Antigen-decorated shell cross-linked nanoparticles: synthesis, characterization, and antibody interactions

Antigen-decorated shell cross-linked knedel-like nanoparticles (SCKs) were synthesized and studied as multivalent nanoscale surfaces from which antibody-binding units were presented in a manner that was designed to approach virus particle surfaces. The SCK nanostructures were fabricated with control over the number of antigenic groups, from mixed micellization of amphiphilic diblock copolymer building blocks that contained either an antigen (2,4-dinitrophenyl) or an ethylpropionate group at the hydrophilic alpha-chain terminus. Amphiphilic diblock copolymers were synthesized by atom transfer radical polymerization of tert-butyl acrylate and methyl acrylate sequentially from either a 2,4-dinitrophenyl-functionalized initiator or ethyl 2-bromopropionate, followed by selective removal of the tert-butyl groups to afford 2,4-dinitrophenyl-poly(acrylic acid)60-b-poly(methyl acrylate)60 (DNP-PAA(60)-b-PMA60) and poly(acrylic acid)70-b-poly(methyl acrylate) (PAA70-b-PMA70). Micelles were assembled via addition of water to THF solutions of the polymers in 0:1, 1:1, and 1:0 molar ratios of DNP-PAA60-b-PMA60 to PAA70-b-PMA70, followed by dialysis against water. The acrylic acid groups of the micelle coronas were partially cross-linked (nominally 50%) with 2,2'-(ethylenedioxy)bis(ethylamine), in the presence of 1-(3'-dimethylaminopropyl)-3-ethylcarbodiimide methiodide. Following extensive dialysis against water, the 0%, 50%, and 100% dinitrophenylated shell cross-linked nanoparticles (DNP-SCKs) were characterized with dynamic light scattering (DLS), transmission electron microscopy (TEM), atomic force microscopy (AFM), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), infrared and UV-vis spectroscopies, and analytical ultracentrifugation (AU). The surface accessibility and bioavailability of the DNP units upon the DNP-SCKs were investigated by performing quenching titrations of fluorescein-labeled IgE antibody in solution and degranulation of IgE sensitized RBL-2H3 cells. The DNP antigens proved to be surface-available and able to form multivalent bonds with IgE antibodies, causing degranulation.     

Low-pH-sensitive PEG-stabilized plasmid-lipid nanoparticles: preparation and characterization

The acid-labile poly(ethyleneglycol)-diorthoester-distearoylglycerol lipid (POD), was used with a cationic lipid-phosphatidylethanolamine mixture to prepare stabilized plasmid-lipid nanoparticles (POD SPLP) that could mediate gene transfer in vitro by a pH triggered escape from the endosome. Nanoparticles of 60 nm diameter were prepared at pH 8.5 using a detergent dialysis method. The DNA encapsulation efficiency in the nanoparticles was optimal between 10 and 13 mol % ratio of cationic lipid and at a POD content of 20 mol %. The apparent zeta potential of the nanoparticles at 1 mM salt and pH 7.5 was positive, indicating cationic lipid on the external surface. However, the external layer of the nanoparticles was depleted in the cationic component compared to the starting mole ratio. Low pH sensitivity of the POD SPLP was characterized by a lag phase followed by a rapid collapse; at pH 5.3 the nanoparticles collapsed in 100 min. Nanoparticles prepared from a pH-insensitive PEG-lipid, PEG-distearoylglycerol had similar physicochemical characteristics as the POD SPLP but did not collapse at low pH. The POD SPLP had up to 3 orders of magnitude greater gene transfer activity than did the pH-insensitive nanoparticles. Both the pH-sensitive and pH-insensitive nanoparticles were internalized to a qualitatively similar extent in a punctate pattern into cultured cells within 2 h of incubation with the cells; thus, increased gene transfer of the POD SPLP was due to a more rapid escape from the endosome rather than to greater cell association of these nanoparticles. These results suggest that the pH-sensitive stabilized plasmid-lipid nanoparticles may be a useful component of a synthetic vector for parenterally administered gene therapy.     

Visualization and characterization of RNA–protein interactions in living cells

RNA–protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA–protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA–protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA–protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA–protein interactions in living cells.     

Atomic force microscopy characterization of silver nanoparticles interactions with marine diatom cells and extracellular polymeric substance

This study highlights the capacity of atomic force microscopy (AFM) for investigating nanoparticle (NP) algal cell interaction with a subnanometer resolution. We designed a set of AFM experiments to characterize NP size, shape, and structure to visualize changes in the cell morphology induced by NPs and to characterize NP interaction with the extracellular polymeric substance (EPS). Samples for AFM imaging were prepared using the same protocol-drop deposition on mica and imaged in air. Here we address the interactions of Ag NPs with ubiquitous, lightly silicified marine diatoms Cylindrotheca fusiformis and Cylindrotheca closterium and their EPS. In natural seawater used throughout this study, the single Ag NPs adopted truncated tetrahedron morphology with particle heights of 10, 20, 30, and 40 nm. This size class Ag NPs penetrates the cell wall through the valve region built of silica NPs embedded in organic matrix. The Ag NPs cause a local damage inside the cell without disintegration of the cell wall. The EPS production has been shown to increase as a feedback response to Ag NP exposure and may contribute to detoxification mechanisms. Imaging EPS at high resolution revealed the incorporation of Ag NPs and their aggregates into the EPS-gel matrix, proving their detoxifying capacity.     

Imaging protein-protein interactions in living cells

The complex organization of plant cells makes it likely that the molecular behaviour of proteins in the test tube and the cell is different. For this reason, it is essential though a challenge to study proteins in their natural environment. Several innovative microspectroscopic approaches provide such possibilities, combining the high spatial resolution of microscopy with spectroscopic techniques to obtain information about the dynamical behaviour of molecules. Methods to visualize interaction can be based on FRET (fluorescence detected resonance energy transfer), for example in fluorescence lifetime imaging microscopy (FLIM). Another method is based on fluorescence correlation spectroscopy (FCS) by which the diffusion rate of single molecules can be determined, giving insight into whether a protein is part of a larger complex or not. Here, both FRET- and FCS-based approaches to study protein-protein interactions in vivo are reviewed.     

Imaging molecular interactions in living cells

Hormones integrate the activities of their target cells through receptor-modulated cascades of protein interactions that ultimately lead to changes in cellular function. Understanding how the cell assembles these signaling protein complexes is critically important to unraveling disease processes, and to the design of therapeutic strategies. Recent advances in live-cell imaging technologies, combined with the use of genetically encoded fluorescent proteins, now allow the assembly of these signaling protein complexes to be tracked within the organized microenvironment of the living cell. Here, we review some of the recent developments in the application of imaging techniques to measure the dynamic behavior, colocalization, and spatial relationships between proteins in living cells. Where possible, we discuss the application of these different approaches in the context of hormone regulation of nuclear receptor localization, mobility, and interactions in different subcellular compartments. We discuss measurements that define the spatial relationships and dynamics between proteins in living cells including fluorescence colocalization, fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, fluorescence resonance energy transfer microscopy, and fluorescence lifetime imaging microscopy. These live-cell imaging tools provide an important complement to biochemical and structural biology studies, extending the analysis of protein-protein interactions, protein conformational changes, and the behavior of signaling molecules to their natural environment within the intact cell.     

Photocrosslinkers illuminate interactions in living cells

Transient and low-affinity interactions among macromolecules underlie many physiological events. Often, these interactions are difficult to study because they are not maintained when the participating molecules are removed from their cellular context. To circumvent this challenge, crosslinking reagents can be used to introduce covalent bonds between interacting macromolecules. Photoactivatable crosslinkers are particularly attractive because they allow crosslinking to proceed in time- and location-specific ways. Once the interacting partners have been crosslinked, they can be isolated and then analyzed by mass spectrometry or other analytical techniques to determine the identity of the interacting molecules and to pinpoint the interacting regions. This review highlights recent methodological developments that make it possible to introduce photocrosslinking groups into polypeptides or glycans as they are synthesized in cells. We also describe how these methods offer a non-invasive way to study macromolecular interactions in a native context.     

Supramolecular structure characterization of molecularly thin cellulose I nanoparticles

Unusual fractions of cellulose microfibrils from woody material with dimensions of hundreds of nanometers in length and single digit angstrom thickness were obtained by intensive sonication of TEMPO-oxidized cellulose fibers. These cellulose microfibril fragments, composed of many mono- and bilayer molecular sheets, were analyzed with scattering and spectroscopy techniques to understand the structural changes at the supramolecular level. XRD data indicated that sonication breaks the cellulose microfibrils along its (200) planes, yet some form of the Iβ crystalline structure is still retained with reduced crystallinity. The Raman and FTIR analysis indicated structural changes to the cellulose microfibrils do not occur until after sonication; furthermore, AFM observation indicates that the structural changes began to occur within 5 min of sonication. An altered supramolecular structure is evident after sonication: major features from cellulose I are preserved, although certain spectral features similar to mercerized and ball milled cellulose appeared in its FTIR and Raman spectra. These spectral differences are traced to changes in the methine environment, hydroxymethyl conformations, and skeletal vibrations. By integrating the present findings and previous research, a cellulose molecular sheet delamination scheme is proposed to describe this microfibril fragmentation along its (200) plane.     

SH-containing cellulose acetate derivatives: preparation and characterization as a shape memory-recovery material

Cellulose derivatives having a cross-linkable mercapto group were prepared by esterification of cellulose acetate (CA) with mercaptoacetic acid. The molecular structure of a series of products (CA-MA) was characterized by (1)H and (1)H- (13)C HMQC NMR spectroscopy and gel permeation chromatography. The solubility of CA-MA in water and organic solvents could be controlled by changing the preparation conditions including the degree of acetyl substitution of the starting CA. The CA-MA samples thus synthesized showed a sol-gel transition in solution and a shape memory-recovery behavior in film form through adequate redox treatments due to the reversible, cross-linking association and dissociation between mercapto groups. Dimethyl sulfoxide was usable as the organic solvent and oxidant, while the major reducing reagent was 2-mercaptoethanol or ammonium mercaptoacetic acid. The progress of the redox reactions was followed by using a confocal depth scanning technique in Raman spectroscopy. It was found that the compatibility between the cellulose derivatives and the redox reagents used was an important factor for the successful reactions, especially in the samples of film form. The cross-linking effect on the thermal and viscoelastic properties of the CA-MA films was also estimated by differential scanning calorimetry and dynamic mechanical analysis. Discussion focused on the alternately declining and recovering behavior of a principal loss tan delta peak, observed following the redox treatments repeated for the CA-MA film specimens.     

Techniques for detecting protein-protein interactions in living cells: principles,limitations, and recent progress

Detecting protein-protein interactions(PPIs) provides fundamental information for understanding biochemical processes such as the transduction of signals from one cellular location to another; however, traditional biochemical techniques cannot provide sufficient spatio-temporal information to elucidate these molecular interactions in living cells. Over the past decade, several new techniques have enabled the identification and characterization of PPIs. In this review, we summarize three main techniques for detecting PPIs in vivo, focusing on their basic principles and applications in biological studies. We place a special emphasis on their advantages and limitations, and, in particular, we introduced some uncommon new techniques, such as single-molecule FRET(smFRET), FRET-fluorescence lifetime imaging microscopy(FRET-FLIM), cytoskeleton-based assay for protein-protein interaction(CAPPI) and single-molecule protein proximity index(smPPI), highlighting recent improvements to the established techniques. We hope that this review will provide a valuable reference to enable researchers to select the most appropriate technique for detecting PPIs.     

Chitosan graft copolymer nanoparticles for oral protein drug delivery: preparation and characterization

Several novel functionalized graft copolymer nanoparticles consisting of chitosan (CS) and the monomer methyl methacrylate (MMA), N-dimethylaminoethyl methacrylate hydrochloride (DMAEMC), and N-trimethylaminoethyl methacrylate chloride (TMAEMC), which show a higher solubility than chitosan in a broader pH range, have been prepared by free radical polymerization. The nanoparticles were characterized in terms of particle size, zeta potential, TEM, and FT-IR. These nanoparticles were 150-280 nm in size and carried obvious positive surface charges. Protein-loaded nanoparticles were prepared, and their maximal encapsulation efficiency was up to 100%. In vitro release showed that these nanoparticles provided an initial burst release followed by a slowly sustained release for more than 24 h. These graft copolymer nanoparticles enhanced the absorption and improved the bioavailability of insulin via the gastrointestinal (GI) tract of normal male Sprague-Dawley (SD) strain rats to a greater extent than that of the phosphate buffer solution (PBS) of insulin.     

Unraveling protein-protein interactions in living cells with fluorescence fluctuation brightness analysis

Fluorescence correlation spectroscopy is a potentially powerful tool for measuring protein-protein interactions directly in single living cells. We previously reported on the detection of homodimer formation in cells using molecular brightness analysis. Here, we extend the technique to detect binding between different proteins. Proteins are labeled with the fluorescent markers YFP and CFP. We first determine the coexpression ratio of both proteins by measuring the intensity ratio with a dual-color setup. The effect of fluorescence resonance energy transfer on the intensity ratio is explicitly taken into account. The brightness of cells coexpressing both proteins is measured in a single-color setup. Selecting the laser wavelength of the two-photon light source allows us to either coexcite both proteins or to selectively excite YFP-labeled proteins. This approach enables us to distinguish between homodimer and heterodimer formation. We first present the theory and then demonstrate experimental feasibility using the ligand binding domains of retinoic acid receptor (RARLBD) and of retinoid X receptor (RXRLBD). Both proteins form heterodimers, and RXRLBD also forms homodimers in the presence of its agonist. We explore binding between these proteins in the presence and absence of RXR agonist. Our results demonstrate that brightness analysis offers a quantitative method for determining protein interactions in cells.     

CdS nanoparticles functionalized colloidal carbon particles: preparation, characterization and application for electrochemical detection of thrombin

A novel and simple method for preparing cadmium sulfide nanoparticles (CdS NPs) functionalized colloidal carbon particles (CPs) has been successfully developed by in situ growing abundant CdS NPs on the surfaces of monodisperse carbon particles (CdS/CPs). The obtained CdS/CPs conjugates as signal amplification labels were further used for the ultrasensitive determination of thrombin. The CdS/CPs conjugates were characterized by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS) and UV-visible absorption spectrum (UV). The protein electrical detection involves a dual binding event, based on thrombin linked to the CdS/CPs tags and glass surface by the specific aptamer-protein affinity interactions and a succedent electrochemical stripping transduction. Owing to the high-content CdS NPs on carbon particles, this assay allowed a desirable detection limit of 6.0 × 10(-17)M, which was 1000 times lower than that of only using CdS NPs as labels in the control experiments. This protocol exhibited excellent selectivity against these common proteins such as bovine plasma albumin, lysozyme and hemoglobin. The signal amplification approach proposed here provides a facile, cost-effective method for the ultrasensitive determination of thrombin in the practical samples.     

Real-time monitoring of receptor and G-protein interactions in living cells

G protein-coupled receptors (GPCRs) represent the largest family of proteins involved in signal transduction. Here we present a bioluminescence resonance energy transfer (BRET) assay that directly monitors in real time the early interactions between human GPCRs and their cognate G-protein subunits in living human cells. In addition to detecting basal precoupling of the receptors to Galpha-, Gbeta- and Ggamma-subunits, BRET measured very rapid ligand-induced increases in the interaction between receptor and Galphabetagamma-complexes (t(1/2) approximately 300 ms) followed by a slower (several minutes) decrease, reflecting receptor desensitization. The agonist-promoted increase in GPCR-Gbetagamma interaction was highly dependent on the identity of the Galpha-subunit present in the complex. Therefore, this G protein-activity biosensor provides a novel tool to directly probe the dynamics and selectivity of receptor-mediated, G-protein activation-deactivation cycles that could be advantageously used to identify ligands for orphan GPCRs.     

Detecting ligand interactions with G protein-coupled receptors in real-time on living cells

G protein-coupled receptors (GPCRs) are a large group of receptors of great biological and clinical relevance. Despite this, the tools for a detailed analysis of ligand–GPCR interactions are limited. The aim of this paper was to demonstrate how ligand binding to GPCRs can be followed in real-time on living cells. This was conducted using two model systems, the radiolabeled porcine peptide YY (pPYY) interacting with transfected human Y2 receptor (hY2R) and the bombesin antagonist RM26 binding to the naturally expressed gastrin-releasing peptide receptor (GRPR). By following the interaction over time, the affinity and kinetic properties such as association and dissociation rate were obtained. Additionally, data were analyzed using the Interaction Map method, which can evaluate a real-time binding curve and present the number of parallel interactions contributing to the curve. It was found that pPYY binds very slowly with an estimated time to equilibrium of approximately 12 h. This may be problematic in standard end-point assays where equilibrium is required. The RM26 binding showed signs of heterogeneity, observed as two parallel interactions with unique kinetic properties. In conclusion, measuring binding in real-time using living cells opens up for a better understanding of ligand interactions with GPCRs.     

Microorganisms living on macroalgae: diversity,interactions, and biotechnological applications

Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.     

Fluorescent proteins for FRET microscopy: monitoring protein interactions in living cells

The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live-cell imaging. In particular, the development of FPs for fluorescence (or F?rster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high fluorescence background, the potential for photoconversion artifacts and the relatively low dynamic range afforded by this technique. Here, we describe the advantages and disadvantages of four methods commonly used in FRET microscopy. We then discuss the selection of FPs for the different FRET methods, identifying the most useful FP candidates for FRET microscopy. The recent success in expanding the FP color palette offers the opportunity to explore new FRET pairs.