Biocompatible Peptide-Coated Ultrasmall Superparamagnetic Iron Oxide Nanoparticles for In Vivo Contrast-Enhanced Magnetic Resonance Imaging

The biocompatibility and performance of reagents for in vivo contrast-enhanced magnetic resonance imaging (MRI) are essential for their translation to the clinic. The quality of the surface coating of nanoparticle-based MRI contrast agents, such as ultrasmall superparamagnetic iron oxide nanoparticles (USPIONs), is critical to ensure high colloidal stability in biological environments, improved magnetic performance, and dispersion in circulatory fluids and tissues. Herein, we report the design of a library of 21 peptides and ligands and identify highly stable self-assembled monolayers on the USPIONs' surface. A total of 86 different peptide-coated USPIONs are prepared and selected using several stringent criteria, such as stability against electrolyte-induced aggregation in physiological conditions, prevention of nonspecific binding to cells, and absence of cellular toxicity and contrast-enhanced in vivo MRI. The bisphosphorylated peptide 2PG-S*VVVT-PEG4-ol provides the highest biocompatibility and performance for USPIONs, with no detectable toxicity or adhesion to live cells. The 2PG-S*VVVT-PEG4-ol-coated USPIONs show enhanced magnetic resonance properties, r₁ (2.4 mM^-1·s^-1) and r₂ (217.8 mM^-1·s^-1) relaxivities, and greater r₂/ r₁ relaxivity ratios (>90) when compared to those of commercially available MRI contrast agents. Furthermore, we demonstrate the utility of 2PG-S*VVVT-PEG4-ol-coated USPIONs as a T₂ contrast agent for in vivo MRI applications. High contrast enhancement of the liver is achieved as well as detection of liver tumors, with significant improvement of the contrast-to-noise ratio of tumor-to-liver contrast. It is envisaged that the reported peptide-coated USPIONs have the potential to allow for the specific targeting of tumors and hence early detection of cancer by MRI.

Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles

The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials.

Specific Internalisation of Gold Nanoparticles into Engineered Porous Protein Cages via Affinity Binding

Porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. Protein cages’ pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. However, strategies based on nanoparticle transport through the pores are largely unexplored, due to the difficulty of tailoring nanoparticles that have diameters commensurate with the pores size and simultaneously displaying specific affinity to the cages’ core and low non-specific binding to the cages’ outer surface. We evaluated the specific internalisation of single small gold nanoparticles, 3.9 nm in diameter, into porous protein cages via affinity binding. The E2 protein cage derived from the Geobacillus stearothermophilus presents 12 pores, 6 nm in diameter, and an empty core of 13 nm in diameter. We engineered the E2 protein by site-directed mutagenesis with oligohistidine sequences exposing them into the cage’s core. Dynamic light scattering and electron microscopy analysis show that the structures of E2 protein cages mutated with bis- or penta-histidine sequences are well conserved. The surface of the gold nanoparticles was passivated with a self-assembled monolayer made of a mixture of short peptidols and thiolated alkane ethylene glycol ligands. Such monolayers are found to provide thin coatings preventing non-specific binding to proteins. Further functionalisation of the peptide coated gold nanoparticles with Ni²⁺ nitrilotriacetic moieties enabled the specific binding to oligohistidine tagged cages. The internalisation via affinity binding was evaluated by electron microscopy analysis. From the various mutations tested, only the penta-histidine mutated E2 protein cage showed repeatable and stable internalisation. The present work overcomes the limitations of currently available approaches and provides a new route to design tailored and well-controlled hybrid nanoparticles.

Photothermally responsive gold nanoparticle conjugated polymer-grafted porous hollow silica nanocapsules

A laser triggered release of encapsulated compounds from gold conjugated polymer-grafted porous hollow silica nanocapsules.

A rapid method to estimate the concentration of citrate capped silver nanoparticles from UV-visible light spectra

We present a generalized table of extinction coefficient data for silver nanoparticles from 8 to 100 nm. This table allows for easy and quick estimation of the concentration and size of modified and mono-dispersed silver nanoparticles from their optical spectra. We obtained data by determining the silver content of citrate-stabilised silver nanoparticles using sodium cyanide to dissolve the nanoparticles, and measuring solution conductivity with a pH meter and a cyanide-ion selective electrode. The quantification of the silver ion concentration enabled the calculation of extinction coefficients. Experimentally calculated extinction coefficients, in the current work, are in good agreement with collated literature values measured by different authors with non-standardized methodology and each for a limited range of particle size. They are also in good agreement with our theoretical calculations using Mie theory. Thus, we provide a highly standardized and comprehensive tabulated reference data-set.

Targeting Cell Membrane Lipid Rafts by Stoichiometric Functionalization of Gold Nanoparticles With a Sphingolipid-Binding Domain Peptide

A non-membrane protein-based nanoparticle agent for the tracking of lipid rafts on live cells is produced by stoichiometric functionalization of gold nanoparticles with a previously characterized sphingolipid- and cell membrane microdomain-binding domain peptide (SBD). The SBD peptide is inserted in a self-assembled monolayer of peptidol and alkane thiol ethylene glycol, on gold nanoparticles surface. The stoichiometric functionalization of nanoparticles with the SBD peptide, essential for single molecule tracking, is achieved by means of non-affinity nanoparticle purification. The SBD-nanoparticles have remarkable long-term resistance to electrolyte-induced aggregation and ligand-exchange and have no detectable non-specific binding to live cells. Binding and diffusion of SBD-nanoparticles bound to the membrane of live cells is measured by real-time photothermal microscopy and shows the dynamics of sphingolipid-enriched microdomains on cells membrane, with evidence for clustering, splitting, and diffusion over time of the SBD-nanoparticle labeled membrane domains. The monofunctionalized SBD-nanoparticle is a promising targeting agent for the tracking of lipid rafts independently of their protein composition and the labelling requires no prior modification of the cells. This approach has potential for further functionalization of the particles to manipulate the organization of, or targeting to microdomains that control signaling events and thereby lead to novel diagnostics and therapeutics.

Designing non-native iron-binding site on a protein cage for biological synthesis of nanoparticles

In biomineralization processes, a supramolecular organic structure is often used as a template for inorganic nanomaterial synthesis. The E2 protein cage derived from Geobacillus stearothermophilus pyruvate dehydrogenase and formed by the self-assembly of 60 subunits, has been functionalized with non-native iron-mineralization capability by incorporating two types of iron-binding peptides. The non-native peptides introduced at the interior surface do not affect the self-assembly of E2 protein subunits. In contrast to the wild-type, the engineered E2 protein cages can serve as size- and shape-constrained reactors for the synthesis of iron nanoparticles. Electrostatic interactions between anionic amino acids and cationic iron molecules drive the formation of iron oxide nanoparticles within the engineered E2 protein cages. The work expands the investigations on nanomaterial biosynthesis using engineered host-guest encapsulation properties of protein cages.

Ferritin-templated synthesis and self-assembly of Pt nanoparticles on a monolithic porous graphene network for electrocatalysis in fuel cells

The monolithic three-dimensional (3D) graphene network is used as the support for Pt nanoparticles (NPs) to fabricate an advanced 3D graphene-based electrocatalyst. Distinct from previous strategies, the monodispersed Pt NPs with ultrafine particle size (∼3 nm) are synthesized using ferritin protein nanocages as the template and subsequently self-assembled on the 3D graphene by leveraging on the hydrophobic interaction between the ferritin and the graphene. Following the self-assembly, the ferritins are removed, resulting in a stable Pt NP/3D graphene composite. The composite exhibits much enhanced electrocatalytic activity for methanol oxidation as compared with both Pt NP/chemically reduced graphene oxide (Pt/r-GO) and state-of-the-art Pt/C catalyst. The observed electrocatalytic activity also shows marked improvement over Pt/3D graphene prepared by pulse electrodeposition of Pt. This study demonstrates that protein nanocage templating and assembly are promising strategies for the fabrication of functional composites in catalysis and fuel cell applications.

Chemical cross-linkers for protein structure studies by mass spectrometry

The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies.

Features of Thiolated Ligands Promoting Resistance to Ligand Exchange in Self-Assembled Monolayers on Gold Nanoparticles

An important feature necessary for biological stability of gold nanoparticles is resistance to ligand exchange. Here, we design and synthesize self-assembled monolayers of mixtures of small ligands on gold nanoparticles promoting high resistance to ligand exchange. We use as ligands short thiolated peptidols, e.g. H-CVVVT-ol, and ethylene glycol terminated alkane thiols (HS-C11-EG4). We present a straightforward method to evaluate the relative stability of each ligand shell against ligand exchange with small thiolated molecules. The results show that a ligand with a ‘thin’ stem, such as HS-C11-EG4, is an important feature to build a highly packed self-assembled monolayer and provide high resistance to ligand exchange. The greatest resistance to ligand exchange was found for the mixed ligand shells of the pentapeptidols H-CAVLT-ol or H-CAVYT-ol and the ligand HS-C11-EG4 at 30:70 (mole/mole). Mixtures of ligands of very different diameters, such as the peptidol H-CFFFY-ol and the ligand HS-C11-EG4, provide only a slightly lower stability against ligand exchange. These ligand shells are thus likely to be suitable for long-term use in biological environments. The method developed here provides a rapid screening tool to identify nanoparticles likely to be suitable for use in biological and biomedical applications.

Synthesis of Silver Nanoparticles with Monovalently Functionalized Self-Assembled Monolayers

The importance of having nanoparticles that are soluble, stable, and that have no non-specific binding is often overlooked, but essential for their use in biology. This is particularly prominent with silver nanoparticles that are susceptible to the effects of aggregation and metal-surface reactivity. Here we use a combination of several small peptidols and short alkanethiol ethylene glycol ligands to develop a ligand shell that is reasonably resistant to ligand exchange and non-specific binding to groups common in biological molecules. The stability of the nanoparticles is not affected by the inclusion of a functional ligand, which is done in the same preparative step. The stoichiometry of the nanoparticles is controlled, such that monofunctional silver nanoparticles can be obtained. Two different sets of nanoparticles, functionalized with either Tris-nitrilotriacetic acid or a hexa-histidine peptide sequence, readily form dimers/oligomers, depending on their stoichiometry of functionalization.

MSX-3D: a tool to validate 3D protein models using mass spectrometry

MOTIVATION

The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking.

RESULTS

We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment.

AVAILABILITY

Freely available at http://proteomics-pbil.ibcp.fr