Modulating the biological function of protein by tailoring the adsorption orientation on nanoparticles

Surface-Engineered Nanoparticles Enhance the Peroxidase Activity of Heme-Containing Proteins

Enzymes interfaced with nanomaterials often lose more than 90% of their activity; yet, some nanomaterials have been shown to enhance enzyme activity. However, these findings are largely observational and lack clear and actionable design principles. Systematic studies are needed to develop nanomaterials that can control and tune enzyme activity. Given that enzyme-nanomaterial interactions are mediated by their surface functional groups, we hypothesized that engineering nanoparticle surfaces could allow for controlled tuning of the enzyme activity. In this study, we used peptide-functionalized gold nanoparticles (PGNPs) as a programmable platform to investigate how surface functionalization affects enzyme activity. By varying the peptide sequences, we examined the effects of charge, hydrophobicity, peptide length, and structure on the peroxidase activity of cytochrome C (Cyt C). Our results showed that carefully designed ligands can significantly enhance enzyme activity, exceeding 10-fold compared with the free enzyme. Molecular dynamics simulations provided insights into the molecular basis of these findings, revealing the preferred orientation of Cyt C upon adsorption and key interaction patterns between the enzyme and peptide ligands, thus bridging experimental results with a mechanistic understanding. Furthermore, PGNPs proved to be a versatile platform for boosting peroxidase activity of other heme-containing proteins such as lactoperoxidase, hemoglobin, and catalase by 13.4-, 3.9-, and 4.2-fold, respectively. This study highlights the potential of nanoparticle surface engineering to activate enzymes at interfaces in a tunable manner, offering a promising alternative to protein engineering for developing biocatalysts.

Computer-aided nanodrug discovery: recent progress and future prospects

Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.

Molecular Dynamics Simulations of Soft and Reactive Landing of Proteins Desorbed by Argon Cluster Bombardment

Reactive molecular dynamics (MD) simulations were conducted to investigate the soft and reactive landing of hyperthermal velocity proteins transferred to a vacuum using large argon clusters. Experimentally, the interaction of argon cluster ion beams (Ar1000-5000+) with a target biofilm was previously used in such a manner to transfer lysozymes onto a collector with the retention of their bioactivity, paving the way to a new solvent-free method for complex biosurface nanofabrication. However, the experiments did not give access to a microscopic view of the interactions needed for their full understanding, which can be provided by the MD model. Our reactive force field simulations clarify the landing mechanisms of the lysozymes and their fragments on collectors with different natures (gold- and hydrogen-terminated graphite). The results highlight the conditions of soft and reactive landing on rigid surfaces, the effects of the protein structure, energy, and incidence angle before landing, and the adhesion forces with the collector substrate. Many of the obtained results can be generalized to other soft and reactive landing approaches used for biomolecules such as electrospray ionization and matrix-assisted laser desorption ionization.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

Molecular Surface Quantification of Multifunctionalized Gold Nanoparticles Using UV-Visible Absorption Spectroscopy Deconvolution

Multifunctional gold nanoparticles (AuNPs) are of great interest, owing to their vast potential for use in many areas including sensing, imaging, delivery, and medicine. A key factor in determining the biological activity of multifunctional AuNPs is the quantification of surface conjugated molecules. There has been a lack of accurate methods to determine this for multifunctionalized AuNPs. We address this limitation by using a new method based on the deconvolution and Levenberg-Marquardt algorithm fitting of UV-visible absorption spectrum to calculate the precise concentration and number of cytochrome C (Cyt C) and zinc porphyrin (Zn Porph) bound to each multifunctional AuNP. Dynamic light scattering (DLS) and zeta potential measurements were used to confirm the functionalization of AuNPs with Cyt C and Zn Porph. Transmission electron microscopy (TEM) was used in conjunction with UV-visible absorption spectroscopy and DLS to identify the AuNP size and confirm that no aggregation had taken place after functionalization. Despite the overlapping absorption bands of Cyt C and Zn Porph, this method was able to reveal a precise concentration and number of Cyt C and Zn Porph molecules attached per AuNP. Furthermore, using this method, we were able to identify unconjugated molecules, suggesting the need for further purification of the sample. This guide provides a simple and effective method to quickly quantify molecules bound to AuNPs, giving users valuable information, especially for applications in drug delivery and biosensors.

Biocompatible metallosurfactant-based nanocolloid-loaded Rose Bengal with excellent singlet oxygen-induced phototoxicity efficiency against cancer cells

Photodynamic therapy (PDT) is facing challenges such as poor solubility, precise delivery, self-aggregation, and photobleaching of photosensitizers with cancer cells due to their less tendency to accumulate in tumor tissues. To address these challenges, we have explored a Rose Bengal (RB)-loaded metallocatanionic vesicles (MCVs) nanosystem for the phototoxicity of cancer cells. Different sets of MCVs were prepared by two different cationic single-chain metallosurfactants, i.e., hexadecylpyridinium trichlorocuprate (CuCPC I) and hexadecylpyridinium trichloroferrate (FeCPC I) in combination with anionic double-chain sodium bis(2-ethylhexyl)sulfosuccinate (AOT) surfactant in phosphate buffer saline of pH 7.4. The RB-loaded CuCPC I:AOT and FeCPC I:AOT vesicles enhanced the maximum singlet oxygen (¹O₂) generation by 1-fold and 3-fold, respectively, compared to pure RB. Upon irradiation with a 532 nm laser for 10 min, these RB-loaded CuCPC I:AOT and FeCPC I:AOT MCVs significantly decreased the metabolic activity of U-251 cells by 70% and 85% at MCVs concentration of 0.75 μM, respectively. Furthermore, RB-loaded MCVs showed the highest intracellular ¹O₂-mediated membrane damage and cell-killing effect as confirmed by singlet oxygen sensor green and differential nuclear staining assay, which is attributed to the cellular uptake profile of different RB-loaded MCVs fractions. Caspase 3/7 assay confirmed the apoptotic pathway of cell death by activating caspase. Therefore, the photoactivation of RB-loaded MCVs led to a significant reduction in the viability of U-251 cells (maximum 85%), which resulted in cell death. Our study demonstrated the advantage of using these dual-charge and biocompatible metallocatanionic vesicles as a promising delivery system of photodynamic therapy that can enhance ¹O₂ generation from PS and can be further utilized in photomedicine.

Nanoparticle protein corona: from structure and function to therapeutic targeting

Nanoparticle (NP)-based therapeutics have ushered in a new era in translational medicine. However, despite the clinical success of NP technology, it is not well-understood how NPs fundamentally change in biological environments. When introduced into physiological fluids, NPs are coated by proteins, forming a protein corona (PC). The PC has the potential to endow NPs with a new identity and alter their bioactivity, stability, and destination. Additionally, the conformation of proteins is sensitive to their physical and chemical surroundings. Therefore, biological factors and protein-NP-interactions can induce changes in the conformation and orientation of proteins in vivo. Since the function of a protein is closely connected to its folded structure, slight differences in the surrounding environment as well as the surface characteristics of the NP materials may cause proteins to lose or gain a function. As a result, this can alter the downstream functionality of the NPs. This review introduces the main biological factors affecting the conformation of proteins associated with the PC. Then, four types of NPs with extensive utility in biomedical applications are described in greater detail, focusing on the conformation and orientation of adsorbed proteins. This is followed by a discussion on the instances in which the conformation of adsorbed proteins can be leveraged for therapeutic purposes, such as controlling protein conformation in assembled matrices in tissue, as well as controlling the PC conformation for modulating immune responses. The review concludes with a perspective on the remaining challenges and unexplored areas at the interface of PC and NP research.

Predicting protein function and orientation on a gold nanoparticle surface using a residue-based affinity scale

The orientation adopted by proteins on nanoparticle surfaces determines the nanoparticle's bioactivity and its interactions with living systems. Here, we present a residue-based affinity scale for predicting protein orientation on citrate-gold nanoparticles (AuNPs). Competitive binding between protein variants accounts for thermodynamic and kinetic aspects of adsorption in this scale. For hydrophobic residues, the steric considerations dominate, whereas electrostatic interactions are critical for hydrophilic residues. The scale rationalizes the well-defined binding orientation of the small GB3 protein, and it subsequently predicts the orientation and active site accessibility of two enzymes on AuNPs. Additionally, our approach accounts for the AuNP-bound activity of five out of six additional enzymes from the literature. The model developed here enables high-throughput predictions of protein behavior on nanoparticles, and it enhances our understanding of protein orientation in the biomolecular corona, which should greatly enhance the performance and safety of nanomedicines used in vivo.

Temperature-Responsive Polymer Brush Coatings for Advanced Biomedical Applications

Modern biomedical technologies predict the application of materials and devices that not only can comply effectively with specific requirements, but also enable remote control of their functions. One of the most prospective materials for these advanced biomedical applications are materials based on temperature-responsive polymer brush coatings (TRPBCs). In this review, methods for the fabrication and characterization of TRPBCs are summarized, and possibilities for their application, as well as the advantages and disadvantages of the TRPBCs, are presented in detail. Special attention is paid to the mechanisms of thermo-responsibility of the TRPBCs. Applications of TRPBCs for temperature-switchable bacteria killing, temperature-controlled protein adsorption, cell culture, and temperature-controlled adhesion/detachment of cells and tissues are considered. The specific criteria required for the desired biomedical applications of TRPBCs are presented and discussed.

Layer-by-Layer Nanoarchitectonics Using Protein-Polyelectrolyte Complexes toward a Generalizable Tool for Protein Surface Immobilization

Layer-by-layer (LbL) self-assembly is an attractive method for the immobilization of macromolecules at interfaces. Integrating proteins in LbL thin films is however challenging due to their polyampholyte nature. Recently, we developed a method to integrate lysozyme into multilayers using protein-polyelectrolytes complexes (PPCs). In this work, we extended this method to a wide range of protein-polyelectrolyte combinations. We demonstrated the robustness and versatility of PPCs as building blocks. LL-37, insulin, lysozyme, and glucose oxidase were complexed with alginate, poly(styrenesulfonate), heparin, and poly(allylamine hydrochloride). The resulting PPCs were then LbL self-assembled with chitosan, PAH, and heparin. We demonstrated that multilayers built with PPCs are thicker compared to the LbL self-assembly of bare protein molecules. This is attributed to the higher mass of protein in the multilayers and/or the more hydrated state of the assemblies. PPCs enabled the self-assembly of proteins that could otherwise not be LbL assembled with a PE or with another protein. Furthermore, the results also show that LbL with PPCs enabled the construction of multilayers combining different proteins, highlighting the formation of multifunctional films. Importantly, we show that the adsorption behavior and thus the multilayer growth strongly depend on the nature of the protein and polyelectrolyte used. In this work, we elaborated a rationale to help and guide the use of PPCs for protein LbL assembly. It will therefore be beneficial to the many scientific communities willing to modify interfaces with hard-to-immobilize proteins and peptides.

Plasmon-Enhanced Antibacterial Activity of Chiral Gold Nanoparticles and In Vivo Therapeutic Effect

d-cysteine (d-cys) has been demonstrated to possess an extraordinary antibacterial activity because of its unique steric configuration. However, inefficient antibacterial properties seriously hinder its wide applications. Here, cysteine-functionalized gold nanoparticles (d-/l-Au NPs) were prepared by loading d-/l-cysteine on the surface of gold nanoparticles for the effective inhibition of Escherichia coli (E. coli) in vitro and in vivo, and the effects on the intestinal microflora in mice were explored during the treatment of E. coli infection in the gut. We found that the antibacterial activity of d-/l-Au NPs was more than 2-3 times higher than pure d-cysteine, l-cysteine and Au NPs. Compared with l-Au NPs, d-Au NPs showed the stronger antibacterial activity, which was related to its unique steric configuration. Chiral Au NPs showed stronger destructive effects on cell membrane compared to other groups, which further leads to the leakage of the cytoplasm and bacterial cell death. The in vivo antibacterial experiment illustrated that d-Au NPs displayed impressive antibacterial activity in the treatment of E. coli-infected mice comparable to kanamycin, whereas they could not affect the balance of intestinal microflora. This work is of great significance in the development of an effective chiral antibacterial agent.