Computational insight on the interaction of common blood proteins with gold nanoparticles

Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems

What can we learn from atomistic simulations of bioactive glasses?

In the last decades, most experimental efforts have been devoted to design bioactive glasses (please consult the Editor’s note in order to clarify the usage of the terms bioglass, bioactive glass and biocompatible glasses) with enhanced biological and mechanical properties by adding specific ions to known bioactive compositions. Concurrently, computational research has been focused to the understanding of the relationships between bioactivity and composition by rationalization of the role of the doping ions. Thus, a deep knowledge of the structural organization of the constituent atoms of the bioactive glasses has been gained by the employment of ab initio and classical molecular dynamics simulations techniques. This chapter reviews the recent successes in this field by presenting, in a concise way, the structure–properties relationships of silicate, phospho-silicate and phosphate glasses with potential bioactive properties

Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to β-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation

O2Activation over Ag-Decorated CeO2(111) and TiO2(110) Surfaces: A Theoretical Comparative Investigation

Periodic spin-polarized hybrid density functional theory calculations have been performed to investigate the reactivity of pristine, O-defective, and Ag-decorated CeO2(111) and TiO2(110) surfaces with a small Ag10 cluster toward O2. The adsorption of O2 and its subsequent dissociation have been studied in order to provide a better understanding of the role of the oxide, the metallic nanoparticle, and their interaction in the reactivity of composite metal/metal oxide materials toward O2, as potential catalysts to this reaction. Structural, energetic, electronic, and vibrational properties of all species involved in the different reaction paths considered have been fully characterized. On the stoichiometric surfaces, Ag10 is oxidized and reduces surface Ce4+/Ti4+ ions, while on the O-defective surfaces, the adhesion of silver is promoted only on CeO2 but unfavored on TiO2. On the other hand, on the silver-free supports, O2 strongly adsorbs at vacancies and preferentially reduces to peroxide. When no O vacancies are considered on the Ag10-decorated supports, the net positive charge on Ag10 actually prevents the adsorption and reduction of O2. Instead, when O vacancies are included, two reaction pathways are observed; oxygen molecules can weakly absorb on the silver cluster as a superoxide moiety or strongly adsorb at the vacancy as peroxide. The dissociation of the O-O bond of the peroxide is favored both from the thermodynamic and kinetic points of view in silver-decorated surfaces, in contrast with the silver-free cases. In addition, Ag10/CeO2 shows higher activity toward the O2 adsorption and dissociation than Ag10/TiO2, which can be related both to the higher ionicity and superior electron storage/release ability of ceria with respect to titania, thus leading to the weakening of the O-O bond and providing lower activation barriers for oxygen reduction. These results deepen the current understanding of the reactivity of metal/metal oxide composites toward O2, especially elucidating how the surface stoichiometry affects the charge state of the metal clusters, and hence the reactivity of these interfaces toward O2, with potential important consequences when such composites are considered for catalytic applications

Computational insights into the binding of monolayer-capped gold nanoparticles onto amyloid-\u3b2 fibrils

Amyloids-\u3b2 (A\u3b2) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with A\u3b2(1-40) and A\u3b2(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-\u3b2 fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions

Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations

Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass–ceramics by atomistic modeling

A DFT approach to the surface-enhanced raman scattering of 4-cyanopyridine adsorbed on silver nanoparticles

A Surface-Enhanced Raman Scattering (SERS) spectrum of 4-cyanopyridine (4CNPy) was recorded on silver plasmonic nanoparticles and analyzed by using Density Functional Theory (DFT) calculations. Two simple molecular models of the metal\u20134CNPy surface complex with a single silver cation or with a neutral dimer (Ag+ \u20134CNPy, Ag2 \u20134CNPy), linked through the two possible interacting sites of 4CNPy (aromatic nitrogen, N, and nitrile group, CN), were considered. The calculated vibrational wavenumbers and intensities of the adsorbate and the isolated species are compared with the experimental Raman and SERS results. The analysis of the DFT predictions and the experimental data indicates that 4CNPy adsorbs preferentially on neutral/charged active sites of the silver nanoparticles through the nitrogen atom of the aromatic ring with a perpendicular orientation