Oriented display of cello-oligosaccharides for pull-down binding assays to distinguish binding preferences of glycan binding proteins

The production of biofuels from lignocellulosic biomass using carbohydrate-active enzymes like cellulases is key to a sustainable energy production. Understanding the adsorption mechanism of cellulases and associated binding domain proteins down to the molecular level details will help in the rational design of improved cellulases. In nature, carbohydrate-binding modules (CBMs) from families 17 and 28 often appear in tandem appended to the C-terminus of several endocellulases. Both CBMs are known to bind to the amorphous regions of cellulose non-competitively and show similar binding affinity towards soluble cello-oligosaccharides. Based on the available crystal structures, these CBMs may display a uni-directional binding preference towards cello-oligosaccharides (based on how the oligosaccharide was bound within the CBM binding cleft). However, molecular dynamics (MD) simulations have indicated no such clear preference. Considering that most soluble oligosaccharides are not always an ideal substrate surrogate to study the binding of CBMs to the native cell wall or cell surface displayed glycans, it is critical to use alternative reagents or substrates. To better understand the binding of type B CBMs towards smaller cello-oligosaccharides, we have developed a simple solid-state depletion or pull-down binding assay. Here, we specifically orient azido-labeled carbohydrates from the reducing end to alkyne-labeled micron-sized bead surfaces, using click chemistry, to mimic insoluble cell wall surface-displayed glycans. Our results reveal that both family 17 and 28 CBMs displayed a similar binding affinity towards cellohexaose-modified beads, but not cellopentaose-modified beads, which helps rationalize previously reported crystal structure and MD data. This may indicate a preferred uni-directional binding of specific CBMs and could explain their co-evolution as tandem constructs appended to endocellulases to increase amorphous cellulose substrate targeting efficiency. Overall, our proposed workflow can be easily translated to measure the affinity of glycan-binding proteins to click-chemistry based immobilized surface-displayed carbohydrates or antigens.

A brief insight to the role of glyconanotechnology in modern day diagnostics and therapeutics

Carbohydrate-protein and carbohydrate-carbohydrate interactions are very important for various biological processes. Although the magnitude of these interactions is low compared to that of protein-protein interaction, the magnitude can be boosted by multivalent approach known as glycocluster effect. Nanoparticle platform is one of the best ways to present diverse glycoforms in multivalent manner and thus, the field of glyconanotechnology has emerged as an important field of research considering their potential applications in diagnostics and therapeutics. Considerable advances in the field have been achieved through development of novel techniques, use of diverse metallic and non-metallic cores for better efficacy and application of ever-increasing number of carbohydrate ligands for site-specific interaction. The present review encompasses the recent developments in the area of glyconanotechnology and their future promise as diagnostic and therapeutic tools.

Quantification of binding affinity of glyconanomaterials with lectins

Carbohydrate-mediated interactions are involved in many cellular activities including immune responses and infections. These interactions are relatively weak, and as such, cells employ multivalency, i.e., the presentation of multiple monovalent carbohydrate ligands within a close proximity, for cooperative binding thus drastically enhanced binding affinity. In the past two decades, the field of glyconanomaterials has emerged where nanomaterials are used as multivalent scaffolds to present multiple copies of carbohydrate ligands on the nanomaterial surface. At the core of glyconanomaterial research is the ability to control and modulate multivalency through ligand display. For the quantitative evaluation of multivalency, the binding affinity must be determined. Quantification of the binding parameters provides insights for not only the fundamental glyconanomaterial-lectin interactions, but also the rational design of effective diagnostics and therapeutics. Several methods have been developed to determine the binding affinity of glyconanomaterials with lectins, including fluorescence competitive assays in solution or on microarrays, Förster resonance energy transfer, fluorescence quenching, isothermal titration calorimetry, surface plasmon resonance spectroscopy, quartz crystal microbalance and dynamic light scattering. This Feature Article discusses each of these techniques, as well as how each technique is applied to determine the binding affinity of glyconanomaterials with lectins, and the data analysis. Although the results differed depending on the specific method used, collectively, they showed that nanomaterials as multivalent scaffolds could amplify the binding affinity of carbohydrate-lectin interactions by several orders of magnitude, the extent of which depending on the structure of the carbohydrate ligand, the ligand density, the linker length and the particle size.

Multivalent Dendrimers and their Differential Recognition of Short Single-Stranded DNAs of Various Length and Sequence

Polycationic dendrimers were generated through simple and versatile reversible amine/aldehyde-imine chemistry. The inherent CD spectroscopic signal arising from the helical structures of single-stranded DNA (ssDNA) undergoes a dramatic amplification in the presence of the synthesised polycationic dendrimers. Compared to the first-generation core molecule, the second-generation dendrimer shows high spectroscopic responses upon chiral recognition of short ssDNA, owing to the combination of self-assembly and multivalency effects. The maximum signal variation is reached at the molar ratio at which the ratio between the negative charges in ssDNA balance the positive charges of the dendrimers, thus the approach enables differential recognition of ssDNAs of different lengths. Altogether, these results accelerate the simple and systematic discovery of efficient adaptive molecules for biomimetic recognition of ssDNA with high accuracy.

Immobilization of glycans on solid surfaces for application in glycomics

Carbohydrates are an important class of biomolecules which are involved in a multitude of cellular functions. In the field of glycomics, the structure and function of various carbohydrates, oligosaccharides, glycans and their conjugates are constantly under investigation. In the continuing quest to understand the roles of carbohydrates in their interactions with proteins, immunogens, and other cell-surface carbohydrates, scientists have developed methods for observing the effects of specific saccharide sequences on various cellular components. Carbohydrate immobilization has allowed researchers to study the impact of specific sequences, leading to a deeper understanding of many cellular processes. The goal of this review is to highlight the chemical reactions and interactions that have been used for glycan immobilization.

Exponential Activation of Carbonic Anhydrase by Encapsulation in Dynameric Host Matrices with Chiral Discrimination

Herein an unexpected exponential activation of bovine carbonic anhydrase (bCA) in aqueous solutions in the presence of dynameric host matrices is reported. Successive experiments confirmed the important role of dynamic imine exchange within the dynameric host structures for direct enzyme activation. This allows for optimal encapsulation of the guest enzyme, whereas the presence of external proton-sponge amino groups is less important. Non-exchanging polymeric sec-amine congeners formed from imine reduction of dynameric structures show no obvious activation on bCA. Although the dynamers synthesized from diamino chiral-pair precursors displayed similar activation constants toward bCA, different activation delay times were observed from these two dynamers of opposite optical activity. The circular dichroism (CD) spectra demonstrate selective structural changes in the secondary structure of bCA upon dynameric encapsulation in aqueous solution. The different interaction molds observed in CD spectra for the dynamers with opposite chirality explain the longer activation time required for one of the dynamers.

Synthetic multivalency for biological applications

Current directions and emerging possibilities under investigation for the integration of synthetic and semi-synthetic multivalent architectures with biology are discussed. Attention is focussed around multivalent interactions, their fundamental role in biology, and current and potential approaches in emulating them in terms of structure and functionality using synthetic architectures.

Glyconanomaterials for biosensing applications

Nanomaterials constitute a class of structures that have unique physiochemical properties and are excellent scaffolds for presenting carbohydrates, important biomolecules that mediate a wide variety of important biological events. The fabrication of carbohydrate-presenting nanomaterials, glyconanomaterials, is of high interest and utility, combining the features of nanoscale objects with biomolecular recognition. The structures can also produce strong multivalent effects, where the nanomaterial scaffold greatly enhances the relatively weak affinities of single carbohydrate ligands to the corresponding receptors, and effectively amplifies the carbohydrate-mediated interactions. Glyconanomaterials are thus an appealing platform for biosensing applications. In this review, we discuss the chemistry for conjugation of carbohydrates to nanomaterials, summarize strategies, and tabulate examples of applying glyconanomaterials in in vitro and in vivo sensing applications of proteins, microbes, and cells. The limitations and future perspectives of these emerging glyconanomaterials sensing systems are furthermore discussed.

Glyconanoparticles with controlled morphologies and their interactions with a dendritic cell lectin

Well-defined amphiphilic block glycopolymers with equal mannose content have been self-assembled in aqueous solution to form glyconanoparticles with different morphologies.

A universal strategy for direct immobilization of intact bioactivity-conserved carbohydrates on gold nanoparticles

Carbohydrate-functioned gold nanoparticles have been highlighted for sensing complicated carbohydrates but their performance is far from ideal due to the lack of bioaffinity-conserved ways to function the particles with intact carbohydrates.

Glyconanomaterials for Combating Bacterial Infections

Bacterial infections constitute an increasing problem to human health in response to build-up of resistance to present antibiotics and sluggish development of new pharmaceuticals. However, a means to address this problem is to pinpoint the drug delivery to-and into-the bacteria. This results in a high local concentration of the drug, circumventing the increasingly high doses otherwise necessary. Combined with other effectors, such as covalent attachment to carriers, rendering the drugs less degradable, and the combination with efflux inhibitors, old drugs can be revived. In this context, glyconanomaterials offer exceptional potential, since these materials can be tailored to accommodate different effectors. In this Concept article, we describe the different advantages of glyconanomaterials, and point to their potential in antibiotic "revitalization".

Biomimetic Approach for Ion Channels Based on Surfactant Encapsulated Spherical Porous Metal-Oxide Capsules

Distinguished hybrid clusters with hydrophilic and hydrophobic interiors embedded within cationic surfactant shells are spontaneously inserted into lipid bilayers, showing well-defined ionic conductance behaviors. The transport via the narrow pore gates acting as selectivity filters is controlled by the dehydration energy of the cations.

Glyconanomaterials: Emerging applications in biomedical research

Carbohydrates constitute the most abundant organic matter in nature, serving as structural components and energy sources, and mediating a wide range of cellular activities. The emergence of nanomaterials with distinct optical, magnetic, and electronic properties has witnessed a rapid adoption of these materials for biomedical research and applications. Nanomaterials of various shapes and sizes having large specific surface areas can be used as multivalent scaffolds to present carbohydrate ligands. The resulting glyconanomaterials effectively amplify the glycan-mediated interactions, making it possible to use these materials for sensing, imaging, diagnosis, and therapy. In this review, we summarize the synthetic strategies for the preparation of various glyconanomaterials. Examples are given where these glyconanomaterials have been used in sensing and differentiation of proteins and cells, as well as in imaging glycan-medicated cellular responses.

Multivalent recognition of concanavalin A by {Mo₁₃₂ } glyconanocapsules--toward biomimetic hybrid multilayers

Herein, we consider Müller's spherical, porous, anionic, molybdenum oxide based capsule, (NH4)42[{(Mo(VI))Mo(VI)5O21(H2O)6}12{Mo(V)2O4(CH3COO)}30]⋅10 CH3COONH4⋅300 H2O≡(NH4)42⋅1 a⋅crystal ingredients≡1, {Mo132}, as an effective sugar-decorated nanoplatform for multivalent lectin recognition. The ion-exchange of NH4(+) ions of 1 with cationic-sugars, D-mannose-ammonium chloride (2) or D-glucose-ammonium chloride (3) results in the formation of glyconanocapsules (NH4)(42-n)2n⋅1 a and (NH4)(42-m)3m⋅1 a. The Mannose (NH4)(42-n)2n⋅1 a capsules bind selectively Concanavalin A (Con A) in aqueous solution, giving an association avidity constant of K(a)(multi)=4.6×10(4) M(-1) and an enhancement factor of β=K(a)(multi)/K(ass)(mono)=21.9, reminiscent of the formation of "glycoside clusters" on the external surface of glyconanocapsule. The glyconanocapsules (NH4)(42-n)2n⋅1 a and (NH4)(42-m)3m⋅1 a self-assemble in "hybrid multilayers" by successive layer-by-layer deposition of (NH4)(42-n)2n⋅1 a or (NH4)(42-m)3m⋅1 a and Con A. These architectures, reminiscent of versatile mimics of artificial tissues, can be easily prepared and quantified by using quartz crystal microgravimetry (QCM). The "biomimetic hybrid multilayers" described here are stable under a continual water flow and they may serve as artificial networks for a greater depth of understanding of various biological mechanisms, which can directly benefit the fields of chemical separations, sensors or storage-delivery devices.

β-Cyclodextrin-bearing gold glyconanoparticles for the development of site specific drug delivery systems

Three novel gold nanoparticles containing multiple long, flexible linkers decorated with lactose, β-cyclodextrin, and both simultaneously have been prepared. The interaction of such nanoparticles with β-d-galactose-recognizing lectins peanut agglutinin (PNA) and human galectin-3 (Gal-3) was demonstrated by UV-vis studies. Gal-3 is well-known to be overexpressed in several human tumors and can act as a biorecognizable target. This technique also allowed us to estimate their loading capability toward the anticancer drug methotrexate (MTX). Both results make these glyconanoparticles potential site-specific delivery systems for anticancer drugs.

Dominant behaviours in the expression of human carbonic anhydrase hCA I activity

Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.

Multivalent glycosylated nanoparticles for studying carbohydrate–protein interactions

Glyconanoparticles decorated with multiple copies of various biologically relevant carbohydrates serve as scaffolds for protein binding assay, molecular imaging, targeted therapy, and bacterium detection.

Single gold nanoparticle localized surface plasmon resonance spectral imaging for quantifying binding constant of carbohydrate-protein interaction

Quantifying carbohydrate-protein (ligand-receptor) interactions is important to understand diverse biological processes and to develop new diagnostic and therapeutic methods. We develop an approach to quantitatively study carbohydrate-protein interactions by Au nanoparticle localized surface plasmon resonance (LSPR) peak position shift at the single particles level. Unlike the previous techniques for single particle LSPR spectral imaging, only the first-order streak of an individual nanoparticle is needed to extract a LSPR spectrum, which has great potential to increase throughput to 500 single particle spectra in each frame. LSPR peak shift of protein modified single Au nanoparticles is found to be a function of its ligand concentration, which can be used to fit the binding constants of the interactions. The moderate interactions of Antithrombin III (AT III) and heparins including low molecular weight heparin (LMWH) are determined as well as the strong interaction of transferrin and antitransferrin and the weak interaction of bovine serum album (BSA) and heparin. The measured binding constants of transferrin to antitransferrin, heparin and LMWH to AT III, and BSA to heparin are (3.0 ± 0.6) × 10(9) M(-1), (3.1 ± 0.3) × 10(6) M(-1), (8.0 ± 0.5) × 10(5) M(-1), and (5.1 ± 0.1) × 10(3) M(-1), respectively, which are in good agreement with the reported values.

Multilayer lectin-glyconanoparticles architectures for QCM enhanced detection of sugar-protein interaction

Multivalent biorecognition of lectin layers by glyconanoparticle sugar-clusters has been used to generate multilayer nanoplatform architectures in a QCM sensing setup.

Multivalent presentation of a hydrolytically stable GM(3) lactone mimetic as modulator of melanoma cells motility and adhesion

A hydrolytically stable mimetic of the tumour antigen GM(3) lactone is used to decorate multivalent scaffolds. Two of them positively interfere on melanoma cell adhesion, migration and resistance to apoptosis (anoikis). Notably, their ability to hamper melanoma-cells adhesion and reduce the metastatic potential is enhanced when the two scaffolds, presenting a different shape, are used in combination.

Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps

Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.

Direct measurement of glyconanoparticles and lectin interactions by isothermal titration calorimetry

Glyconanomaterials have shown high potential in applications including bioanalysis and nanomedicine. Here, a quantitative analytical technique, based on isothermal titration calorimetry, was developed to characterize the interactions between glyconanoparticles and lectins. By titrating lectins into the glyconanoparticle solution, the apparent dissociation constant, thermodynamic parameters, and the number of binding sites were derived simultaneously. For the glyconanoparticles-lectin binding pairs investigated, a 3-5 order of magnitude affinity enhancement over the free ligand-lectin interactions was observed which can be attributed to the multivalent ligand presentation on the nanoparticles. The impact of ligand density was also studied, and results showed that the affinity increased with the number of glycans on the nanoparticle.

Site-selective modification of proteins for the synthesis of structurally defined multivalent scaffolds

A combination of classical site-directed mutagenesis, genetic code engineering and bioorthogonal reactions delivered a chemically modified barstar protein with one or four carbohydrates installed at specific residues. These protein conjugates were employed in multivalent binding studies, which support the use of proteins as structurally defined scaffolds for the presentation of multivalent ligands.

Dynamic light scattering as an efficient tool to study glyconanoparticle-lectin interactions

Glyconanomaterials, an emerging class of bio-functional nanomaterials, have shown promise in detecting, imaging and targeting proteins, bacteria, and cells. In this article, we report that dynamic light scattering (DLS) can be used as an efficient tool to study glyconanoparticle (GNP)--lectin interactions. Silica and Au nanoparticles (NPs) conjugated with D-mannose (Man) and D-galactose (Gal) were treated with the lectins Concanavalin A (Con A) and Ricinus communis agglutinin (RCA(120)), and the hydrodynamic volumes of the resulting aggregates were measured by DLS. The results showed that the particle size grew with increasing lectin concentration. The limit of detection (LOD) was determined to be 2.9 nM for Con A with Man-conjugated and 6.6 nM for RCA(120) with Gal-conjugated silica NPs (35 nm), respectively. The binding affinity was also determined by DLS and the results showed 3-4 orders of magnitude higher affinity of GNPs than the free ligands with lectins. The assay sensitivity and affinity were particle size dependent and decreased with increasing particle diameter. Because the method relies on the particle size growth, it is therefore general and can be applied to nanomaterials of different compositions.