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1. Biomolecular corona formation on CuO nanoparticles in plant xylem fluid

   https://doi.org/10.1039/D1EN00140J  

   Borgatta, Jaya R.; Lochbaum, Christian A.; Elmer, Wade H.; White, Jason C.; Pedersen, Joel A.; Hamers, Robert J. (January 2021, Environmental Science: Nano)

   null (Ed.)

   Biomolecular coatings (coronas) that form on nanomaterials have been widely investigated in animal and bacterial cell culture and in the extracellular and intracellular fluids of animals. Such coronas influence the distribution of nanoparticles within organisms, their uptake by cells, and their storage in intracellular compartments. Plants can be exposed to nanoparticles via either intentional application of nanomaterials in agriculture or inadvertently due, for example, to biosolids amendment of soils. Development of a mechanistic understanding of nanoparticle transport and fate within plants requires consideration of corona acquisition within plants, particularly within the vascular fluids that transport nanoparticles throughout plants. Here, we examine the interactions between copper oxide (CuO) nanoparticles and pumpkin xylem fluid to understand corona formation in an important part of the plant vasculature system. We used CuO nanoparticles because they have emerged as a promising micronutrient source for the suppression of fungal diseases. The corona was composed primarily of proteins, despite the higher abundance of carbohydrates in xylem fluid. We used X-ray photoelectron spectroscopy to determine the thickness of the protein corona. Polyacrylamide gel electrophoresis revealed that protein binding to the CuO nanoparticle surface was selective; the most abundant proteins in the corona were not the most abundant ones in the xylem fluid. We used in situ attenuated total reflectance Fourier-transform infrared spectroscopy to show that the protein–CuO NP interactions were quasi-irreversible, while carbohydrate–CuO interactions were reversible. Corona formation is expected to influence the distribution and transformation of nanomaterials in plants. 

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2. Influence of Sensor Coating and Topography on Protein and Nanoparticle Interaction with Supported Lipid Bilayers

   https://doi.org/10.1021/acs.langmuir.0c02662  

   Yin, Hui; Mensch, Arielle C.; Lochbaum, Christian A.; Foreman-Ortiz, Isabel U.; Caudill, Emily R.; Hamers, Robert J.; Pedersen, Joel A. (January 2021, Langmuir)

   null (Ed.)

   Supported lipid bilayers (SLBs) have proven to be valuable model systems for studying the interactions of proteins, peptides, and nanoparticles with biological membranes. The physicochemical properties (e.g., topography, coating) of the solid substrate may affect the formation and properties of supported phospholipid bilayers, and thus, subsequent interactions with biomolecules or nanoparticles. Here, we examine the influence of support coating (SiO2 vs Si3N4) and topography [sensors with embedded vs protruding gold nanodisks for nanoplasmonic sensing (NPS)] on the formation and subsequent interactions of supported phospholipid bilayers with the model protein cytochrome c and with cationic polymer-wrapped quantum dots using quartz crystal microbalance with dissipation monitoring and NPS techniques. The specific protein and nanoparticle were chosen because they differ in the degree to which they penetrate the bilayer. We find that bilayer formation and subsequent non-penetrative association with cytochrome c were not significantly influenced by substrate composition or topography. In contrast, the interactions of nanoparticles with SLBs depended on the substrate composition. The substrate-dependence of nanoparticle adsorption is attributed to the more negative zeta-potential of the bilayers supported by the silica vs the silicon nitride substrate and to the penetration of the cationic polymer wrapping the nanoparticles into the bilayer. Our results indicate that the degree to which nanoscale analytes interact with SLBs may be influenced by the underlying substrate material. 

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

   https://doi.org/10.1038/s41467-022-34749-w  

   Xu, Joanna Xiuzhu; Alom, Md. Siddik; Yadav, Rahul; Fitzkee, Nicholas C. (November 2022, Nature Communications)

   Abstract 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. 

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4. Cell-penetrating protein-recognizing polymeric nanoparticles through dynamic covalent chemistry and double imprinting

   https://doi.org/10.1038/s41467-024-48131-5  

   Ghosh, Avijit; Sharma, Mansi; Zhao, Yan (May 2024, Nature Communications)

   Abstract Molecular recognition of proteins is key to their biological functions and processes such as protein–protein interactions (PPIs). The large binding interface involved and an often relatively flat binding surface make the development of selective protein-binding materials extremely challenging. A general method is reported in this work to construct protein-binding polymeric nanoparticles from cross-linked surfactant micelles. Preparation involves first dynamic covalent chemistry that encodes signature surface lysines on a protein template. A double molecular imprinting procedure fixes the binding groups on the nanoparticle for these lysine groups, meanwhile creating a binding interface complementary to the protein in size, shape, and distribution of acidic groups on the surface. These water-soluble nanoparticles possess excellent specificities for target proteins and sufficient affinities to inhibit natural PPIs such as those between cytochrome c (Cytc) and cytochrome c oxidase (CcO). With the ability to enter cells through a combination of energy-dependent and -independent pathways, they intervene apoptosis by inhibiting the PPI between Cytc and the apoptotic protease activating factor-1 (APAF1). Generality of the preparation and the excellent molecular recognition of the materials have the potential to make them powerful tools to probe protein functions in vitro and in cellulo. 

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5. Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques

   https://doi.org/10.1002/ijch.201900080  

   Randika Perera, Y.; Hill, Rebecca A.; Fitzkee, Nicholas C. (September 2019, Israel Journal of Chemistry)

   Abstract In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub‐categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small‐molecule interactions are easily probed using NMR spectroscopy, studying protein‐NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP‐protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique forin situanalysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces. 

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