Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption

Hydration and Antibiofouling Behavior of Zwitterionic Polycarboxybetaine-Grafted Surfaces Studied with Atomistic Simulations

Fouling-resistant coating materials have important applications in marine industry and biomedicine. Zwitterionic carboxybetaine polymers have demonstrated robust antibiofouling functionalities in experiments. In this work, we performed atomistic molecular dynamics simulations to study the molecular mechanism of hydration and antibiofouling of poly(carboxybetaine acrylamide) (polyCBAA) brush surfaces. We focused on the zwitterionic carboxybetaine, which has only a short methylene spacer between the positive quaternary ammonium and the negative carboxylate groups. Our study shows that a large amount of water is present within the polyCBAA surface, and a condensed water layer of single-molecular thickness covers the top of the polymer surface. Moreover, the clustering of the zwitterionic chains results in an amorphous structure of the polymer surface, a reduced degree of order in the interfacial water molecules, and weak protein attachment. The low protein desorption free energy demonstrates that the polyCBAA surface exhibits strong fouling resistance due to its significant interfacial hydration and the small dipole moment of the carboxybetaine group, minimizing protein-surface electrostatic interactions. Our study at the molecular level will be important to the future development of zwitterionic materials.

Unveiling the potential of RADA16-I peptide-coated silver nanoparticles for biomedical uses: a computational study

Nanomaterials, specifically silver nanoparticles (AgNPs), have demonstrated great potential in biomedical applications due to their unique properties, such as antimicrobial activity and conductivity. One promising strategy to improve their biocompatibility and functional specificity is through the functionalization of AgNPs with peptides. By attaching peptides to the surface of AgNPs, their interaction with biological systems can be enhanced and tailored for specific applications. This computational study uses classical molecular dynamics and enhancement sampling techniques to investigate the interaction between AgNPs and RADA16-I peptides, as well as their derivative CLKRADA16-I. It utilizes classical molecular dynamics and enhanced sampling methods to gain insights into the structural information and details of their interaction. Furthermore, this study addresses the need for a better understanding of the interaction between composite materials made of nanoparticles and peptides. Our results demonstrate that the incorporation of the CLK motif significantly augments both structural stability and the binding affinity of peptides to silver nanoparticles. Through computational simulations, we observed that peptides modified with the CLK motif (CLKRADA16-I) exhibit a higher binding affinity toward a silver surface model, with the adsorption energy increasing by up to 4.2 kcal mol-1 relative to unmodified peptides. This calculated interaction energy boosts adsorption and surface coverage, facilitating a packed and more effective peptide coating on the silver nanoparticles. These findings pave the way for the advancement of AgNPs as versatile agents in nanomedicine, particularly necessitating precise molecular recognition and robust bioactive scaffolding. Our study enhances the understanding of nanoparticle-peptide conjugates and their implications for designing next-generation nanomaterials.

Biosynthesis and Characterization of Silver Nanoparticles and Simvastatin Association in Titanium Biofilms

INTRODUCTION

Simvastatin is an antilipidemic drug that has already demonstrated antibacterial activities on oral and non-oral microorganisms. Silver nanoparticles also exhibit antimicrobial properties, particularly for coating implant surfaces. In this study, we evaluated the effects of combining simvastatin with silver nanoparticles on the formation and viability of biofilms consolidated on titanium discs.

METHODS

Silver nanoparticles were first biosynthesized using the fungus Fusarium oxysporum and then characterized using Dynamic Light Scattering, X-ray Diffraction, Transmission Electron Microscopy, and energy dispersive spectroscopy. Species of Streptococcus oralis, Streptococcus mutans, Porphyromonas gingivalis, Methicillin-sensitive Staphylococcus aureus, and Methicillin-resistant Staphylococcus aureus were used and tested using Minimum Inhibitory Concentration assays with concentrations of silver nanoparticles and simvastatin alone and in combination. Biofilm inhibition and viability tests were performed on titanium surfaces. Toxicity tests were also performed on Galleria mellonella moth larvae.

RESULTS

The silver nanoparticles had a spherical shape without the formation of aggregates as confirmed by Transmission Electron Microscopy. Dynamic Light Scattering revealed nanoparticles with an average diameter of 53.8 nm (±1.23 nm), a polydispersity index of 0.23 and a zeta potential of -25 mV (±2.19 mV). The silver nanoparticles inhibited the growth of the strains tested in the range of 0.001592 and 63.75, while simvastatin alone inhibited the growth of the same strains in the range of 3.125-62.5 µg/mL. The antibacterial activity test of the combination of the two substances showed a reduction in the Minimum Inhibitory Concentration of about two to eight times, showing synergistic effects on Staphylococcus aureus and additive effects on Streptococcus oralis and Porphyromonas gingivalis. As for biofilm, sub-inhibitory concentrations of the combination of substances showed better antibacterial activity in inhibiting the formation of Streptococcus oralis biofilm, and this combination also proved effective in eradicating already established biofilms compared to the substances alone. The combination of silver nanoparticles and simvastatin showed low toxicity to Galleria mellonella moth larvae.

CONCLUSIONS

The results presented indicate that the combination of the two substances could be an alternative for the prevention and reduction of biofilms on implants. These findings open up new possibilities in the search for alternatives for the treatment of peri-implant infections, as well as the possibility of using lower doses compared to single drugs, achieving the same results and reducing potential toxic effects.

Recent Advances in Simulation Studies on the Protein Corona

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on the nanoparticle surface, known as the "protein corona". Since the protein corona influences the size, shape, and surface properties of nanoparticles, it can modulate their circulating lifetime, cytotoxicity, and targeting efficiency. Therefore, understanding the mechanism of protein corona formation at the atomic scale is crucial, which has become possible due to advances in computer power and simulation methodologies. This review covers the following topics: (1) the structure, dynamics, and composition of protein corona on nanoparticles; (2) the effects of protein concentration and ionic strength on protein corona formation; (3) the effects of particle size, morphology, and surface properties on corona formation; (4) the interactions among lipids, membranes, and nanoparticles with the protein corona. For each topic, mesoscale, coarse-grained, and all-atom molecular dynamics simulations since 2020 are discussed. These simulations not only successfully reproduce experimental observations but also provide physical insights into the protein corona formation. In particular, these simulation findings can be applied to manipulate the formation of a protein corona that can target specific cells, aiding in the rational design of nanomedicines for drug delivery applications.

Highly elastic, fatigue-resistant, antibacterial, conductive, and nanocellulose-enhanced hydrogels with selenium nanoparticles loading as strain sensors

The fabrication of highly elastic, fatigue-resistant and conductive hydrogels with antibacterial properties is highly desirable in the field of wearable devices. However, it remains challenging to simultaneously realize the above properties within one hydrogel without compromising excellent sensing ability. Herein, we fabricated a highly elastic, fatigue-resistant, conductive, antibacterial and cellulose nanocrystal (CNC) enhanced hydrogel as a sensitive strain sensor by the synergistic effect of biosynthesized selenium nanoparticles (BioSeNPs), MXene and nanocellulose. The structure and potential mechanism to generate biologically synthesized SeNPs (BioSeNPs) were systematically investigated, and the role of protease A (PrA) in enhancing the adsorption between proteins and SeNPs was demonstrated. Additionally, owing to the incorporation of BioSeNPs, CNC and MXene, the synthesized hydrogels showed high elasticity, excellent fatigue resistance and antibacterial properties. More importantly, the sensitivity of hydrogels determined by the gauge factor was as high as 6.24 when a high strain was applied (400-700 %). This study provides a new horizon to synthesize high-performance antibacterial and conductive hydrogels for soft electronics applications.

Superoxide Dismutase Catalyzed Size-Adjustable Selenium Nanoparticles in Saccharomyces boulardii

Selenium nanoparticles (SeNPs) are important and safe food and feed additives that can be used for dietary supplementation. In this study, a mutagenic strain of Saccharomyces boulardii was employed to obtain biologically synthesized SeNPs (BioSeNPs) with the desired particle size by controlling the dosage and duration of sodium selenite addition, and the average particle size achieved was 55.8 nm with protease A encapsulation. Transcriptomic analysis revealed that increased expression of superoxide dismutase 1 (SOD1) in the mutant strain effectively promoted the synthesis of BioSeNPs and the formation of smaller nanoparticles. Under sodium selenite stress, the mutant strain exhibited significantly increased expression of glutathione peroxidase 2 (GPx2), which was significantly greater in the mutant strain than in the wild type, facilitating the synthesis of glutathione selenol and providing abundant substrates for the production of BioSeNPs. Furthermore, based on the experimental results and transcriptomic analysis of relevant genes such as sod1, gpx2, the thioredoxin reductase 1 gene (trr1) and the thioredoxin reductase 2 gene (trr2), a yeast model for the size-controlled synthesis of BioSeNPs was constructed. This study provides an important theoretical and practical foundation for the green synthesis of controllable-sized BioSeNPs or other metal nanoparticles with potential applications in the fields of food, feed, and biomedicine.

Determination of protein conformation and orientation at buried solid/liquid interfaces

Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.

Understanding Conformational Changes in Human Serum Albumin and Its Interactions with Gold Nanorods: Do Flexible Regions Play a Role in Corona Formation?

The importance of protein-nanoparticle (NP) conjugates for biomedical applications has seen an exponential growth in the past few years. The protein corona formation on NPs with human serum albumin (HSA), being the most abundant protein in blood serum, has become one of the most studied protein analyses under NP-protein interactions as HSA is readily adsorbed on the surface of the NPs. Understanding the fate of the NPs in physiological media along with the change in biological responses due to the formation of the protein corona thus becomes important. We analyzed the HSA protein corona formation on gold nanorods (AuNRs) through different spectroscopic studies in addition to the effects of change in the protein concentration on the protein-NP interactions. Different imaging techniques such as high-resolution transmission electron microscopy, field emission scanning electron microscopy, and atomic force microscopy were used to determine the morphology and the dimensions of the nanorods and the protein-nanorod conjugates. Fourier-transform infrared data showed a reduction in the α-helix content and an increase in β-sheet content for the HSA-AuNR conjugate compared to the native protein. A decrease in steady-state fluorescence intensity occurred with instant addition of AuNR to HSA showing better and efficient quenching of Trp fluorescence for the lower concentration of protein. Time-correlated single photon counting results showed greater energy transfer efficiency and faster decay rate for higher concentrations of proteins. The circular dichroism study gives insight into the secondary structural changes due to unfolding, and a greater change was observed for lower concentrations of protein due to a thermodynamically stable protein corona formation. Surface-enhanced Raman spectroscopy (SERS) indicated the presence of aromatic residues such as Phe, Tyr, and Cys that appear to be close to the surface of the AuNRs in addition to hydrophobic interactions between AuNR and the protein. The disordered and flexible regions mapped onto HSA (PDB: 1AO6), predicted by the intrinsically disordered region predictors, point toward the interactions of similar residues with the nanorods observed from SERS and fluorescence studies. These studies could provide a clearer understanding of the interactions between HSA and AuNRs for possible biological applications.

Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface

Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a Go̅-like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low-dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the π-π stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.