanomolecules in medicine [ 26 ]. MD simulations represent a powerful tool to investigate such interactions [ 55 ]. Starting from the docking pose, 100 ns of molecular dynamics simulations was carried out.…”

Carbon Nanomaterials Modified Biomimetic Dental Implants for Diabetic Patients

“…Carbon nanomaterials (CNMs) have unique features that make them one of the most promising nanomaterials in dentistry and are used as drugs themselves or gene carriers [147,148]. For example, graphene has been applied as a nano drug with a high pharmaceutical efficiency, and low toxicity of the CNMs and anti-inflammatory properties have been achieved by combining CNMs with different drugs, proteins, nucleic acids, and bioactive peptides [138].…”