Protein-carbohydrate Complexes Research Articles

Quantifying Carbohydrate–Protein Interactions by Electrospray Ionization Mass Spectrometry Analysis

The development of analytical methods capable of characterizing carbohydrate-protein interactions, which are critical for many biological processes, represents an active area of research. Recently, the direct electrospray ionization mass spectrometry (ESI-MS) assay has emerged as a valuable tool for identifying and quantifying carbohydrate-protein complexes in vitro. The assay boasts a number of strengths, including its simplicity, speed, low level of sample consumption, and the unique ability to directly probe binding stoichiometry and to measure multiple binding equilibria simultaneously. Here, we describe the implementation of the direct ESI-MS assay for the determination of carbohydrate-protein binding stoichiometries and affinities. Common sources of error encountered with direct ESI-MS analysis of carbohydrate-protein interactions are identified along with strategies for minimizing their effects. The application of ESI-MS and a catch-and-release strategy for carbohydrate library screening are also described. The utility of the direct ESI-MS assay can be extended by combining the technique with competitive protein or ligand binding. An overview of these "indirect" ESI-MS methods is given, as well as examples of recent applications.

The Antiproliferative Activity of Sclerotia ofLignosus rhinocerus(Tiger Milk Mushroom)

Lignosus rhinocerus, the tiger milk mushroom, is one of the most important medicinal mushrooms used by the indigenous people of Southeast Asia and China. It has been used to treat breast cancer. A cold water extract (LR-CW) prepared from the sclerotia of L. rhinocerus cultivar was found to exhibit antiproliferative activity against human breast carcinoma (MCF-7) and human lung carcinoma (A549), with IC50 of 96.7 μg/mL and 466.7 μg/mL, respectively. In comparison, LR-CW did not show significant cytotoxicity against the two corresponding human normal cells, 184B5 (human breast cell) and NL 20 (human lung cell). DNA fragmentation studies suggested that the cytotoxic action of LR-CW against cancer cells is mediated by apoptosis. Sephadex G-50 gel filtration fractionation of LR-CW yielded a high-molecular-weight and a low-molecular-weight fraction. The high-molecular-weight fraction contains mainly carbohydrate (68.7%) and small amount of protein (3.6%), whereas the low-molecular-weight fraction contains 31% carbohydrate and was devoid of protein. Only the high-molecular-weight fraction exhibited antiproliferative activity against cancer cells, with IC50 of 70.0 μg/mL and 76.7 μg/mL, respectively. Thus, the cytotoxic action of the LR-CW is due to the high-molecular-weight fraction, either the proteins or protein-carbohydrate complex.

Conformational flexibility of a protein–carbohydrate complex and the structure and ordering of surrounding water

Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.

Applications of a Catch and Release Electrospray Ionization Mass Spectrometry Assay for Carbohydrate Library Screening

Applications of a catch and release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against target proteins are described. Direct ESI-MS measurements were performed on solutions containing a target protein (a single chain antibody, an antigen binding fragment, or a fragment of a bacterial toxin) and a library of carbohydrates containing multiple specific ligands with affinities in the 10(3) to 10(6) M(-1) range. Ligands with moderate affinity (10(4) to 10(6) M(-1)) were successfully detected from mixtures containing >200 carbohydrates (at concentrations as low as 0.25 μM each). Additionally, the absolute affinities were estimated from the abundance of free and ligand-bound protein ions determined from the ESI mass spectrum. Multiple low affinity ligands (~10(3) M(-1)) were successfully detected in mixtures containing >20 carbohydrates (at concentrations of ~10 μM each). However, identification of specific interactions required the use of the reference protein method to correct the mass spectrum for the occurrence of nonspecific carbohydrate-protein binding during the ESI process. The release of the carbohydrate ligands, as ions, was successfully demonstrated using collision-induced dissociation performed on the deprotonated ions of the protein-carbohydrate complexes. The use of ion mobility separation, performed on deprotonated carbohydrate ions following their release from the complex, allowed for the positive identification of isomeric ligands.

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2007–2008

This review is the fifth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2008. The first section of the review covers fundamental studies, fragmentation of carbohydrate ions, use of derivatives and new software developments for analysis of carbohydrate spectra. Among newer areas of method development are glycan arrays, MALDI imaging and the use of ion mobility spectrometry. The second section of the review discusses applications of MALDI MS to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, biopharmaceuticals, glycated proteins, glycolipids, glycosides and various other natural products. There is a short section on the use of MALDI mass spectrometry for the study of enzymes involved in glycan processing and a section on the use of MALDI MS to monitor products of the chemical synthesis of carbohydrates with emphasis on carbohydrate-protein complexes and glycodendrimers. Corresponding analyses by electrospray ionization now appear to outnumber those performed by MALDI and the amount of literature makes a comprehensive review on this technique impractical. However, most of the work relating to sample preparation and glycan synthesis is equally relevant to electrospray and, consequently, those proposing analyses by electrospray should also find material in this review of interest.

Modelling the Effect of Solvents on Carbohydrates

Carbohydrates are polar molecules and their conformational and anomeric equilibrium can be strongly influenced by solvents. This review provides examples of studies addressing different issues of glycochemistry, such as anomeric equilibrium, conformational changes in rings, modelling of inter-residue linkages or complex carbohydrates and formation of carbohydrate-protein complexes. All these phenomena provide benchmark systems for testing of different solvent models.

Infrared spectroscopy study of Gleditsia macracantha seeds

Seeds of Gleditsia macracantha were shown to contain a protein—carbohydrate complex using IR spectroscopy. It was found that the carbohydrate composition was heterogeneous and included a neutral polysaccharide and a carboxypolysaccharide containing acetyl, ester, and ionized carboxylic groups.

Novel Fold and Carbohydrate Specificity of the Potent Anti-HIV Cyanobacterial Lectin from Oscillatoria agardhii

Oscillatoria agardhii agglutinin (OAA) is a recently discovered cyanobacterial lectin that exhibits potent anti-HIV activity. Up to now, only its primary structure and carbohydrate binding data have been available. To elucidate the structural basis for the antiviral mechanism of OAA, we determined the structure of this lectin by x-ray crystallography at 1.2 Å resolution and mapped the specific carbohydrate recognition sites of OAA by NMR spectroscopy. The overall architecture of OAA comprises 10 β-strands that fold into a single, compact, β-barrel-like domain, creating a unique topology compared with all known protein structures in the Protein Data Bank. OAA sugar binding was tested against Man-9 and various disaccharide components of Man-9. Two symmetric carbohydrate-binding sites were located on the protein, and a preference for Manα(1-6)Man-linked sugars was found. Altogether, our structural results explain the antiviral activity OAA and add to the growing body of knowledge about antiviral lectins.

Effect of carbohydrate-protein complex supplementation immediately after intermittent cycling on recovery of fatigue.

Effect of carbohydrate-protein complex supplementation immediately after intermittent cycling on recovery of fatigue.

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for the period 2005–2006

This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.

Conformational changes and sequence analysis in cellulase from Aspergillus niger with cationic surfactant

The present study evaluates the binding of cetylpyridinium chloride (CPC) with cellulase in various experimental conditions using potentiometric, fluorescence spectroscopy and turbidimetric techniques. The analysis of binding curves revealed the existence of two sets of binding sets for CPC. The binding parameters were estimated and interpreted in terms of structural viewpoints of cellulase. The observation of turbidity suggests that CPC molecules individually nucleate around cellulase/CMC complex to form micelle-like structures. Fluorescence spectroscopy analysis of cellulase/CMC-surfactant system showed that these complexes could be compact to elucidate the mechanism of binding cellulase/CMC complex to CPC. The differential response of the enzyme/CMC to surfactant, indicates that the interaction on the complex surface is strongly ionic and hydrophobic(cooperative) in nature. A sequencing analysis was also conducted on β-1, 4-endoglucanase from A. niger (EglA) and others from family 12 in order to examine the nature of interaction involved in binding process and structure of carbohydrate-protein complexes. The results suggest that the conserved residues are located in a more hydrophobic microenvironment and apolar area energy is more than polar within enzyme structure.

Isopropylamino and Isobutylamino Groups as Recognition Sites for Carbohydrates: Acyclic Receptors with Enhanced Binding Affinity toward β-Galactosides

Binding motifs observed in the crystal structures of protein-carbohydrate complexes, in particular the participation of the isopropyl/isobutyl side chain of valine/leucine in the formation of van der Waals contacts, have inspired the design of new artificial carbohydrate receptors. The new compounds, containing a trisubstituted triethylbenzene core, were expected to recognize sugar molecules through a combination of NH···O and OH···N hydrogen bonds, CH···π interactions, and numerous van der Waals contacts. (1)H NMR spectroscopic titrations in competitive and noncompetitive media, as well as binding studies in two-phase systems, such as dissolution of solid carbohydrates in apolar media and phase transfer of sugars from aqueous into organic solvents, revealed effective recognition of neutral carbohydrates and β- vs α-anomer binding preferences in the recognition of glycosides as well as significantly increased binding affinity of the receptors toward β-galactoside in comparison with the previously described receptors.

PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB), (ii) Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii) CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate-protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery.

Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates.

Compounds 4 and 5, including both 4(5)-substituted imidazole or 3-substituted indole units as the entities used in nature, and 2-aminopyridine group as a heterocyclic analogue of the asparagine/glutamine primary amide side chain, were prepared and their binding properties towards carbohydrates were studied. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein–carbohydrate complexes. 1H NMR spectroscopic titrations in competitive and non-competitive media as well as binding studies in two-phase systems, such as dissolution of solid carbohydrates in apolar media, revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of these acyclic compounds. Compared to the previously described acyclic receptors, compounds 4 and 5 showed significantly increased binding affinity towards β-galactoside. Both receptors display high β- vs. α-anomer binding preferences in the recognition of glycosides. It has been shown that both hydrogen bonding and interactions of the carbohydrate CH units with the aromatic rings of the receptors contribute to the stabilization of the receptor–carbohydrate complexes. The molecular modeling calculations, synthesis and binding properties of 4 and 5 towards selected carbohydrates are described and compared with those of the previously described receptors.

Exploring the Conformational Space for the Interactions of Aromatic Residue Analogs with Biologically Important Saccharides

Proteins interacting with carbohydrate ligands are getting a great deal of attention because of its important role in various biological processes. The crystal structures of several lectin-saccharide complexes have shown the presence of an aromatic residue in the binding site. The C-H hydrophobic patch of saccharide “stacks” against pi-cloud of aromatic residues forming CH-pi interactions, which are governed by dispersive and charge transfer interactions. The energetics of saccharide - aromatic residue interactions are dictated by their mutual position-orientations. It is conceivable that there exist low-energy position-orientations other than those found in the limited number of crystal structures of protein-carbohydrate complexes known to date. Hence, we have explored the conformational space for the interactions of 3-methylindole (3-MeIn), p-hydroxytoluene (p-OHTol) and toluene (Tol) (analogs of tryptophan, tyrosine and phenylalanine, respectively) with six saccharides. A Monte Carlo conformational search method was used to explore the features of the molecular potential energy surfaces. We found that the saccharides are densely populated above and below the pi-cloud of the aromatic ring of the amino acid residue but not along the edges. Clustering of conformers indicate the aromatic residues are spread out when interacting with C-H atoms as compared to that with -OH groups. The saccharides were capable of sliding on the surface of the aromatic residue. Four C-H groups can simultaneously participate in CH-pi interaction in 3-MeIn systems owing to its larger surface area. The β-D-Galactose and β-L-Fucose have been found to interact only through their b- and a-faces, respectively. Our ability to understand molecular flexibility through conformational search will further lead to advances in the design of drugs and to understand the advantages of selective choice of aromatic residues viz., tryptophan, tyrosine or phenylalanine in different carbohydrate binding proteins.

Structural modifications of sugar beet pectin and the relationship of structure to functionality

The emulsifying properties of sugar beet pectin (SBP) were investigated in relation to its molecular structure. SBP has been subjected to an enhancement process, and this material was here compared with conventional non-enhanced SBP. The oil-in-water emulsification properties of both were compared at 1.5% concentration at pH 3.25, using 15% middle-chain triglyceride as the oil phase. Their emulsification behavior after various enzyme treatments decreased in the order: protease > arabinanase/galactanase mixture > polygalacturonase. The enzyme treatment also decreased the molecular weight of SBP. Protease degraded the high molecular weight carbohydrate–protein complex. Arabinanase/galactanase mixture was more effective in decreasing the emulsification performance than polygalacturonase. The results confirm the key role of protein as the anchor for the oil droplets and identify also the contribution of the neutral lateral chains in stabilizing emulsions by forming a hydrated layer. Protein also aggregates, which functions as a linker for the association of the carbohydrate chains consequent to the enhancement process.

Heat capacity changes in carbohydrates and protein–carbohydrate complexes

Carbohydrates are crucial for living cells, playing myriads of functional roles that range from being structural or energy-storage devices to molecular labels that, through non-covalent interaction with proteins, impart exquisite selectivity in processes such as molecular trafficking and cellular recognition. The molecular bases that govern the recognition between carbohydrates and proteins have not been fully understood yet. In the present study, we have obtained a surface-area-based model for the formation heat capacity of protein-carbohydrate complexes, which includes separate terms for the contributions of the two molecular types. The carbohydrate model, which was calibrated using carbohydrate dissolution data, indicates that the heat capacity contribution of a given group surface depends on its position in the saccharide molecule, a picture that is consistent with previous experimental and theoretical studies showing that the high abundance of hydroxy groups in carbohydrates yields particular solvation properties. This model was used to estimate the carbohydrate's contribution in the formation of a protein-carbohydrate complex, which in turn was used to obtain the heat capacity change associated with the protein's binding site. The model is able to account for protein-carbohydrate complexes that cannot be explained using a previous model that only considered the overall contribution of polar and apolar groups, while allowing a more detailed dissection of the elementary contributions that give rise to the formation heat capacity effects of these adducts.

Identifying Nonspecific Ligand Binding in Electrospray Ionization Mass Spectrometry Using the Reporter Molecule Method

The application of the reporter molecule (M(rep)) method for identifying nonspecific complexes in the ES-MS analysis of protein-ligand and DNA-ligand interactions in vitro is described. To test the reliability of the method, it was applied to the ES-MS analysis of protein-carbohydrate complexes originating from specific interactions in solution and from nonspecific interactions in the ES process. These control experiments confirm the basic assumptions underlying the M(rep) method, namely that nonspecific ligand binding is a random process, and that the ES droplet histories for specific and nonspecific complexes are distinct. The application of the M(rep) method to the ES-MS analysis of the sequential binding of the ethidium cation, a DNA intercalator, to single and double strand oligodeoxynucleotides is also described, and highlights the general utility of the method.

Analysis and validation of carbohydrate three-dimensional structures.

Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.