Sequential structural changes upon zinc and calcium binding to metal-free concanavalin A

Selective interactions of Co2+-Ca2+-concanavalin A with high mannose N-glycans

Concanavalin A (ConA) has an intrinsic binding affinity to carbohydrates. Here, we obtained Co2+-Ca2+-ConA (2.83 Å, PDB: 8I7Q) via X-ray crystallography by substituting native ConA (Mn2+-Ca2+); it has binding selectivity for high-mannose N-glycan similar to native ConA. Our findings may thus inform antiviral reagent design.

Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences

The binding ability of lectins has gained attention owing to the carbohydrate-specific interactions of these proteins. Such interactions can be applied to diverse fields of biotechnology, including the detection, isolation, and concentration of biological target molecules. The physiological aspects of the lectin concanavalin A (ConA) have been intensively studied through structural and functional investigations. X-ray crystallography studies have proven that ConA has two β-sheets and a short α-helix and that it exists in the form of a metalloprotein containing Mn²⁺ and Ca²⁺. These heterometals are coordinated with side chains located in a metal-coordinated domain (MCD), and they affect the structural environment in the carbohydrate-binding domain (CBD), which interacts with carbohydrates through hydrogen bonds. Recent studies have shown that ConA can regulate biophysical interactions with glycoproteins in virus envelopes because it specifically interacts with diverse polysaccharides through its CBD (Tyr, Asn, Asp, and Arg residues positioned next to the MCD). Owing to their protein-protein interaction abilities, ConA can form diverse self-assembled complexes including monomers, dimers, trimers, and tetramers, thus affording unique results in different applications. In this regard, herein, we present a review of the structural modifications in ConA through metal-ion coordination and their effect on complex formation. In recent approaches, ConA has been applied for viral protein detection, on the basis of the interactions of ConA. These aspects indicate that lectins should be thoroughly investigated with respect to their biophysical interactions, for avoiding unexpected changes in their interaction abilities.

Concanavalin A targeting N-linked glycans in spike proteins influence viral interactions

Lectins, which exhibit viral-interaction abilities, have garnered attention in the current pandemic era as potential neutralizing agents and vaccine candidates. Viral invasion through envelope proteins is modulated by N-linked glycosylation in the spike (S) protein. This study demonstrates the biophysical aspects between lectins and high-mannose and -galactose N-glycans to provide insights into binding events.

Therapeutic Potentials of Antiviral Plants Used in Traditional African Medicine With COVID-19 in Focus: A Nigerian Perspective

The coronavirus disease 2019 (COVID-19) pandemic is caused by an infectious novel strain of coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was earlier referred to as 2019-nCoV. The respiratory disease is the most consequential global public health crisis of the 21st century whose level of negative impact increasingly experienced globally has not been recorded since World War II. Up till now, there has been no specific globally authorized antiviral drug, vaccines, supplement or herbal remedy available for the treatment of this lethal disease except preventive measures, supportive care and non-specific treatment options adopted in different countries via divergent approaches to halt the pandemic. However, many of these interventions have been documented to show some level of success particularly the Traditional Chinese Medicine while there is paucity of well reported studies on the impact of the widely embraced Traditional African Medicines (TAM) adopted so far for the prevention, management and treatment of COVID-19. We carried out a detailed review of publicly available data, information and claims on the potentials of indigenous plants used in Sub-Saharan Africa as antiviral remedies with potentials for the prevention and management of COVID-19. In this review, we have provided a holistic report on evidence-based antiviral and promising anti-SARS-CoV-2 properties of African medicinal plants based on in silico evidence, in vitro assays and in vivo experiments alongside the available data on their mechanistic pharmacology. In addition, we have unveiled knowledge gaps, provided an update on the effort of African Scientific community toward demystifying the dreadful SARS-CoV-2 micro-enemy of man and have documented popular anti-COVID-19 herbal claims emanating from the continent for the management of COVID-19 while the risk potentials of herb-drug interaction of antiviral phytomedicines when used in combination with orthodox drugs have also been highlighted. This review exercise may lend enough credence to the potential value of African medicinal plants as possible leads in anti-COVID-19 drug discovery through research and development.

Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Human galectin-7 (Gal-7; also termed p53-induced gene 1 product) is a multifunctional effector by productive pairing with distinct glycoconjugates and protein counter-receptors in the cytoplasm and nucleus, as well as on the cell surface. Its structural analysis by NMR spectroscopy detected doubling of a set of particular resonances, an indicator of Gal-7 existing in two conformational states in slow exchange on the chemical shift time scale. Structural positioning of this set of amino acids around the P4 residue and loss of this phenomenon in the bioactive P4L mutant indicated cis-trans isomerization at this site. Respective resonance assignments confirmed our proposal of two Gal-7 conformers. Mapping hydrogen bonds and considering van der Waals interactions in molecular dynamics simulations revealed a structural difference for the N-terminal peptide, with the trans-state being more exposed to solvent and more mobile than the cis-state. Affinity for lactose or glycan-inhibitable neuroblastoma cell surface contact formation was not affected, because both conformers associated with an overall increase in order parameters (S2). At low µM concentrations, homodimer dissociation is more favored for the cis-state of the protein than its trans-state. These findings give direction to mapping binding sites for protein counter-receptors of Gal-7, such as Bcl-2, JNK1, p53 or Smad3, and to run functional assays at low concentration to test the hypothesis that this isomerization process provides a (patho)physiologically important molecular switch for Gal-7.

Insight into Erythrina Lectins: Properties, Structure and Proposed Physiological Significance

The genus Erythrina, collectively known as “coral tree”, are pantropical plants, comprising of more than 112 species. Since the early 1980s, seven of these have been found to possess hemagglutinating activity, although not yet characterized. However, around two dozen galactose-binding lectins have been isolated and fully characterized with respect to their sugar specificity, glycoconjugates agglutination, dependence of activity on metal ions, primary and secondary structures and stability. Three lectins have been fully sequenced and the crystal structures of the two proteins have been solved with and without the haptenic sugar. Lectins isolation and characterization from most of these species usually originated from the seeds, although the proteins from other vegetative tissues have also been reported. The main objective of this review is to summarize the physicochemical and biological properties of the reported purified Erythrina lectins to date. Structural comparisons, based on available lectins sequences, are also made to relate the intrinsic physical and chemical properties of these proteins. Particular attention is also given to the proposed biological significance of the lectins from the genus Erythrina.

Polyethyleneimine-modified graphene oxide nanocomposites for effective protein functionalization

A facile method to prepare a biocompatible graphene oxide (GO)-based substrate for protein immobilization was developed to overcome the drawbacks of GO, such as the strong electrostatic and hydrophobic interactions which could potentially alter the conformation and biological activity of proteins. The GO was coated with hydrophilic branched polyethyleneimine (BPEI), while Concanavalin A (Con A) as a model lectin protein was employed to fabricate the functionalized composites to evaluate the feasibility of this strategy. The composites exhibit an extremely high binding capacity for glycoproteins (i.e. IgG 538.3 mg g(-1)), which are superior to other immobilized materials. Moreover, they can work well in 500-fold non-glycoprotein interference and even in complex biological samples. All these data suggest that the GO@BPEI composites will have great potential as scaffolds for proteins fully exerting their biofunctions.

Biosensor based on lectin and lipid membranes for detection of serum glycoproteins in infected patients with dengue

In this work, we developed a biosystem based on Concanavalin A (ConA) and lipid membranes to recognize glycoproteins from the serum of patients contaminated with dengue serotypes 1, 2 and 3 (DENV1, DENV2 and DENV3). The modified gold electrode was characterized using cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and atomic force microscopy. Morphological analyses of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), DPPC-ConA, DPPC-ConA-DENV1, DPPC-ConA-DENV2 and DPPC-ConA-DENV3 revealed the existence of a non-uniform covering and large globules. EIS and CV measurements have shown that redox probe reactions on the modified gold electrodes were partially blocked due to the adsorption of lipid-ConA system and reveal the interaction response of the immobilized ConA to the presence of glycoproteins of dengue serum. The biosystem exhibited a wide linear response to different concentrations of sera of dengue serotypes 1, 2 and 3. A higher impedimetric response to glycoproteins present in dengue serotype 3 was observed. Our results demonstrate the applicability of lectin and lipid membranes to the development of biosensors for dengue infections.

Plant as a plenteous reserve of lectin

Lectins are clusters of glycoproteins of nonimmune foundation that combine specifically and reversibly to carbohydrates, mainly the sugar moiety of glycoconjugates, resulting in cell agglutination and precipitation of glycoconjugates. They are universally distributed in nature, being established in plants, fungi, viruses, bacteria, crustacea, insects, and animals, but leguminacae plants are rich source of lectins. The present review reveals the structure, biological properties, and application of plant lectins.

Ultrasensitive impedimetric lectin biosensors with efficient antifouling properties applied in glycoprofiling of human serum samples

Ultrasensitive impedimetric lectin biosensors recognizing different glycan entities on serum glycoproteins were constructed. Lectins were immobilized on a novel mixed self-assembled monolayer containing 11-mercaptoundecanoic acid for covalent immobilization of lectins and betaine terminated thiol to resist nonspecific interactions. Construction of biosensors based on Concanavalin A (Con A), Sambucus nigra agglutinin type I (SNA), and Ricinus communis agglutinin (RCA) on polycrystalline gold electrodes was optimized and characterized with a battery of tools including electrochemical impedance spectroscopy, various electrochemical techniques, quartz crystal microbalance (QCM), Fourier transform infrared (FT-IR) spectroscopy, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS) and compared with a protein/lectin microarray. The lectin biosensors were able to detect glycoproteins from 1 fM (Con A), 10 fM (Ricinus communis agglutinin (RCA), or 100 fM (SNA) with a linear range spanning 6 (SNA), 7 (RCA), or 8 (Con A) orders of magnitude. Furthermore, a detection limit for the Con A biosensor down to 1 aM was achieved in a sandwich configuration. A nonspecific binding of proteins for the Con A biosensor was only 6.1% (probed with an oxidized invertase) of the signal toward its analyte invertase and a negligible nonspecific interaction of the Con A biosensor was observed in diluted human sera (1000×), as well. The performance of the lectin biosensors was finally tested by glycoprofiling of human serum samples from healthy individuals and those having rheumatoid arthritis, which resulted in a distinct glycan pattern between these two groups.

Ligand accessibility to receptor binding sites enhanced by movable polyrotaxanes

Functionalized polyrotaxanes are utilized to investigate the relation to multivalent interactions between the mannose moiety and Con A immobilized surfaces. According to the results of SPR spectroscopy, the mannose-conjugated polyrotaxanes show a higher response than any other mannose conjugate on both surfaces of high- and low-density Con A. Moreover, the results of the FRET analysis suggest that the mobility of α-cyclodextrins in the polyrotaxane more efficiently contributes to their binding interactions in a multivalent manner. This well-defined polyrotaxane system provides control over ligand density, ligand mobility, and gives an efficient response to the biological interaction receptor, which has not been easy to achieve in covalently bound polymeric systems.

Protein adsorption on a glycosylated polyacrylonitrile surface: monitoring with QCM and SPR

A simple and efficient method to fabricate a glycosylated surface on a polyacrylonitrile-based film is described. Construction and protein adsorption processes were monitored in situ using a QCM. A PANCHEMA film was deposited on the gold surface of the quartz crystal, and the glycosylated surface was then constructed through surface modification. Con A and BSA were used as probes to study the specificity of this surface to proteins. It can recognize Con A, while showing no specific interaction with BSA. The binding affinity indicates the presence of strong multivalent interactions between Con A and the glucose residues (cluster glycoside effect). Reproducibility and repeatability of the glycosylated polymer surface are sufficient to allow specific adsorption of Con A.

Polydispersity as a parameter for indicating the thermal stability of proteins by dynamic light scattering

A physical parameter for predicting the thermal stability of proteins was provided by a new approach using dynamic light scattering (DLS). The relationship between the melting point measured by differential scanning calorimetry (DSC) and the polydispersity of the hydrodynamic diameter determined by DLS analysis was examined. Calmodulin (CaM) and concanavalin A (ConA) were used as model proteins. The melting point measured by DSC, an indicator for thermal stability, increased and the polydispersity decreased on binding of the proteins to specific ligands, suggesting that the polydispersity could be used an indicator to predict thermal stability. In addition, the increase of thermal stability that resulted from forming a complex could be quantified by polydispersity analysis even when the melting point changed only slightly.

Electrochemical determination of carbohydrate-binding proteins using carbohydrate-stabilized gold nanoparticles and silver enhancement

A highly sensitive electrochemical lectin biosensor has been developed for the first time using carbohydrate-stabilized gold nanoparticles and silver-enhancement technique. A target lectin protein, Concanavalin A (Con A), was specifically bound to the self-assembled monolayer of thiolated mannose on a gold electrode. Mannose-stabilized gold nanoparticles were added to form a sandwich-type complex with the Con A and were followed by silver-enhancement process to coat the mannose-stabilized gold nanoparticles with silver metal. The coated metallic silver was dissolved in an acidic solution and the resulting silver ions were detected by anodic stripping voltammetry. The present lectin biosensor gave a linear response (R(2)=0.999) for Con A concentration from 0.084 μg/mL to 50.0 μg/mL with a remarkable detection limit (S/N=3) of 0.070 μg/mL, which is much lower compared to those obtained with the reported microgravimetric and colorimetric detection methods.

NMR studies of zinc binding in a multi-histidinic peptide fragment

A multi-histidinic peptide and its minimal models have been investigated for Zn(ii) binding. We have used NMR spectroscopy to probe the binding of zinc to the three repeats (T(1)R(2)S(3)R(4)S(5)H(6)T(7)S(8)E(9)G(10))(3) and to its mono-histidinic minimal models, the 9- and 10-aminoacid fragment. (1)H-(1)H TOCSY, (1)H-(13)C HSQC, (1)H-(1)H NOESY and (1)H-(1)H ROESY multidimensional NMR techniques were performed to understand the details of metal binding sites and the conformational behaviour of the peptides at different pH values and at different ligand to metal molar ratios. Zinc coordination involves imidazole N(delta) of His6 and carboxyl gamma-O of Glu9 residues; interaction with peptide oxygens of the His6-Thr7 or Thr7-Ser8 bonds in a tetrahedral arrangement with the minimal model peptides, cannot be excluded. Zinc coordination involves, at physiologic pH, all the three imidazole N(delta) donors of His6, His16 and His26 as well as carboxyl gamma-O of Glu residues in a tetra, penta or octahedral arrangement with the three repeats, the 30-aminoacid fragment. Zinc complexation induces important structural changes with the C-terminal portion of the ligand, constraining it to leave its disordered conformation. Our results give rise to a model of the induced structure of the peptides when bound to zinc. At high pH, amide deprotonation does not take place and hydroxo or high molecular weight polymeric species may be formed.

Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36

VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.

Carbohydrate-Coated Supramolecular Structures: Transformation of Nanofibers into Spherical Micelles Triggered by Guest Encapsulation

Triblock rigid-flexible dendritic block molecules consisting of a rigid aromatic segment as a stem segment, carbohydrate-branched dendrons as a flexible head, and a hydrophobic alkyl chain were synthesized and characterized. The carbohydrate conjugate molecule based on a methyl group as a hydrophobic tail, in the solid state, self-assembles into a 1D nanostructure, whereas the molecule based on a longer hydrophobic tail self-assembles into 2D nanosheets, as confirmed by X-ray scatterings. In aqueous solution, however, both molecules were observed to self-assemble into carbohydrate-coated cylindrical aggregates with a uniform diameter, as confirmed by dynamic light scatterings and transmission electron microscopic (TEM) investigations. Notably, these cylindrical objects reversibly transformed into spherical objects on addition of guest molecules. Investigation of the interactions of the carbohydrate-coated nanostructures with E. coli cells showed that both nano-objects could immobilize bacterial cells, while the degrees of immobilization were significantly dependent on the shape of nanostructure. These results demonstrated that the supramolecular materials that are responsive to external stimuli can provide novel opportunities to control many biological activities.

Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin

The interplay between metal binding, carbohydrate binding activity, stability and structure of the lectin from Pterocarpus angolensis was investigated. Removal of the metals leads to a more flexible form of the protein with significantly less conformational stability. Crystal structures of this metal-free form show significant structural rearrangements, although some structural features that allow the binding of sugars are retained. We propose that substitution of an asparagine residue at the start of the C-terminal beta-strand of the legume lectin monomer hinders the trans-isomerization of the cis-peptide bond upon demetallization and constitutes an intramolecular switch governing the isomer state of the non-proline bond and ultimately the lectin phenotype.

Flexibility of metal binding sites in proteins on a database scale

Protein metal binding sites in the pre-bound (apo) state, and their rearrangements upon metal binding were not analyzed previously at a database scale. Such a study may provide valuable information for metal binding site prediction and design. A high resolution, nonredundant dataset of 210 metal binding sites was created, containing all available representatives of apo-holo pairs for the most populated metals in the PDB. More than 40% of the sites underwent rearrangements upon metal binding. In 30 cases rearrangements involved the backbone. The tendency for side-chain rearrangement inversely correlates with the number of first-shell residues. Analysis of side-chain reorientations as a result of metal binding showed that in 95% of the rigid-backbone binding sites at most one side chain moved. Thus, in general, part of the first coordination shell is already in place in the pre-bound form. The frequencies of side-chain reorientation directly correlated with metal ligand flexibility and solvent accessibility in the apo state.

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p

Emp46p and Emp47p are type I membrane proteins, which cycle between the endoplasmic reticulum (ER) and the Golgi apparatus by vesicles coated with coat protein complexes I and II (COPI and COPII). They are considered to function as cargo receptors for exporting N-linked glycoproteins from the ER. We have determined crystal structures of the carbohydrate recognition domains (CRDs) of Emp46p and Emp47p of Saccharomyces cerevisiae, in the absence and presence of metal ions. Both proteins fold as a beta-sandwich, and resemble that of the mammalian ortholog, p58/ERGIC-53. However, the nature of metal binding is distinct from that of Ca(2+)-dependent p58/ERGIC-53. Interestingly, the CRD of Emp46p does not bind Ca(2+) ion but instead binds K(+) ion at the edge of a concave beta-sheet whose position is distinct from the corresponding site of the Ca(2+) ion in p58/ERGIC-53. Binding of K(+) ion to Emp46p appears essential for transport of a subset of glycoproteins because the Y131F mutant of Emp46p, which cannot bind K(+) ion fails to rescue the transport in disruptants of EMP46 and EMP47 genes. In contrast the CRD of Emp47p binds no metal ions at all. Furthermore, the CRD of Emp46p binds to glycoproteins carrying high mannosetype glycans and the is promoted by binding not the addition of Ca(2+) or K(+) ion in These results suggest that Emp46p can be regarded as a Ca(2+)-independent intracellular lectin at the ER exit sites.

Redox-responsive and calcium-dependent switching of glycosyldisulfide interactions with Concanavalin A

Glycosyldisulfides can interact efficiently with carbohydrate-binding entities. This has been shown for a range of thiosaccharide dimers when tested for their effects against the lectin Concanavalin A using a modified quartz crystal microbalance-technique. Contrary to the thiosaccharide monomers, showing no significant binding up to 10 mM, several of the dimers showed IC(50)-values in the low millimolar range. Three of the glycosyldisulfides tested also displayed very high positive apparent cooperativity effects that were found to be both calcium-dependent and redox-responsive.

Proteins that bind high-mannose sugars of the HIV envelope

A broad range of proteins bind high-mannose carbohydrates found on the surface of the envelope protein gp120 of the human immunodeficiency virus and thus interfere with the viral life cycle, providing a potential new way of controlling HIV infection. These proteins interact with the carbohydrate moieties in different ways. A group of them interacts as typical C-type lectins via a Ca2+ ion. Another group interacts with specific single, terminal sugars, without the help of a metal cation. A third group is involved in more intimate interactions, with multiple carbohydrate rings and no metal ion. Finally, there is a group of lectins for which the interaction mode has not yet been elucidated. This review summarizes, principally from a structural point of view, the current state of knowledge about these high-mannose binding proteins and their mode of sugar binding.

Inorganic cations mediate plant PR5 protein antifungal activity through fungal Mnn1- and Mnn4-regulated cell surface glycans

Antimicrobial activities of many defense proteins are profoundly altered by inorganic cations, thereby controlling disease pathologies in a number of mammalian systems, such as cystic fibrosis in humans. Protein-based active defense systems in plants also are influenced by cations; however, little is known of how these cation effects are mediated. Cytotoxicity of the pathogenesis-related protein osmotin against the model fungus Saccharomyces cerevisiae was progressively abolished by K+. By the use of S. cerevisiae mannosylation mutants, this effect was shown to require mannosephosphate residues in the cell wall. However, osmotin activity was not suppressed by even high concentrations of Ca2+. Rather, submillimolar levels of Ca2+ specifically facilitated osmotin's activity, as well as its binding to the cell surface. This effect also was dependent on mannosephosphate groups on the cell surface, and appeared to require negative charge on a portion of the osmotin protein. Results suggest that Ca2+ modulates osmotin action by facilitating its binding to the fungal cell surface, but that K+ blocks this interaction by competing for binding to mannosephosphate groups. Therefore, we have identified glycan interaction as a mechanism for antimicrobial protein activity modulation by cations, a pattern that may apply to diverse innate defense responses.

The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated with Calcium Ion Binding

p58/ERGIC-53 is a calcium-dependent animal lectin that acts as a cargo receptor, binding to a set of glycoproteins in the endoplasmic reticulum (ER) and transporting them to the Golgi complex. It is similar in structure to calcium-dependent leguminous lectins. We have determined the structure of the carbohydrate-recognition domain of p58/ERGIC-53 in its calcium-bound form. The structure reveals localized but large conformational changes in relation to the previously determined metal ion-free structure, mapping mostly to the ligand-binding site. It reveals the presence of two calcium ion-binding sites located 6A apart, one of which has no equivalent in the plant lectins. The second metal ion-binding site present in that class of lectins, binding Mn(2+), is absent from p58/ERGIC-53. The absence of a short loop in the ligand-binding site in this protein suggests that it has adapted to optimally bind the high-mannose Man(8)(GlcNAc)(2) glycan common to glycoproteins at the ER exit stage.

Calcium modulates protease resistance and carbohydrate binding of a plant defense legume lectin, Griffonia simplicifolia lectin II (GSII)

Site-directed mutagenesis previously identified the residues responsible for the biological activity of the plant defense legume lectin, Griffonia simplicifolia lectin II (GSII) [Proc. Natl. Acad. Sci. USA 95, (1998) 15123-15128]. However, these results were inconclusive as to whether these residues function as direct defense determinants through carbohydrate binding, or whether substantial changes of the protein structure had occurred in mutated proteins, with this structural disruption actually causing the loss of biochemical and biological functions. Evidence shown here supports the former explanation: circular dichroism and fluorescence spectra showed that mutations at carbohydrate-binding residues of GSII do not render it dysfunctional because of substantial secondary or tertiary structure modifications; and trypsin treatment confirmed that rGSII structural integrity is retained in these mutants. Reduced biochemical stability was observed through papain digestion and urea denaturation in mutant versions that had lost carbohydrate-binding ability, and this was correlated with lower Ca(2+) content. Accordingly, the re-addition of Ca(2+) to demetalized proteins could recover resistance to papain in the carbohydrate-binding mutant, but not in the non-binding mutant. Thus, both carbohydrate binding (presumably to targets in the insect gut) and biochemical stability to proteolytic degradation in situ indeed contribute to anti-insect activity, and these activities are Ca(2+)-dependent.

Isolectins I-A and I-B of Griffonia (Bandeiraea) simplicifolia. Crystal structure of metal-free GS I-B(4) and molecular basis for metal binding and monosaccharide specificity

Seeds from the African legume shrub Griffonia simplicifolia contain several lectins. Among them the tetrameric lectin GS I-B(4) has strict specificity for terminal alpha Gal residues, whereas the closely related lectin GS I-A(4) can also bind to alpha GalNAc. These two lectins are commonly used as markers in histology or for research in xenotransplantation. To elucidate the basis for the fine difference in specificity, the amino acid sequences of both lectins have been determined and show 89% identity. The crystal structure of GS I-B(4), determined at 2.5-A resolution, reveals a new quaternary structure that has never been observed in other legume lectins. An unexpected loss of both Ca(2+) and Mn(2+) ions, which are necessary for carbohydrate binding in legume lectins, may be related to a particular amino acid sequence Pro-Glu-Pro in the metal binding loop. Comparison with demetallized concanavalin A reveals a different process for the loss of metal ions and for the subsequent loss of carbohydrate binding activity. The GS I-A x alpha GalNAc and GS I-B x alpha Gal complexes were constructed using homology modeling and docking approaches. The unusual presence of an aromatic amino acid at position 47 (Tyr in I-A and Trp in I-B) explains the strong preference for alpha-anomeric sugars in both isolectins. Alteration at one amino acid position, Ala(106) in I-A versus Glu(106) in I-B, is the basis for the observed specificities toward alpha GalNAc and alpha Gal.

The structural features of concanavalin A governing non-proline peptide isomerization

The reversible binding of manganese and calcium to concanavalin A determines the carbohydrate binding of the lectin by inducing large conformational changes. These changes are governed by the isomerization of a non-proline peptide bond, Ala-207-Asp-208, positioned in a beta-strand in between the calcium binding site S2 and the carbohydrate specificity-determining loop. The replacement of calcium by manganese allowed us to investigate the structures of the carbohydrate binding, locked state and the inactive, unlocked state of concanavalin A, both with and without metal ions bound. Crystals of unlocked metal-free concanavalin A convert to the locked form with the binding of two Mn(2+) ions. Removal of these ions from the crystals traps metal-free concanavalin A in its locked state, a minority species in solution. The ligation of a metal ion in S2 to unlocked concanavalin A causes bending of the beta-strand foregoing the S2 ligand residues Asp-10 and Tyr-12. This bending disrupts conventional beta-sheet hydrogen bonding and forces the Thr-11 side chain against the Ala-207-Asp-208 peptide bond. The steric strain exerted by Thr-11 is presumed to drive the trans-to-cis isomerization. Upon isomerization, Asp-208 flips into its carbohydrate binding position, and the conformation of the carbohydrate specificity determining loop changes dramatically.

Non-proline cis peptide bonds in proteins

In a non-redundant set of 571 proteins from the Brookhaven Protein Data Base, a total of 43 non-proline cis peptide bonds were identified. Average geometrical parameters of the well-defined cis peptide bonds in proteins determined at high resolution show that some parameters, most notably the bond angle at the amide bond nitrogen, deviate significantly from the corresponding one in the trans conformation. Since the same feature was observed in cis amide bonds in small molecule structures found in the Cambridge Structural Data Base, a new set of parameters for the refinement of protein structures containing non-Pro cis peptide bonds is proposed.A striking preference was observed for main-chain dihedral angles of the residues involved in cis peptide bonds. All residues N-terminal and most residues C-terminal to a non-Pro cis peptide bond (except Gly) are located in the beta-region of a phi/psi plot. Also, all of the few C-terminal residues (except Gly) located in the alpha-region of the phi/psi plot constitute the start of an alpha-helix in the respective structure. In the majority of cases, an intimate side-chain/side-chain interaction was observed between the flanking residues, often involving aromatic side-chains. Interestingly, most of the cases found occur in functionally important regions such as close to the active site of proteins. It is intriguing that many of the proteins containing non-proline cis peptide bonds are carbohydrate-binding or processing proteins. The occurrence of these unusual peptide bonds is significantly more frequent in structures determined at high resolution than in structures determined at medium and low resolution, suggesting that these bonds may be more abundant than previously thought. On the basis of our experience with the structure determination of coagulation factor XIII, we developed an algorithm for the identification of possibly overlooked cis peptide bonds that exploits the deviations of geometrical parameters from ideality. A few likely candidates based on our algorithm have been identified and are discussed.

Ca2+-dependent structural changes in C-type mannose-binding proteins

C-type animal lectins are a diverse family of proteins which mediate cell-surface carbohydrate-recognition events through a conserved carbohydrate-recognition domain (CRD). Most members of this family possess a carbohydrate-binding activity that depends strictly on the binding of Ca2+ at two sites, designated 1 and 2, in the CRD. The structural transitions associated with Ca2+ binding in C-type lectins have been investigated by determining high-resolution crystal structures of rat serum mannose-binding protein (MBP) bound to one Ho3+ in place of Ca2+, and the apo form of rat liver MBP. The removal of Ca2+ does not affect the core structure of the CRD, but dramatic conformational changes occur in the loops. The most significant structural change in the absence of Ca2+ is the isomerization of a cis-peptide bond preceding a conserved proline residue in Ca2+ site 2. This bond adopts the cis conformation in all Ca2+-bound structures, whereas both cis and trans conformations are observed in the absence of Ca2+. The pattern of structural changes in the three loops that interact with Ca2+ is dictated in large part by the conformation of the prolyl peptide bond. The highly conserved nature of Ca2+ site 2 suggests that the transitions observed in MBPs are general features of Ca2+ binding in C-type lectins.

Analysis of zinc binding sites in protein crystal structures

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.

Legume lectin structure

The legume lectins are a large family of homologous carbohydrate binding proteins that are found mainly in the seeds of most legume plants. Despite their strong similarity on the level of their amino acid sequences and tertiary structures, their carbohydrate specificities and quaternary structures vary widely. In this review we will focus on the structural features of legume lectins and their complexes with carbohydrates. These will be discussed in the light of recent mutagenesis results when appropriate. Monosaccharide specificity seems to be achieved by the use of a conserved core of residues that hydrogen bond to the sugar, and a variable loop that determines the exact shape of the monosaccharide binding site. The higher affinity for particular oligosaccharides and monosaccharides containing a hydrophobic aglycon results mainly from a few distinct subsites next to the monosaccharide binding site. These subsites consist of a small number of variable residues and are found in both the mannose and galactose specificity groups. The quaternary structures of these proteins form the basis of a higher level of specificity, where the spacing between individual epitopes of multivalent carbohydrates becomes important. This results in homogeneous cross-linked lattices even in mixed precipitation systems, and is of relevance for their effects on the biological activities of cells such as mitogenic responses. Quaternary structure is also thought to play an important role in the high affinity interaction between some legume lectins and adenine and a series of adenine-derived plant hormones. The molecular basis of the variation in quaternary structure in this group of proteins is poorly understood.

A structure of the complex between concanavalin A and methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside reveals two binding modes

The structure of concanavalin A in complex with the trimannoside methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside has been determined in a novel space group. In three of the four subunits of the concanavalin A tetramer, the interactions between the protein and the bound saccharide are essentially identical to those reported previously by other authors (Naismith, J. H., and Field, R. A. (1996) J. Biol. Chem. 271, 972-976). In the fourth subunit, however, the alpha1-->3 linkage has a different conformation, resulting in a different part of the alpha1-->3-linked mannose interacting with essentially the same surface of the protein. Furthermore, significant differences are observed in the quaternary associations of the subunits compared with the saccharide-free structures and other carbohydrate complexes, suggesting that the concanavalin A tetramer is a rather flexible entity.