Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design

Omics-driven bioinformatics for plant lectins discovery and functional annotation - A comprehensive review

Lectins are known for their specific and reversible binding capacity to carbohydrates. These molecules have been particularly explored in plants due to their reported properties, highlighting antimicrobial, antiviral, anticancer, antiparasitic, insecticidal, and immunoregulatory actions. The increasing availability of lectin and lectin-like sequences in omics data banks provides an opportunity to identify important candidates, inferring their roles in essential signaling pathways and processes in plants. Bioinformatics enables a fast and low-cost scenario for elucidating sequences and predicting functions in the lectinology universe. Thus, this review addresses the state of the art of annotation, structural characterization, classification, and predicted applications of plant lectins. Their allergenic and toxic properties are also discussed, as well as tools for predicting such effects from the primary structure. This review uncovers a promising scenario for plant lectins and new study possibilities, particularly for studies in lectinology in the omics era.

19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3

Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.

Exploring the role of the residues into catalytic cavity of inulosucrase from Leuconostoc citreum CW28

Inulosucrases are enzymes capable of synthesizing inulin polymers using sucrose as the main substrate. The enzymatic activity relies on the catalytic triad within the active site and residues responsible for substrate recognition and orientation, termed carbohydrate-binding subsites. This study investigates the role of specific residues within the catalytic cavity of a truncated version of IslA4 in enzymatic catalysis. Mutants at residues S425, L499, A602, R618, F619, Y676, Y692, and R696 were constructed and characterized. Characterization results, and in silico structural comparison with other fructansucrases, reveal these residues' functional significance in catalysis. Residue S425 belongs to subsite -1; residues R618 and Y692 are part of subsite +1, and residue R696 belongs to subsites +1 and +2. Residues L499 and A602 are support residues; the former favors the formation of the fructosyl-enzyme intermediate, while the latter stabilizes the acid/base catalyst during catalysis. Residues Y676 and F619 may participate in stabilizing residues at -1/+1 subsites. This study represents the first comprehensive exploration of the structural determinants essential for enzymatic function in the inulosucrase of Leuconostoc citreum, and proposes the identity of residues involved in the -1 to +2 subsites.

Investigating extrusion impact on functional, textural properties, morphological structure, and molecular interactions in hulless barley-based extruded snacks supplemented with mung bean

The effect of varying extrusion conditions on the functional properties of hulless barley-mung bean (70:30) extruded snacks was investigated using response surface methodology with feed moisture (FM), barrel temperature (BT), and screw speed (SS) as process variables. Results revealed significant impacts on functional characteristics with varying extrusion conditions. Bulk density (BD) of extruded snacks ranged from 0.24 to 0.42 g/cm3, showing that lower FM and higher BT results in lower BD while it increased with increasing FM, SS, and BT. The expansion ratio (ER) of extruded snacks ranged between 2.03 and 2.33, showing BT and SS had a desirable positive effect, whereas increasing FM led to decreased ER. Increasing BT and SS depicted a negative effect on water absorption index, whereas FM showed positive effect, which ranged between 4.21 and 4.82 g/g. A positive effect on water solubility index was depicted by BT and SS, which ranges between 9.01% and 13.45%, as higher SS and BT led to starch degradation and increased solubility suggesting better digestibility. The hardness of extruded snacks ranged from 32.56 to 66.88 Newton (N), showing increasing FM increased hardness, whereas higher SS and BT resulted in lowering the hardness. Scanning electronic microscope (SEM) analysis revealed structural changes in extrudates in comparison with nonextruded flour, indicating starch gelatinization and pore formation affected by varying processing parameters. Shifts in absorption bands were observed in Fourier transform infrared spectroscopy (FT-IR), suggesting structural changes in starch and protein. Understanding the effects of extrusion parameters on product properties can help tailored production to meet consumers' preferences and the development of functional snacks with improved nutritional quality.

Effects of adding proteins from different sources during heat-moisture treatment on corn starch structure, physicochemical and in vitro digestibility

Proteins impact starch digestion, but the specific mechanism under heat-moisture treatment remains unclear. This study examined how proteins from various sources-white kidney bean, soybean, casein, whey-altered corn starch's structure, physicochemical properties, and digestibility during heat-moisture treatment (HMT). HMT and protein addition could significantly reduce starch's digestibility. The kidney bean protein-starch complex under HMT had the highest resistant starch at 19.74 %. Most proteins effectively inhibit α-amylase, with kidney bean being the most significantly (IC50 = 1.712 ± 0.085 mg/mL). HMT makes starch obtain a more rigid structure, limits its swelling ability, and reduces paste viscosity and amylose leaching. At the same time, proteins also improve starch's short-range order, acting as a physical barrier to digestion. Rheological and low-field NMR analyses revealed that protein enhanced the complexes' shear stability and water-binding capacity. These findings enrich the understanding of how proteins from different sources affect starch digestion under HMT, aiding the creation of nutritious, hypoglycemic foods.

Synthesis and unexpected binding of monofluorinated N,N'-diacetylchitobiose and LacdiNAc to wheat germ agglutinin

Fluorination of carbohydrate ligands of lectins is a useful approach to examine their binding profile, improve their metabolic stability and lipophilicity, and convert them into 19F NMR-active probes. However, monofluorination of monovalent carbohydrate ligands often leads to a decreased or completely lost affinity. By chemical glycosylation, we synthesized the full series of methyl β-glycosides of N,N'-diacetylchitobiose (GlcNAcβ(1-4)GlcNAcβ1-OMe) and LacdiNAc (GalNAcβ(1-4)GlcNAcβ1-OMe) systematically monofluorinated at all hydroxyl positions. A competitive enzyme-linked lectin assay revealed that the fluorination at the 6'-position of chitobioside resulted in an unprecedented increase in affinity to wheat germ agglutinin (WGA) by one order of magnitude. For the first time, we have characterized the binding profile of a previously underexplored WGA ligand LacdiNAc. Surprisingly, 4'-fluoro-LacdiNAc bound WGA even stronger than unmodified LacdiNAc. These observations were interpreted using molecular dynamic calculations along with STD and transferred NOESY NMR techniques, which gave evidence for the strengthening of CH/π interactions after deoxyfluorination of the side chain of the non-reducing GlcNAc. These results highlight the potential of fluorinated glycomimetics as high-affinity ligands of lectins and 19F NMR-active probes.

Impact of red kidney bean protein on starch digestion and exploring its underlying mechanism

This study aimed to investigate the effect of different proportions of red kidney bean protein (RKP) on the digestibility of co-gelatinized wheat starch (WS) and corn starch (CS), as well as explore the potential underlying mechanisms. The results showed a significant reduction in both the rate and extent of digestion for WS and CS after adding the RKP during co-gelatinization. Furthermore, incorporating RKP at 0 % to 20 % levels increased the content of resistant starch (RS) by 34.89 % and 14.43 % in the digested systems of wheat starch and maize starch, respectively, while decreasing the concentration of rapidly digestible starch (RDS) by 12.24 % and 20.39 %, respectively. Furthermore, RKP was found to inhibit α-amylase in a dose-dependent and non-competitive manner. Its interaction with starch occurred through hydrogen bonds and hydrophobic interactions, resulting in a modification of the short-range ordered structure of starch and ultimately leading to inhibition of starch digestion. The physical barrier effect of RKP on starch digestion also contributed to its inhibitory action. Considering the health-related delay in the rate and extent of postprandial starch digestion, Our findings have important inspirational value for the use of red kidney bean protein in hypoglycemic foods.

Imaging Saturation Transfer Difference (STD) NMR: Affinity and Specificity of Protein-Ligand Interactions from a Single NMR Sample

We have combined saturation transfer difference NMR (STD NMR) with chemical shift imaging (CSI) and controlled concentration gradients of small molecule ligands to develop imaging STD NMR, a new tool for the assessment of protein-ligand interactions. Our methodology allows the determination of protein-ligand dissociation constants (K_D) and assessment of the binding specificity in a single NMR tube, avoiding time-consuming titrations. We demonstrate the formation of suitable and reproducible concentration gradients of ligand along the vertical axis of the tube, against homogeneous protein concentration, and present a CSI pulse sequence for the acquisition of STD NMR experiments at different positions along the sample tube. Compared to the conventional methodology in which the [ligand]/[protein] ratio is increased manually, we can perform STD NMR experiments at a greater number of ratios and construct binding epitopes in a fraction (∼20%) of the experimental time. Second, imaging STD NMR also allows us to screen for non-specific binders, by monitoring any variation of the binding epitope map at increasing [ligand]/[protein] ratios. Hence, the proposed method does carry the potential to speed up and smooth out the drug discovery process.

Structure-based neural network protein-carbohydrate interaction predictions at the residue level

Carbohydrates dynamically and transiently interact with proteins for cell-cell recognition, cellular differentiation, immune response, and many other cellular processes. Despite the molecular importance of these interactions, there are currently few reliable computational tools to predict potential carbohydrate-binding sites on any given protein. Here, we present two deep learning (DL) models named CArbohydrate-Protein interaction Site IdentiFier (CAPSIF) that predicts non-covalent carbohydrate-binding sites on proteins: (1) a 3D-UNet voxel-based neural network model (CAPSIF:V) and (2) an equivariant graph neural network model (CAPSIF:G). While both models outperform previous surrogate methods used for carbohydrate-binding site prediction, CAPSIF:V performs better than CAPSIF:G, achieving test Dice scores of 0.597 and 0.543 and test set Matthews correlation coefficients (MCCs) of 0.599 and 0.538, respectively. We further tested CAPSIF:V on AlphaFold2-predicted protein structures. CAPSIF:V performed equivalently on both experimentally determined structures and AlphaFold2-predicted structures. Finally, we demonstrate how CAPSIF models can be used in conjunction with local glycan-docking protocols, such as GlycanDock, to predict bound protein-carbohydrate structures.

Study on the mechanism of various exogenous proteins with different inhibitions on wheat starch digestion: From the distribution behaviors of protein in the starch matrix

This study aimed to compare the effect of various exogenous proteins on wheat starch (WS) digestion and assess the relevant mechanisms based on the distribution behaviors of exogenous proteins in the starch matrix. Rice protein (RP), soy protein isolate (SPI), and whey protein isolate (WPI) all effectively suppressed the rapid digestion of WS but with different modes. RP increased the slowly digestible starch content, while SPI and WPI increased the resistant starch content. Fluorescence images showed that RP aggregated and competed for effective space with starch granules, while SPI and WPI formed continuous network structures among the starch matrix. These distribution behaviors endowed different reductions in starch digestion by influencing the gelatinization and ordered structure of starch. Pasting and water mobility results suggested all exogenous proteins inhibited the water migration and swelling of starch. Simultaneously, X-ray diffraction and Fourier transform infrared spectroscopy analysis showed that exogenous proteins improved the ordered structures of starch. RP had a more significant effect on the long-term ordered structure, while SPI and WPI had a more effective effect on the short-term ordered structure. These findings will enrich the theory of exogenous protein inhibiting starch digestion and inspire the applications in low-glycemic index food.

Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems

Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.

Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

Carbohydrates dynamically and transiently interact with proteins for cell-cell recognition, cellular differentiation, immune response, and many other cellular processes. Despite the molecular importance of these interactions, there are currently few reliable computational tools to predict potential carbohydrate binding sites on any given protein. Here, we present two deep learning models named CArbohydrate-Protein interaction Site IdentiFier (CAPSIF) that predict carbohydrate binding sites on proteins: (1) a 3D-UNet voxel-based neural network model (CAPSIF:V) and (2) an equivariant graph neural network model (CAPSIF:G). While both models outperform previous surrogate methods used for carbohydrate binding site prediction, CAPSIF:V performs better than CAPSIF:G, achieving test Dice scores of 0.597 and 0.543 and test set Matthews correlation coefficients (MCCs) of 0.599 and 0.538, respectively. We further tested CAPSIF:V on AlphaFold2-predicted protein structures. CAPSIF:V performed equivalently on both experimentally determined structures and AlphaFold2 predicted structures. Finally, we demonstrate how CAPSIF models can be used in conjunction with local glycan-docking protocols, such as GlycanDock, to predict bound protein-carbohydrate structures.

Exploring the interaction sites in glucose and galactose using phenol as a probe

Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.

Phosphorylation of IGFBP-3 by Casein Kinase 2 Blocks Its Interaction with Hyaluronan, Enabling HA-CD44 Signaling Leading to Increased NSCLC Cell Survival and Cisplatin Resistance

Cisplatin is a platinum agent used in the treatment of non-small cell lung cancer (NSCLC). Much remains unknown regarding the basic operative mechanisms underlying cisplatin resistance in NSCLC. In this study, we found that phosphorylation of IGFBP-3 by CK2 (P-IGFBP-3) decreased its binding to hyaluronan (HA) but not to IGF-1 and rendered the protein less effective at reducing cell viability or increasing apoptosis than the non-phosphorylated protein with or without cisplatin in the human NSCLC cell lines, A549 and H1299. Our data suggest that blocking CD44 signaling augmented the effects of cisplatin and that IGFBP-3 was more effective at inhibiting HA-CD44 signaling than P-IGFBP-3. Blocking CK2 activity and HA-CD44 signaling increased cisplatin sensitivity and more effectively blocked the PI3K and AKT activities and the phospho/total NFκB ratio and led to increased p53 activation in A549 cells. Increased cell sensitivity to cisplatin was observed upon co-treatment with inhibitors targeted against PI3K, AKT, and NFκB while blocking p53 activity decreased A549 cell sensitivity to cisplatin. Our findings shed light on a novel mechanism employed by CK2 in phosphorylating IGFBP-3 and increasing cisplatin resistance in NSCLC. Blocking phosphorylation of IGFBP-3 by CK2 may be an effective strategy to increase NSCLC sensitivity to cisplatin.

Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies

Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed carbohydrate-based ionic liquids. Subsequently, we employed MD simulations to obtain information about the interactions of these known and designed ILs with the cell membrane. In our approach, we adopted QM and MD studies and illustrated that there could be a link between the QM and MD results.

Carbohydrate-based drugs launched during 2000-2021

Carbohydrates are fundamental molecules involved in nearly all aspects of lives, such as being involved in formating the genetic and energy materials, supporting the structure of organisms, constituting invasion and host defense systems, and forming antibiotics secondary metabolites. The naturally occurring carbohydrates and their derivatives have been extensively studied as therapeutic agents for the treatment of various diseases. During 2000 to 2021, totally 54 carbohydrate-based drugs which contain carbohydrate moities as the major structural units have been approved as drugs or diagnostic agents. Here we provide a comprehensive review on the chemical structures, activities, and clinical trial results of these carbohydrate-based drugs, which are categorized by their indications into antiviral drugs, antibacterial/antiparasitic drugs, anticancer drugs, antidiabetics drugs, cardiovascular drugs, nervous system drugs, and other agents.

Investigation of the Binding of Lectins with Polymer Glycoconjugates and the Glycoconjugates Containing Silver Nanoparticles by Means of Optical Spectroscopy and Light Scattering

The synthesis of glycoconjugates, lectin-specific polymers containing a carbohydrate ligand (spacered residue of N-acetyl-D-glucosamine, β-N-Gly-GlcNAc) has been carried out. Glyconanoparticles (glycol-NPs) containing a label detectable by means of spectrophotometry, silver nanoparticles, have been prepared on the basis of the glycoconjugates. Copolymers of maleic anhydride with ethylene or N-vinylpyrrolidone have been used as a carrier to introduce the carbohydrate ligand and a stabilizer of silver nanoparticles. Solutions of the glycoconjugates and the silver glyconanoparticles have been characterized by means of light scattering, UV-visible spectroscopy, and TEM. The interaction of the obtained glycoconjugates and silver glyconanoparticles with N-acetyl-D-glucosamine-specific lectins of Solanum tuberosum agglutinin (STA) and wheat germ agglutinin (WGA) has been investigated by means of light scattering and UV-visible spectro-scopy. The data obtained via these physical methods using the carbohydrate-containing derivatives labeled with silver nanoparticles have been in agreement. It has been shown that the glycoconjugates and silver glyconanoparticles based on more hydrophilic copolymer of maleic acid with N-vinylpyrrolidone are more sensitive than the respective systems based on more hydrophobic copolymer of maleic acid with ethylene. It has been also shown that the considered systems are more sensitive to the STA lectin than to the WGA lectin. The silver glyconanoparticles have allowed more accurate and reliable detection of the lectins by means of light scattering, as compared to the glycopolymer.

Preparation of Natural Food-Grade Core-Shell Starch/Zein Microparticles by Antisolvent Exchange and Transglutaminase Crosslinking for Reduced Digestion of Starch

The purpose of this study was to slow down the digestibility of starch granules by encapsulating it in zein shells. Drop of the preformed swollen corn starch (CS) granule suspension into thermal-treated zein ethanolic solution enables antisolvent precipitation of thermal-treated zein on the surface of the preformed swollen CS granules, leading to the formation of core-shell starch/zein microparticles. Confocal laser scanning microscopy images showed that the preformed swollen CS granules were coated by thermal-treated zein shells with a thickness of 0.48–0.95 μm. The volume average particle diameter of core-shell starch/zein microparticles was 14.70 μm and reached 18.59–30.98 μm after crosslinking by transglutaminase. The results of X-ray diffraction and Fourier transform infrared spectroscopy demonstrated that an interaction occurred between the preformed swollen CS granules and the thermal-treated zein. The results for thermodynamic characteristics, pasting properties, and swelling power indicated that the compact network structure of core-shell starch/zein microparticles crosslinked by transglutaminase could improve starch granule thermal stability and resistance to shearing forces. Compared to native CS, the peak gelatinization temperatures of core-shell starch/zein microparticles increased significantly (p < 0.05), with a maximum value of 76.64°C. The breakdown values and the swelling power at 95°C of core-shell starch/zein microparticles significantly (p < 0.05) decreased by 52.83–85.66% and 0.11–0.28%, respectively. The in vitro digestibility test showed that the contents of slowly digestible starch and resistant starch in the core-shell starch/zein microparticles increased to ∼42.66 and ∼34.75%, respectively, compared to those of native CS (9.56 and 2.48%, respectively). Our research supports the application of food-grade core-shell starch/zein microparticles to formulate low-digestibility food products.

Influenza A virus diffusion through mucus gel networks

Mucus in the lung plays an essential role as a barrier to infection by viral pathogens such as influenza A virus (IAV). Previous work determined mucin-associated sialic acid acts as a decoy receptor for IAV hemagglutinin (HA) binding and the sialic-acid cleaving enzyme, neuraminidase (NA), facilitates virus passage through mucus. However, it has yet to be fully addressed how the physical structure of the mucus gel influences its barrier function and its ability to trap viruses via glycan mediated interactions to prevent infection. To address this, IAV and nanoparticle diffusion in human airway mucus and mucin-based hydrogels is quantified using fluorescence video microscopy. We find the mobility of IAV in mucus is significantly influenced by the mesh structure of the gel and in contrast to prior reports, these effects likely influence virus passage through mucus gels to a greater extent than HA and NA activity. In addition, an analytical approach is developed to estimate the binding affinity of IAV to the mucus meshwork, yielding dissociation constants in the mM range, indicative of weak IAV-mucus binding. Our results provide important insights on how the adhesive and physical barrier properties of mucus influence the dissemination of IAV within the lung microenvironment.

Influenza A virus movement in mucus is found to be affected by the mesh structure of the gel network and further analysis reveals weak IAV-mucus binding.

A review on the antimicrobial properties of lectins

Lectins are biologically versatile biomolecules with remarkable antimicrobial effects, notably against bacteria, fungi and protozoa, in addition to modulating host immunity. For this, the lectins bind to carbohydrates on the surface of the pathogen, which can cause damage to the cell wall and prevent the attachment of microorganisms to host cells. Thus, this study intends to review the biological activities of lectins, with an emphasis on antimicrobial activity. Lectins of plant stood out for its antimicrobial effects, demonstrating that they act against a variety of strains, where in vitro were able to inhibit their development and affect their morphology. In vivo, they modulated host immunity, signaling and activating defense cells. Some of these lectins were capable to modulate the action of antibiotics, indicating their potential to minimize the antibiotic resistance. The results suggest that lectins have antimicrobial activity with potential to be used in drug development.

Plant protein-based fibers: Fabrication, characterization, and potential food applications

Proteins from plants have been considered as safer, healthier, and more sustainable resources than their animal counterparts. However, incomplete amino acid composition and relatively poor functionality limit their applications in foods. Structuring plant proteins to fibrous architectures enhances their physicochemical properties, which can favor various food applications. This review primarily focuses on fabrication of fibers from plant proteins via self-assembly, electrospinning, solution blow spinning, wet spinning, and high-temperature shear, as well as on several applications where such fibrous proteins assemble in quality foods. The changes of protein structure and protein-protein interactions during fiber production are discussed in detail, along with the effects of fabrication conditions and protein sources on the morphology and function of the fibers. Self-assembly requires proteolysis and subsequent peptide aggregation under specific conditions, which can be influenced by pH, salt and protein type. The spinning strategy is more scalable and produces uniformed fibers with larger length scales suitable for encapsulation, food packaging and sensor substrates. Significant progress has been made on high-temperature shear (including extrusion)-induced fibers responsible for desirable texture in meat analogues. Structuring plant proteins adds values for broadened food applications, but it remains challenging to keep processes cost-effective and environmentally friendly using food grade solvents.

CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins

Elucidating protein rigidity offers insights about protein conformational changes. An understanding of protein motion can help speed drug development, and provide general insights into the dynamic behaviors of biomolecules. Existing rigidity analysis techniques employ fine-grained, all-atom modeling, which has a costly run-time, particularly for proteins made up of more than 500 residues. In this work, we introduce coarse-grained rigidity analysis, and showcase that it provides flexibility information about a protein that is similar in accuracy to an all-atom modeling approach. We assess the accuracy of the coarse-grained method relative to an all-atom approach via a comparison metric that reasons about the largest rigid clusters of the two methods. The apparent symmetry between the all-atom and coarse-grained methods yields very similar results, but the coarse-grained method routinely exhibits 40% reduced run-times. The CGRAP web server outputs rigid cluster information, and provides data visualization capabilities, including a interactive protein visualizer.

NMR spectroscopy of wastewater: A review, case study, and future potential

NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (¹³C, ¹⁵N, ¹⁹F, ³¹P, ²⁹Si) as well as other environmentally relevant nuclei and metals such as ²⁷Al, ⁵¹V, ²⁰⁷Pb and ¹¹³Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.

Conformational and Structural characterization of carbohydrates and their interactions studied by NMR

Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.

Comparison of Carbohydrate Force Fields in Molecular Dynamics Simulations of Protein-Carbohydrate Complexes

In this paper, we present the results of molecular dynamics simulations aimed at critical comparison of classical, biomolecular force fields (FFs) in the context of their capabilities to describe the structural and thermodynamic features of carbohydrate-protein interactions. We have considered the three main families of FFs (CHARMM, GROMOS, and GLYCAM/AMBER) by applying them to investigate the seven different carbohydrate-protein complexes. The results indicate that although the qualitative pattern of several structural descriptors (intermolecular hydrogen bonding, ligand dynamic location, etc.) is conserved among the compared FFs, there also exists a number of significant divergences (mainly the patterns of contacts between particular amino acid residues and bound carbohydrate). The carbohydrate-protein unbinding free energies also vary from one FF to another, displaying diversified trends in deviations from the experimental data. The magnitude of those deviations is not negligible and indicates the need for refinement in the currently existing combinations of carbohydrate- and protein-dedicated biomolecular force fields. In spite of the lack of explicit functional terms responsible for the corresponding intermolecular forces, all tested FFs are capable of adequately reproducing the CH-π interactions, crucial for carbohydrate-protein binding.

A Simple Biomimetic Receptor Selectively Recognizing the GlcNAc2 Disaccharide in Water

GlcNAc₂ is the core disaccharide fragment present in N-glycans exposed on the surface of enveloped viruses of high health concern, such as coronaviruses. Because N-glycans are directly involved in the docking of viruses to host cells, recognition of GlcNAc₂ by a biomimetic receptor may be a convenient alternative to the use of lectins to interfere with viral entry and infection. Herein, we describe a simple biomimetic receptor recognizing the methyl-β-glycoside of GlcNAc₂ in water with an unprecedented affinity of 160 μM, exceeding that of more structurally complex receptors reported in the literature. The tweezers-shaped acyclic structure exhibits marked selectivity among structurally related disaccharides, and complete discrimination between mono- and disaccharides. Molecular modelling calculations supported by NOE data provided a three-dimensional description of the binding mode, shedding light on the origin of the affinities and selectivities exhibited by the receptor.

Starch-protein interplay varies the multi-scale structures of starch undergoing thermal processing

This work concerns how starch-protein interplay affects the multi-scale structures (e.g., short- and long-range orders, nanoscale structure and morphology) of starch undergoing thermal processing (pasting) involving heating and cooling at high water content. An indica rice starch (IRS) and three proteins (whey protein isolate, WPI; soy protein isolate, SPI; casein, CS) were used. By inspecting rheological profiles of mixed systems before and after adding chemicals, IRS-WPI and IRS-CS showed mainly hydrophobic molecular interaction; and IRS-SPI exhibited hydrophobic, hydrogen bonding and electrostatic interactions. The RVA results revealed that, with starch and proteins as controls, starch-globular protein (WPI or SPI) interplay accelerated the swelling of starch granules (faster viscosity increase at initial pasting stage), and reduced the paste stability during heating (higher breakdown) and during cooling (higher setback); however, the starch-casein interactions resulted in opposed effects. Moreover, starch-protein interactions varied the multi-scale chain reassembly of starch into different structures during cooling. Observed could be fewer short- and long-range starch orders, and larger nonperiod structure (or colloidal clusters) on the nanoscale. On even larger scale to micron, IRS-globular protein molecules generated larger grids (with reduced number) in the gel network, and IRS-casein formed a more continuous gel network with less prominent tunnel-like features.

Overcoming challenges in developing small molecule inhibitors for GPVI and CLEC-2

GPVI and CLEC-2 have emerged as promising targets for long-term prevention of both arterial thrombosis and thrombo-inflammation with a decreased bleeding risk relative to current drugs. However, while there are potent blocking antibodies of both receptors, their protein nature comes with decreased bioavailability, making formulation for oral medication challenging. Small molecules are able to overcome these limitations, but there are many challenges in developing antagonists of nanomolar potency, which is necessary when considering the structural features that underlie the interaction of CLEC-2 and GPVI with their protein ligands. In this review, we describe current small-molecule inhibitors for both receptors and strategies to overcome such limitations, including considerations when it comes to in silico drug design and the importance of complex compound library selection.

Carbohydrate-Protein Interactions: Advances and Challenges

A carbohydrate, also called saccharide in biochemistry, is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. For example, sugars are low molecular-weight carbohydrates, and starches are high molecular-weight carbohydrates. Carbohydrates are the most abundant organic substances in nature and essential constituents of all living things. Protein-carbohydrate interactions play important roles in many biological processes, such as cell growth, differentiation, and aggregation. They also have broad applications in pharmaceutical drug design. In this review, we will summarize the characteristic features of protein-carbohydrate interactions and review the computational methods for structure prediction, energy calculations, and kinetic studies of protein-carbohydrate complexes. Finally, we will discuss the challenges in this field.

A Glucose binding lectin from Leucaena leucocephala seeds and its mitogenic activity against human lymphocytes

Lectins are a specialized group of proteins with immense biological properties and applications. This study describes the purification and characterization of a lectin from Leucaena leucocephala seeds, a plant belonging to the Fabaceae family. Leucaena leucocephala lectin (LLL) was purified by a two-step purification method involving DEAE-cellulose anion exchange chromatography and Sephadex G-75 size exclusion chromatography. The isolated lectin displayed a high haemagglutination titre upon treatment with rabbit erythrocytes. SDS-PAGE and Reverse-Phase High performance liquid chromatography (RP-HPLC) analysis experimentally revealed the presence of three bands corresponding to 37, 27 and 20 kDa indicating the presence of isolectins. Periodic Acid Schiff's (PAS) staining of LLL confirmed the presence of glycoprotein. Various biochemical parameters were analysed to study its effect on the haemagglutination activity. Sugar inhibition studies experimentally revealed that Glucose was the most potent inhibitor. Fluorescence spectrometric analysis of LLL and Glucose indicated a strong interaction with an association constant of 0.159 × 10³ M^-1. Circular Dichroism spectroscopy indicated a higher alpha helical content (25.27%). LLL was observed to possess mitogenic activity against Peripheral blood mononuclear cells (PBMC). The present investigation reports the isolation of a novel lectin from this plant which could contribute towards the diagnostic studies of certain diseases and for its therapeutic potential.

Effects of Stereochemistry and Hydrogen Bonding on Glycopolymer-Amyloid-β Interactions

Saccharide stereochemistry plays an important role in carbohydrate functions such as biological recognition processes and protein binding. Synthetic glycopolymers with pendant saccharides of controlled stereochemistry provide an attractive approach for the design of polysaccharide-inspired biomaterials. Acrylamide-based polymers containing either β,d-glucose or β,d-galactose pendant groups, designed to mimic GM1 ganglioside saccharides, and their small-molecule analogues were used to evaluate the effect of stereochemistry on glycopolymer solution aggregation processes alone and in the presence of Aβ42 peptide using dynamic light scattering, gel permeation chromatography-multiangle laser light scattering, and fluorescence assays. Fourier transform infrared and nuclear magnetic resonance (NMR) were employed to determine hydrogen bonding patterns of the systems. The galactose-containing polymer displayed significant intramolecular hydrogen bonding and self-aggregation and minimal association with Aβ42, while the glucose-containing glycopolymers showed intermolecular interactions with the surrounding environment and association with Aβ42. Saturation transfer difference NMR spectroscopy demonstrated different binding affinities for the two glycopolymers to Aβ42 peptide.

Neurological disorders-associated anti-glycosphingolipid IgG-antibodies display differentially restricted IgG subclass distribution

Antibodies against several self-glycans on glycosphingolipids are frequently detected in different neurological disorders. Their pathogenic role is profusely documented, but the keys for their origin remain elusive. Additionally, antibodies recognizing non-self glycans appear in normal human serum during immune response to bacteria. Using HPTLC-immunostaining we aimed to characterize IgM and IgG subclass antibody responses against glycosphingolipids carrying self glycans (GM1/GM2/GM3/GD1a/GD1b/GD3/GT1b/GQ1b) and non-self glycans (Forssman/GA1/“A” blood group/Nt7) in sera from 27 randomly selected neurological disorder patients presenting IgG reactivity towards any of these antigens. Presence of IgG2 (p = 0.0001) and IgG1 (p = 0.0078) was more frequent for IgG antibodies against non-self glycans, along with less restricted antibody response (two or more simultaneous IgG subclasses). Contrariwise, IgG subclass distribution against self glycans showed clear dominance for IgG3 presence (p = 0.0017) and more restricted IgG-subclass distributions (i.e. a single IgG subclass, p = 0.0133). Interestingly, anti-self glycan IgG antibodies with simultaneous IgM presence had higher proportion of IgG2 (p = 0.0295). IgG subclass frequencies were skewed towards IgG1 (p = 0.0266) for “anti-self glycan A” subgroup (GM2/GM1/GD1b) and to IgG3 (p = 0.0007) for “anti-self glycan B” subgroup (GM3/GD1a/GD3/GT1b/GQ1b). Variations in players and/or antigenic presentation pathways supporting isotype (M-G) and IgG-subclass pattern differences in the humoral immune response against glycosphingolipids carrying non-self versus self-glycans are discussed.

Biochemical determinants of the IGFBP-3-hyaluronan interaction

IGFBP-3, the most abundant IGFBP and the main carrier of insulin-like growth factor I (IGF-I) in the circulation, can bind IGF-1 with high affinity, which attenuates IGF/IGF-IR interactions, thereby resulting in antiproliferative effects. The C-terminal domain of insulin-like growth factor-binding protein-3 (IGFBP-3) is known to contain an 18-basic amino acid motif capable of interacting with either humanin (HN) or hyaluronan (HA). We previously showed that the 18-amino acid IGFBP-3 peptide is capable of binding either HA or HN with comparable affinities to the full-length IGFBP-3 protein and that IGFBP-3 can compete with the HA receptor, CD44, for binding HA. Blocking the interaction between HA and CD44 reduced viability of A549 human lung cancer cells. In this study, we set out to better characterize IGFBP-3-HA interactions. We show that both stereochemistry and amino acid identity are important determinants of the interaction between the IGFBP-3 peptide and HA and for the peptide's ability to exert its cytotoxic effects. Binding of IGFBP-3 to either HA or HN was unaffected by glycosylation or reduction of IGFBP-3, suggesting that the basic 18-amino acid residue sequence of IGFBP-3 remains accessible for interaction with either HN or HA upon glycosylation or reduction of the full-length protein. Removing N-linked oligosaccharides from CD44 increased its ability to compete with IGFBP-3 for binding HA, while reduction of CD44 rendered the protein relatively ineffective at blocking IGFBP-3-HA interactions. We conclude that both deglycosylation and disulfide bond formation are important for CD44 to compete with IGFBP-3 for binding HA.

Rational identification and characterisation of peptide ligands for targeting polysialic acid

The alpha-2,8-linked form of the polysaccharide polysialic acid (PSA) has widespread implications in physiological and pathological processes, ranging from neurological development to disease progression. Though the high electronegativity and excluded volume of PSA often promotes interference of biomolecular interactions, PSA-binding ligands have important implications for both biological processes and biotechnological applications. As such, the design, identification, and characterisation of novel ligands towards PSA is critical for expanding knowledge of PSA interactions and achieving selective glycan targeting. Here, we report on a rational approach for the identification of alpha-2,8-PSA-binding peptides, involving design from the endogenous ligand Siglec-11 and multi-platform characterisation of peptide binding. Microarray-based examination of peptides revealed charge and sequence characteristics influencing peptide affinity to PSA, and carbohydrate-peptide binding was further quantified with a novel fluorescence anisotropy assay. PSA-binding peptides exhibited specific binding to polymeric SA, as well as different degrees of selective binding in various conditions, including competition with PSA of alternating 2,8/9-linkages and screening with PSA-expressing cells. A computational study of Siglec-11 and Siglec-11-derived peptides offered synergistic insight into ligand binding. These results demonstrate the potential of PSA-binding peptides for selective targeting and highlight the importance of the approaches described herein for the study of carbohydrate interactions.

IGFBP-3 Blocks Hyaluronan-CD44 Signaling, Leading to Increased Acetylcholinesterase Levels in A549 Cell Media and Apoptosis in a p53-Dependent Manner

Insulin-like growth factor binding protein-3 (IGFBP-3) belongs to a family of six IGF binding proteins. We previously found that IGFBP-3 exerts its cytotoxic effects on A549 (p53 wild-type) cell survival through a mechanism that depends on hyaluronan-CD44 interactions. To shed light on the mechanism employed, we used CD44-negative normal human lung cells (HFL1), A549, and H1299 (p53-null) lung cancer cells. A synthetic IGFBP-3 peptide (²¹⁵-KKGFYKKKQCRPSKGRKR-²³²) but not the mutant (K228AR230A), was able to bind hyaluronan more efficiently than the analogous sequences from the other IGFBPs. In a manner comparable to that of the IGFBP-3 protein, the peptide blocked hyaluronan-CD44 signaling, and more effectively inhibited viability of A549 cells than viability of either H1299 or HFL1 cell lines. Treatment with the IGFBP-3 protein or its peptide resulted in increased acetylcholinesterase concentration and activity in the A549 cell media but not in the media of either HFL1 or H1299, an effect that correlated with increased apoptosis and decreased cell viability. These effects were diminished upon the same treatment of A549 cells transfected with either p53 siRNA or acetylcholinesterase siRNA. Taken together, our results show that IGFBP-3 or its peptide blocks hyaluronan-CD44 signaling via a mechanism that depends on both p53 and acetylcholinesterase.

Comparative Study of Aryl O-, C-, and S-Mannopyranosides as Potential Adhesion Inhibitors toward Uropathogenic E. coli FimH

A set of three mannopyranoside possessing identical 1,1'-biphenyl glycosidic pharmacophore but different aglyconic atoms were synthesized using either a palladium-catalyzed Heck cross coupling reaction or a metathesis reaction between their corresponding allylic glycoside derivatives. Their X-ray structures, together with their calculated 3D structures, showed strong indicators to explain the observed relative binding abilities against E. coli FimH as measured by a improved surface plasmon resonance (SPR) method. Amongst the O-, C-, and S-linked analogs, the C-linked analog showed the best ability to become a lead candidate as antagonist against uropathogenic E. coli with a Kd of 11.45 nM.

NMR Methods to Characterize Protein-Ligand Interactions

Structural information pertaining to the interactions between biological macromolecules and ligands is of potential significance for understanding of molecular mechanisms in key biological processes. Recently, nuclear magnetic resonance (NMR) spectroscopic techniques has come of age and has widened its scope to characterize binding interactions of small molecules with biological macromolecules especially, proteins. NMR spectroscopy-based techniques are versatile due to their ability to examine weak binding interactions and for rapid screening the binding affinities of ligands with proteins at atomic resolution. In this review, we provide a broad overview of some of the important NMR approaches to investigate interactions of small organic molecules with proteins.

Spatially Resolved STD-NMR Applied to the Study of Solute Transport in Biphasic Systems: Application to Protein-Ligand Interactions

Fluid biphasic systems are one of the most interesting dynamic systems in chemistry and biochemistry. In nuclear magnetic resonance (NMR) spectroscopy, the study of the solute dynamics across fluid biphasic systems requires the introduction of dedicated NMR methods, due to their intrinsic heterogeneity. Diffusion and spatially resolved NMR techniques represent a useful approach for dealing with the study of solutes in biphasic systems and have been applied lately with success. Nevertheless, other potential applications of NMR spectroscopy for biphasic systems remain to be explored. In this proof-of-concept communication, we specifically aimed to investigate whether solute exchange between two immiscible phases can be followed by NMR experiments involving transfer of magnetization. To that aim, we have used spatially resolved saturation transfer difference NMR (SR-STD NMR) experiments to analyze solute exchange by transfer of saturation from one phase to the other in a biphasic system and have explored which are the underlying mechanisms leading to the transfer of magnetization between phases and the limits of the approach. We hereby demonstrate that SR-STD NMR is feasible and that it might be implemented in pharmacological screening for binders of biological receptors or in the study of chemical and biochemical reactions occurring at interfaces.

Novel model of secreted human tau protein reveals the impact of the abnormal N-glycosylation of tau on its aggregation propensity

Alzheimer’s disease (AD) is the most common neurodegenerative disorder and has no disease-modifying treatment yet. The hallmarks of AD are two amyloidogenic proteins: tau and amyloid β (Aβ). Tau undergoes several posttranslational modifications, including N-glycosylation. Tau was reported to be N-glycosylated in AD brains, but not in healthy counterparts, which may affect AD etiology. Here, we aimed to examine the effect of N-glycosylation on aggregation propensity of tau. To that end, a novel SH-SY5Y cell-based model was generated in which recombinant human tau (htau) is forced to be secreted from the cells. Secreted htau was found to localize in the secretory pathway compartments and to undergo N-glycosylation. Following N-glycan cleavage of the secreted htau, various biophysical results collectively indicated that the untreated N-glycosylated secreted htau is markedly less aggregative, contains thinner and shorter fibrils, as compared to treated de-glycosylated secreted htau. This finding shows that N-glycans attached to htau may affect its aggregation. This could help to better understand the effect of N-glycosylated htau on AD progression.

Cations brought together by hydrogen bonds: the protonated pyridine–boronic acid dimer explained

Stable dimers of protonated pyridine–boronic acid are found in the gas phase and solvent models. The importance of electrostatics is discussed.

Interaction of Insulin-Like Growth Factor-Binding Protein 3 With Hyaluronan and Its Regulation by Humanin and CD44

Insulin-like growth factor-binding protein-3 (IGFBP-3) belongs to a family of IGF-binding proteins. Humanin is a peptide known to bind residues 215-232 of mature IGFBP-3 in the C-terminal region of the protein. This region of IGFBP-3 was shown earlier to bind certain glycosaminoglycans including hyaluronan (HA). Here, we characterized the binding affinities of the IGFBP-3 protein and peptide (²¹⁵-KKGFYKKKQCRPSKGRKR-²³²) to HA and to humanin and found that HA binds with a weaker affinity to this region than does humanin. Either HA or humanin could bind to this IGFBP-3 segment, but not simultaneously. The HA receptor, CD44, blocked HA binding to IGFBP-3 but had no effect on binding of humanin to either IGFBP-3 or its peptide. Upon incubation of HA with CD44 and either IGFBP-3 protein or peptide, humanin was effective at binding and sequestering IGFBP-3 or peptide, thereby enabling access of CD44 to HA. We show that IGFBP-3 and humanin in the medium of A549 lung cancer cells can immunoprecipitate in a complex. However, the fraction of IGFBP-3 in the medium that is able to bind HA was not complexed with humanin suggesting that HA binding to the 215-232 segment renders it inaccessible for binding to humanin. Moreover, while the cytotoxic effects of IGFBP-3 on cell viability were reversed by humanin, blocking HA-CD44 interaction with an anti-CD44 antibody in combination with IGFBP-3 did not have an additive negative effect on cell viability suggesting that IGFBP-3 exerts its cytotoxic effects on cell survival through a mechanism that depends on HA-CD44 interactions.

The recognition of glycans by protein receptors. Insights from NMR spectroscopy

Carbohydrates (glycans, saccharides, sugars) are everywhere. In fact, glycan-protein interactions are involved in many essential processes of life and disease. The understanding of the key structural details at the atomic and molecular level is of paramount importance to effectively design molecules for therapeutic purposes. Different approximations may be employed to decipher these molecular recognition processes with high resolution. Advances in cryo-electron microscopy are providing exquisite details on different biological mechanisms involving sugars, while better and better protocols for structural refinement in the application of X-ray methods for protein-sugar complexes and glycoproteins are also permitting fantastic advances in the glycoscience arena. Alternatively, NMR spectroscopy remains as one of the most rewarding techniques to explore protein-carbohydrate interactions. In fact, given the intrinsic dynamic nature of saccharides, NMR can afford exquisite structural information at the atomic detail, not accessible by other techniques. However, the access to this information is sometimes intricate, and requires careful analysis and well-defined strategies. In this review, we have highlighted these issues and presented an overview of different modern NMR approaches with a focus on the latest developments and challenges.