Modular assembly of proteins on nanoparticles

Generation of biparatopic antibody through two-step targeting of fragment antibodies on antigen using SpyTag and SpyCatcher

Biparatopic fragment antibodies can overcome deficiencies in avidity of conventional antibody fragments. Here, we describe a technology for generating biparatopic antibodies through two-step targeting using a pair of polypeptides, SpyTag and SpyCatcher, that spontaneously react to form a covalent bond between antibody fragments. In this method, two antibody fragments, each targeting different epitopes of the antigen, are fused to SpyTag and to SpyCatcher. When the two polypeptides are serially added to the antigen, their proximity on the antigen results in covalent bond formation and generation of a biparatopic antibody. We validated the system with purified recombinant antigen. Results in antigen-overexpressing cells were promising although further optimization will be required. Because this strategy results in high-affinity targeting with a bipartite molecule that has considerably lower molecular weight than an antibody, this technology is potentially useful for diverse applications.

Oriented Immobilization on Gold Nanoparticles of a Recombinant Therapeutic Zymogen

Direct immobilization of functional proteins on gold nanoparticles (AuNPs) affects their structure and function. Changes may vary widely and range from strong inhibition to the enhancement of protein function. More often though the outcome of direct protein immobilization results in protein misfolding and the loss of protein activity. Additional complications arise when the protein being immobilized is a zymogen which requires and relies on additional protein-protein interactions to exert its function. Here we describe molecular design of a glutathione-S-transferase-Staphylokinase fusion protein (GST-SAK) and its conjugation to AuNPs. The multivalent AuNP-(GST-SAK)n complexes generated show plasminogen activation activity in vitro. The methods described are transferable and could be adapted for conjugation and functional analysis of other plasminogen activators, thrombolytic preparations or other functional enzymes.

Protein Immobilization on Gold Nanoparticles: Quantitative Analysis

Conjugation of gold nanoparticles (AuNPs) with biologically relevant molecules underpins many applications in medicine and biochemistry. Immobilization of functional proteins on AuNPs often affects protein structure and function. Such effects are protein dependent and require thorough investigation using suitable quantitative tests. Good experimental design and the use of a comprehensive set of control samples are essential when characterizing the consequences of protein immobilization and its effect on protein structure and function. However, traditional approaches to making control samples, that is, immobilized protein versus protein in solution in absence of any nanoparticles, do not provide sufficiently identical reaction conditions and complicate interpretation of the results. Accurate quantification of protein conjugation to AuNPs and ensuring complete removal of unconjugated protein remain the two key challenges in such functional assays. This report describes a simple and straightforward procedure allowing for quantitative analysis of protein conjugation to AuNPs. The principles are illustrated using fluorescence and circular dichroism measurements, and can be applied to other analytical techniques or be adapted with minor modifications for use with other proteins.

The Molecular Dynamics Simulation of Peptides on Gold Nanosurfaces

This chapter contributes a short tutorial on the preparation of molecular dynamics (MD) simulations for a peptide in solution at the interface of an uncoated gold nanosurface. Specifically, the step-by-step procedure will give guidance to set up the simulation of a 16 amino acid long antimicrobial peptide on a gold layer using the program Gromacs for MD simulations.

Novel fluorescein polymer-based nanoparticles: facile and controllable one-pot synthesis, assembly, and immobilization of biomolecules for application in a highly sensitive biosensor

A key aspect of biochip and biosensor preparation is optimization of the optical or electrochemical techniques that combine high sensitivity and specificity. Among them, optical techniques such as the use of fluorescent polymeric nanoparticles have resulted in dramatic progress in the field of diagnostics due to their range of advantages. We herein report a facile approach for the development of novel fluorescein polymeric nanoparticles (FPNPs) with immobilization of specific biomolecules for application in a highly sensitive optical biosensor. A series of three amphiphilic fluorescein polymers (poly(FMA-r-NAS-r-MA)), comprising hydrophobic fluorescein O-methacrylate (FMA), hydrophilic N-acryloxysuccinimide (NAS), and methacrylic acid (MA) monomers were synthesized through radical polymerization. In an aqueous environment, these fluorescein polymers self-assembled into spherical shaped nanoparticles with a well-defined particle size, narrow particle size distribution, and enhanced fluorescence properties. The bio-immobilization properties of the FPNPs were also tunable by control of the activated N-hydroxysuccinimide ester group in the polymer series. Furthermore, the fluorescence sensitivity of bovine serum albumin detection by the FPNPs indicates that the limit of detection and sensitivity were improved compared to conventional fluorescence dye-labelled proteins. These novel FPNPs therefore represent a suitable technology for disease diagnosis and biomarker detection to ultimately improve the sensitivity of existing analytical methodologies in a facile and cost-effective manner.

We report a facile approach for the development of novel fluorescein polymeric nanoparticles (FPNPs) with immobilization of specific biomolecules for application in a highly sensitive optical biosensor.

Directed and Modular Protein Immobilization on Gold and Silver Nanoparticles

Conjugation of proteins to gold nanoparticles (AuNP), silver nanoparticles (AgNP), or other metal nanoparticles (NPs) can often be achieved using passive adsorption. Although such an approach is simple and effective, there is usually no control over the orientation of the protein and denaturation due to close contact with the metal surface. The method described here makes use of adapter proteins which have the ability to adsorb to the NP surface in an oriented and stable way and at the same time enable straightforward attachment to other proteins of interest.

Immobilized Enzymes on Gold Nanoparticles: From Enhanced Stability to Cleaning of Heritage Textiles

Enzyme-based treatments are used in heritage conservation for the effective removal of glues and other damaging organic layers from the surfaces of historic and artistic works. Despite their potential, however, the application of enzymatic treatments is currently limited because of their poor efficiency and low operational and environmental stability. We demonstrate the use of α-amylase immobilized on gold nanoparticles to improve the efficacy of enzymatic treatments enhancing both the reactivity and the stability of the formulations. Gold nanoparticles coated with α-amylase exhibit significant advantages compared to free enzymes. We report up to 5× greater resistance to environmental changes, up to 2× higher efficacy toward removal of starch-based glues from textiles and deeper penetration through the fibers, without causing damage or inducing salt precipitation. These results offer exciting prospects for the development of enzymatic formulations, both for heritage conservation and the wider application of enzymes, such as in medicine, the detergent industry, and green chemistry.

Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives

Injection of nanoparticles (NP) into the bloodstream leads to the formation of a so-called "nano-bio" interface where dynamic interactions between nanoparticle surfaces and blood components take place. A common consequence is the formation of the protein corona, that is, a network of adsorbed proteins that can strongly alter the surface properties of the nanoparticle. The protein corona and the resulting structural changes experienced by adsorbed proteins can lead to substantial deviations from the expected cellular uptake as well as biological responses such as NP aggregation and NP-induced protein fibrillation, NP interference with enzymatic activity, or the exposure of new antigenic epitopes. Achieving a detailed understanding of the nano-bio interface is still challenging due to the synergistic effects of several influencing factors like pH, ionic strength, and hydrophobic effects, to name just a few. Because of the multiscale complexity of the system, modeling approaches at a molecular level represent the ideal choice for a detailed understanding of the driving forces and, in particular, the early events at the nano-bio interface. This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature.

Protein-functionalized nanoparticles derived from end-functional polymers and polymer prodrugs for crossing the blood-brain barrier

Nanoparticles may provide a viable way for neuroprotective drugs to cross the blood-brain barrier (BBB), which limits the passage of most drugs from the peripheral circulation to the brain. Heterotelechelic polymer prodrugs comprising a neuroprotective model drug (adenosine) and a maleimide functionality were synthesized by the "drug-initiated" approach and subsequent nitroxide exchange reaction. Nanoparticles were obtained by nanoprecipitation and exhibited high colloidal stability with diameters in the 162-185 nm range and narrow size distributions. Nanoparticles were then covalently surface-conjugated to different proteins (albumin, α2-macroglobulin and fetuin A) to test their capability of enhancing BBB translocation. Their performances in terms of endothelial permeability and cellular uptake in an in vitro BBB model were compared to that of similar nanoparticles with surface-adsorbed proteins, functionalized or not with the drug. It was shown that bare NPs (i.e., NPs not surface-functionalized with proteins) without the drug exhibited significant permeability and cellular uptake, which were further enhanced by NP surface functionalization with α2-macroglobulin. However, the presence of the drug at the polymer chain-end prevented efficient passage of all types of NPs through the BBB model, likely due to adecrease in the hydrophobicity of the nanoparticle surface and alteration of the protein binding/coupling, respectively. These results established a new and facile synthetic approach for the surface-functionalization of polymer nanoparticles for brain delivery purposes.

Catching a SPY: Using the SpyCatcher-SpyTag and Related Systems for Labeling and Localizing Bacterial Proteins

The SpyCatcher-SpyTag system was developed seven years ago as a method for protein ligation. It is based on a modified domain from a Streptococcus pyogenes surface protein (SpyCatcher), which recognizes a cognate 13-amino-acid peptide (SpyTag). Upon recognition, the two form a covalent isopeptide bond between the side chains of a lysine in SpyCatcher and an aspartate in SpyTag. This technology has been used, among other applications, to create covalently stabilized multi-protein complexes, for modular vaccine production, and to label proteins (e.g., for microscopy). The SpyTag system is versatile as the tag is a short, unfolded peptide that can be genetically fused to exposed positions in target proteins; similarly, SpyCatcher can be fused to reporter proteins such as GFP, and to epitope or purification tags. Additionally, an orthogonal system called SnoopTag-SnoopCatcher has been developed from an S. pneumoniae pilin that can be combined with SpyCatcher-SpyTag to produce protein fusions with multiple components. Furthermore, tripartite applications have been produced from both systems allowing the fusion of two peptides by a separate, catalytically active protein unit, SpyLigase or SnoopLigase. Here, we review the current state of the SpyCatcher-SpyTag and related technologies, with a particular emphasis on their use in vaccine development and in determining outer membrane protein localization and topology of surface proteins in bacteria.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

The Role of Ligands in the Chemical Synthesis and Applications of Inorganic Nanoparticles

The design of nanoparticles is critical for their efficient use in many applications ranging from biomedicine to sensing and energy. While shape and size are responsible for the properties of the inorganic nanoparticle core, the choice of ligands is of utmost importance for the colloidal stability and function of the nanoparticles. Moreover, the selection of ligands employed in nanoparticle synthesis can determine their final size and shape. Ligands added after nanoparticle synthesis infer both new properties as well as provide enhanced colloidal stability. In this article, we provide a comprehensive review on the role of the ligands with respect to the nanoparticle morphology, stability, and function. We analyze the interaction of nanoparticle surface and ligands with different chemical groups, the types of bonding, the final dispersibility of ligand-coated nanoparticles in complex media, their reactivity, and their performance in biomedicine, photodetectors, photovoltaic devices, light-emitting devices, sensors, memory devices, thermoelectric applications, and catalysis.

Stereoselective Double Reduction of 3-Methyl-2-cyclohexenone, by Use of Palladium and Platinum Nanoparticles, in Tandem with Alcohol Dehydrogenase

The combination of metal nanoparticles (Pd or Pt NPs) with NAD-dependent thermostable alcohol dehydrogenase (TADH) resulted in the one-flask catalytic double reduction of 3-methyl-2-cyclohexenone to 3-(1S,3S)-methylcyclohexanol. In this article, some assumptions about the interactions between a chemocatalyst and a biocatalyst have been proposed. It was demonstrated that the size of the NPs was the critical parameter for the mutual inhibition: the bigger the NPs, the more harmful for the enzyme they were, even if the NPs themselves were only moderately inactivated. Conversely, the smaller the NPs, the more minimal the TADH denaturation, although they were dramatically inhibited. Resuming, the chemocatalysts were very sensitive to deactivation, which was not related to the amount of enzyme used, while the inhibition of the biocatalyst can be strongly reduced by minimizing the NPs/TADH ratio used to catalyze the reaction. Among some methods to avoid direct binding of NPs with TADH, we found that using large Pd NPs and protecting their surfaces with a silica shell, the overall yield of 3-(1S,3S)-methylcyclohexanol was maximized (36%).