Crystal structure of a platelet-agglutinating factor isolated from the venom of Taiwan habu (Trimeresurus mucrosquamatus)

The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans

Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.

Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts

Predatory bacteria, like the model endoperiplasmic bacterium Bdellovibrio bacteriovorus, show several adaptations relevant to their requirements for locating, entering and killing other bacteria. The mechanisms underlying prey recognition and handling remain obscure. Here we use complementary genetic, microscopic and structural methods to address this deficit. During invasion, the B. bacteriovorus protein CpoB concentrates into a vesicular compartment that is deposited into the prey periplasm. Proteomic and structural analyses of vesicle contents reveal several fibre-like proteins, which we name the mosaic adhesive trimer (MAT) superfamily, and show localization on the predator surface before prey encounter. These dynamic proteins indicate a variety of binding capabilities, and we confirm that one MAT member shows specificity for surface glycans from a particular prey. Our study shows that the B. bacteriovorus MAT protein repertoire enables a broad means for the recognition and handling of diverse prey epitopes encountered during bacterial predation and invasion.

The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans

Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.

C-type lectin-(like) fold - Protein-protein interaction patterns and utilization

The C-type lectin-like fold (CTL fold) is a building block of many proteins, including saccharide-binding lectins, natural killer cell receptors, macrophage mannose receptor, selectins, collectins, snake venoms and others. Some are important players in innate immunity and are involved in the first-line response to virally infected cells or cancer cells, some play a role in antimicrobial defense, and some are potential targets for fight against problems connected with allergies, obesity, and autoimmunity. The structure of a CTL domain typically contains two α-helices, two small β-sheets and a long surface loop, with two or three disulfide bridges stabilizing the structure. This small domain is often involved in interactions with a target molecule, however, utilizing varied parts of the domain surface, with or without structural modifications. More than 500 three-dimensional structures of CTL fold-containing proteins are available in the Protein Data Bank, including a significant number of complexes with their key interacting partners (protein:protein complexes). The amount of available structural data enables a detailed analysis of the rules of interaction patterns utilized in activation, inhibition, attachment and other pathways or functionalities. Interpretation of known CTL receptor structures and all other CTL-containing proteins and complexes with described three-dimensional structures, complemented with sequence/structure/interaction correlation analysis offers a comprehensive view of the rules of interaction patterns of the CTL fold. The results are of value for prediction of interaction behavior of so far not understood CTL-containing proteins and development of new protein binders based on this fold, with applications in biomedicine or biotechnologies. It follows from the available structural data that almost the whole surface of the CTL fold is utilized in protein:protein interactions, with the heaviest frequency of utilization in the canonical interaction region. The individual categories of interactions differ in the interface buildup strategy. The strongest CTL binders rely on interfaces with large interaction area, presence of hydrophobic core, or high surface complementarity. The typical interaction surfaces of the fold are not conserved in amino acid sequence and can be utilized in design of new binders for biotechnological applications.

Inflammation Induced by Platelet-Activating Viperid Snake Venoms: Perspectives on Thromboinflammation

Envenomation by viperid snakes is characterized by systemic thrombotic syndrome and prominent local inflammation. To date, the mechanisms underlying inflammation and blood coagulation induced by Viperidae venoms have been viewed as distinct processes. However, studies on the mechanisms involved in these processes have revealed several factors and signaling molecules that simultaneously act in both the innate immune and hemostatic systems, suggesting an overlap between both systems during viper envenomation. Moreover, distinct classes of venom toxins involved in these effects have also been identified. However, the interplay between inflammation and hemostatic alterations, referred as to thromboinflammation, has never been addressed in the investigation of viper envenomation. Considering that platelets are important targets of viper snake venoms and are critical for the process of thromboinflammation, in this review, we summarize the inflammatory effects and mechanisms induced by viper snake venoms, particularly from the Bothrops genus, which strongly activate platelet functions and highlight selected venom components (metalloproteases and C-type lectins) that both stimulate platelet functions and exhibit pro-inflammatory activities, thus providing insights into the possible role(s) of thromboinflammation in viper envenomation.

Structurally Robust and Functionally Highly Versatile-C-Type Lectin (-Related) Proteins in Snake Venoms

Snake venoms contain an astounding variety of different proteins. Among them are numerous C-type lectin family members, which are grouped into classical Ca²⁺- and sugar-binding lectins and the non-sugar-binding snake venom C-type lectin-related proteins (SV-CLRPs), also called snaclecs. Both groups share the robust C-type lectin domain (CTLD) fold but differ in a long loop, which either contributes to a sugar-binding site or is expanded into a loop-swapping heterodimerization domain between two CLRP subunits. Most C-type lectin (-related) proteins assemble in ordered supramolecular complexes with a high versatility of subunit numbers and geometric arrays. Similarly versatile is their ability to inhibit or block their target molecules as well as to agonistically stimulate or antagonistically blunt a cellular reaction triggered by their target receptor. By utilizing distinct interaction sites differentially, SV-CLRPs target a plethora of molecules, such as distinct coagulation factors and receptors of platelets and endothelial cells that are involved in hemostasis, thrombus formation, inflammation and hematogenous metastasis. Because of their robust structure and their high affinity towards their clinically relevant targets, SV-CLRPs are and will potentially be valuable prototypes to develop new diagnostic and therapeutic tools in medicine, provided that the molecular mechanisms underlying their versatility are disclosed.

Snake venom components in medicine: From the symbolic rod of Asclepius to tangible medical research and application

Both mythologically and logically, snakes have always fascinated man. Snakes have attracted both awe and fear not only because of the elegant movement of their limbless bodies, but also because of the potency of their deadly venoms. Practically, in 2017, the world health organization (WHO) listed snake envenomation as a high priority neglected disease, as snakes inflict up to 2.7 million poisonous bites, around 100.000 casualties, and about three times as many invalidities on man. The venoms of poisonous snakes are a cocktail of potent compounds which specifically and avidly target numerous essential molecules with high efficacy. The individual effects of all venom toxins integrate into lethal dysfunctions of almost any organ system. It is this efficacy and specificity of each venom component, which after analysis of its structure and activity may serve as a potential lead structure for chemical imitation. Such toxin mimetics may help in influencing a specific body function pharmaceutically for the sake of man's health. In this review article, we will give some examples of snake venom components which have spurred the development of novel pharmaceutical compounds. Moreover, we will provide examples where such snake toxin-derived mimetics are in clinical use, trials, or consideration for further pharmaceutical exploitation, especially in the fields of hemostasis, thrombosis, coagulation, and metastasis. Thus, it becomes clear why a snake captured its symbolic place at the Asclepius rod with good reason still nowadays.

Lebecin, a new C-type lectin like protein from Macrovipera lebetina venom with anti-tumor activity against the breast cancer cell line MDA-MB231

C-type lectins like proteins display various biological activities and are known to affect especially platelet aggregation. Few of them have been reported to have anti-tumor effects. In this study, we have identified and characterized a new C-type lectin like protein, named lebecin. Lebecin is a heterodimeric protein of 30 kDa. The N-terminal amino acid sequences of both subunits were determined by Edman degradation and the entire amino acid sequences were deduced from cDNAs. The precursors of both lebecin subunits contain a 23-amino acid residue signal peptide and the mature α and β subunits are composed of 129 and 131 amino acids, respectively. Lebecin is shown to be a potent inhibitor of MDA-MB231 human breast cancer cells proliferation. Furthermore, lebecin dose-dependently inhibited the integrin-mediated attachment of these cells to different adhesion substrata. This novel C-type lectin also completely blocked MDA-MB231 cells migration towards fibronectin and fibrinogen in haptotaxis assays.

Identification of inhibitors of α2β1 integrin, members of C-lectin type proteins, in Echis sochureki venom

Snake venom antagonists of α2β1 integrin have been identified as members of a C-lectin type family of proteins (CLP). In the present study, we characterized three new CLPs isolated from Echis sochureki venom, which interact with this integrin. These proteins were purified using a combination of gel filtration, ion exchange chromatography and reverse phase HPLC. Sochicetin-A and sochicetin-B potently inhibited adhesion of cells expressing α2β1 integrin and binding of isolated α2β1 ectodomain to collagen I, as well as bound to recombinant GST-α2A domain in ELISA, whereas activity of sochicetin-C in these assays was approximately two orders of magnitude lower. Structurally, sochicetin-B and sochicetin-C are typical heterodimeric αβ CLPs, whereas sochicetin-A exhibits a trimer of its subunits (αβ)₃ in the quaternary structure. Immobilized sochicetins supported adhesion of glioma cell lines, LN18 and LBC3, whereas in a soluble form they partially inhibited adhesion of these cells to collagen I. Glioma cells spread very poorly on sochicetin-A, showing no cytoskeleton rearrangement typical for adhesion to collagen I or fibronectin. Adhesion on CLP does not involve focal adhesion elements, such as vinculin. Sochicetin-A also inhibited collagen-induced platelet aggregation, similar to other CLPs' action on the blood coagulation system.

Haemostatically active proteins in snake venoms

Snake venom proteins that affect the haemostatic system can cause (a) lowering of blood coagulability, (b) damage to blood vessels, resulting in bleeding, (c) secondary effects of bleeding, e.g. hypovolaemic shock and organ damage, and (d) thrombosis. These proteins may, or may not, be enzymes. We review the data on the most relevant haemostatically active proteinases, phospholipases A₂, L-amino acid oxidases and 5'-nucleotidases from snake venoms. We also survey the non-enzymatic effectors of haemostasis from snake venoms--disintegrins, C-type lectins and three-finger toxins. Medical applications have already been found for some of these snake venom proteins. We describe those that have already been approved as drugs to treat haemostatic disorders or are being used to diagnose such health problems. No clinical applications, however, currently exist for the majority of snake venom proteins acting on haemostasis. We conclude with the most promising potential uses in this respect.

A novel platelet glycoprotein Ib-binding protein with human platelet aggregation-inhibiting activity from Trimeresurus jerdonii venom

Platelet glycoprotein Ib (GPIb) is a primary adhesion receptor and involved in platelet-related disorders. However, it is difficult to study GPIb-specific platelet stimulation using physiological ligands in vivo. GPIb-binding snake C-type lectins (snaclecs) are useful tools for exploring GPIb in vitro because they act on platelets differently. In the present study, a novel GPIb-binding snaclec, named jerdonibitin, was purified, molecular cloned and characterized from Trimeresurus jerdonii venom. On SDS-polyacrylamide gel electrophoresis, it showed a single band with an apparent molecular weight of 25 kDa under non-reducing conditions and two distinct bands with apparent molecular weights of 15 kDa (α-subunit) and 13 kDa (β-subunit) under reducing conditions. The cDNA sequences of each subunit of jerdonibitin were identified and both deduced amino acid sequences were confirmed by N-terminal protein sequencing and trypsin-digested peptide mass fingerprinting of MALDI-TOF. Sequence alignment showed that jerdonibitin is a snaclec and has sequence similarity with TSV-GPIb-BP (a GPIb-inhibitory snaclec). Jerdonibitin dose-dependently inhibited platelet aggregation induced by ristocetin or low-dose thrombin, but not by high-dose thrombin. The GPIbα was detected by affinity chromatography on jerdonibitin. In vivo, jerdonibitin also dose-dependently induced thrombocytopenia of mice and platelet counts remained at very low level after 18 h intravenous injection. In summary, a novel GPIb-inhibitory snaclec was molecular cloned and characterized, which might provide insights into investigation of how GPIb-inhibitory snaclecs work and development of new antiplatelet agents.

Structure and function of snake venom proteins affecting platelet plug formation

Many snake venom proteins have been isolated that affect platelet plug formation by interacting either with platelet integrins, membrane glycoprotein Ib (GPIb), or plasma von Willebrand factor (VWF). Among them, disintegrins purified from various snake venoms are strong inhibitors of platelet aggregation. Botrocetin and bitiscetin derived from Bothrops jararaca and Bitis arietans venom, respectively, induce VWF-dependent platelet agglutination in vitro. Several GPIb-binding proteins have also been isolated from snake venoms. In this review, we focus on the structure and function of those snake venom proteins that influence platelet plug formation. These proteins are potentially useful as reagents for the sub-diagnosis of platelet disorder or von Willebrand disease, as well as for clinical and basic research of thrombosis and hemostasis.

Mining the secretome of the root-knot nematode Meloidogyne chitwoodi for candidate parasitism genes

Parasite proteins secreted at the interface of nematode and host are believed to play an essential role in parasitism. Here, we present an efficient pipeline of bio-informatic algorithms and laboratory experiments to identify candidate parasitism genes within nematode secretomes, i.e. the repertoire of secreted proteins in an organism. We performed our approach on 12 218 expressed sequence tags (ESTs) originating from three life stages of the plant parasitic nematode Meloidogyne chitwoodi--a molecularly unexplored root-knot nematode species. The ESTs from M. chitwoodi were assembled into 5880 contigs and open reading frames translated from the consensus sequences were searched for features of putative signal peptides for protein secretion and trans-membrane regions, resulting in the identification of 398 secretome members. The products of parasitism genes are secreted by a range of organs, including the oesophageal, amphidial and rectal glands, the intestine, and the hypodermis. To localize the site of expression in M. chitwoodi, we subjected the most abundant secretome members to in situ hybridization microscopy. We found hybridization of one tag in the dorsal oesophageal gland, seven in the two subventral oesophageal glands, two in the intestine and one tag hybridized to the tail tip in the proximity of the phasmids. Four sequences showed similarity to putative parasitism genes from other nematode species, whereas seven represented pioneering sequences. Our approach presents an efficient method to identify candidate parasitism genes, which does not require sophisticated cDNA isolation and selection protocols, and can therefore be used as a powerful starting point for the molecular investigation of parasites.

Snake venomics: Comparative analysis of the venom proteomes of the Tunisian snakesCerastes cerastes, Cerastes vipera andMacrovipera lebetina

The protein composition of the crude venoms of the three most important vipers of Tunisia was analyzed by RP-HPLC, N-terminal sequence analysis, MALDI-TOF mass determination, and in-gel tryptic digestion followed by PMF and CID-MS/MS of selected peptide ions in a quadrupole-linear IT instrument. Our results show that the venom proteomes of Cerastes cerastes, Cerastes vipera, and Macrovipera lebetina are composed of proteins belonging to a few protein families. However, each venom showed distinct degree of protein composition complexity. The three venoms shared a number of protein classes though the relative occurrence of these toxins was different in each snake species. On the other hand, the venoms of the Cerastes species and Macrovipera lebetina each contained unique components. The comparative proteomic analysis of Tunisian snake venoms provides a comprehensible catalogue of secreted proteins, which may contribute to a deeper understanding of the biological effects of the venoms, and may also serve as a starting point for studying structure-function correlations of individual toxins.

Snake venom C-type lectins interacting with platelet receptors. Structure–function relationships and effects on haemostasis

Snake venoms contain components that affect the prey either by neurotoxic or haemorrhagic effects. The latter category affect haemostasis either by inhibiting or activating platelets or coagulation factors. They fall into several types based upon structure and mode of action. A major class is the snake C-type lectins or C-type lectin-like family which shows a typical folding like that in classic C-type lectins such as the selectins and mannose-binding proteins. Those in snake venoms are mostly based on a heterodimeric structure with two subunits alpha and beta, which are often oligomerized to form larger molecules. Simple heterodimeric members of this family have been shown to inhibit platelet functions by binding to GPIb but others activate platelets via the same receptor. Some that act via GPIb do so by inducing von Willebrand factor to bind to it. Another series of snake C-type lectins activate platelets by binding to GPVI while yet another series uses the integrin alpha(2)beta(1) to affect platelet function. The structure of more and more of these C-type lectins have now been, and are being, determined, often together with their ligands, casting light on binding sites and mechanisms. In addition, it is relatively easy to model the structure of the C-type lectins if the primary structure is known. These studies have shown that these proteins are quite a complex group, often with more than one platelet receptor as ligand and although superficially some appear to act as inhibitors, in fact most function by inducing thrombocytopenia by various routes. The relationship between structure and function in this group of venom proteins will be discussed.

Structures and functions of snake venom CLPs (C-type lectin-like proteins) with anticoagulant-, procoagulant-, and platelet-modulating activities

C-type lectin-like proteins (CLPs) have a variety of biological activities, including anticoagulant- and platelet-modulating activities but have no lectin activity. CLPs are made up of heterodimers or oligomers of heterodimers, while C-type lectins from snake venom are composed exclusively of homodimers or homooligomers. In the last decade, numerous CLPs, such as blood coagulation factor IX/X-binding protein and botrocetin, have been isolated from various snake venoms, sequenced, and characterized. In addition, RVV-X (factor X activator) and carinactivase-1 (prothrombin activator) are metalloproteases composed of two C-type lectin-like domains that recognize the Gla domain of factor X and prothrombin, respectively. The basic structures of these CLPs include two homologous subunits: subunit alpha (A chain) of 14-15 kDa and subunit beta (B chain) of 13-14 kDa. CLPs occur in a variety of oligomeric forms, including alphabeta, (alphabeta)(2), and (alphabeta)(4). The basic homologous dimer (alphabeta) of these CLPs is formed by three-dimensional (3D) domain swapping. The CLPs constitute a new protein family and are useful tools for elucidating the mechanisms involved in clotting and platelet activation as well as the structure-function relationships of both blood clotting factors and platelet glycoproteins.

Snake venom probes of platelet adhesion receptors and their ligands

Snake venom proteins that modulate platelet adhesive interactions are chiefly from either of two main structural families: the C-type lectin-like family, or the metalloproteinase-disintegrins. Snake venom probes from both families selectively target platelet adhesion receptors, including glycoprotein (GP) Ib-IX-V, GP VI, alpha2beta1 and alphaIIbbeta3 (GP IIb-IIIa). These receptors act together to mediate platelet adhesion, activation and aggregation (thrombus formation) under hydrodynamic shear stress in flowing blood. The receptors are members of the leucine-rich repeat family (GP Ib-IX-V), the immunoglobulin superfamily (GP VI), or integrins (alpha2beta1, alphaIIbbeta3). In addition, adhesive glycoproteins in matrix and/or plasma such as von Willebrand factor (that binds GP Ibalpha and alphaIIbbeta3), collagen (that binds GP V, GP VI and alpha2beta1), or fibrinogen (that binds alphaIIbbeta3), are also targeted by C-type lectin family or metalloproteinase-disintegrin snake venom proteins. Emerging structural and functional evidence is beginning to explain how interactions between the conserved structural module-domains that make up these mammalian and snake proteins are regulated. Whether homologous adhesion/counter-receptors on platelets and other vascular cells are also potential snake venom targets is as yet largely unexplored.

Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom

The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. Crystals of agkicetin-C suitable for structure determination were obtained from 1.8 M ammonium sulfate, 40 mM MES pH 6.5 with 2%(v/v) PEG 400. Interestingly, low buffer concentrations of MES seem to be necessary for crystal growth. The crystals of agkicetin-C belong to space group C2, with unit-cell parameters a = 177.5, b = 97.7, c = 106.8 A, beta = 118.5 degrees, and diffract to 2.4 A resolution. Solution of the phase problem by the molecular-replacement method shows that there are four agkicetin-C molecules in the asymmetric unit, with a VM value of 3.4 A3 Da(-1), which corresponds to a high solvent content of approximately 64%. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that may represent additional elements of non-crystallographic symmetry.