Structural basis for disparate sugar-binding specificities in the homologous cargo receptors ERGIC-53 and VIP36

Clinical, Laboratory, Molecular, and Reproductive Aspects of Combined Deficiency of Factors V and VIII

Congenital combined deficiency of factor V (FV) and factor VIII (FVIII; F5F8D, OMIM 227300) is a rare hereditary coagulopathy and accounts for approximately 3% of cases of rare coagulation disorders. The prevalence of this disease in the general population is estimated to be 1:1,000,000 and is significantly higher in regions where consanguineous marriages are permitted, such as the Mideast and South Asia. The disease has an autosomal recessive mode of inheritance and therefore occurs with an equal incidence among males and females. Heterozygous mutation carriers usually do not have clinical manifestations. The molecular basis of this disease differs from that of stand-alone congenital deficiencies of FVIII and FV. F5F8D is caused by mutations in either LMAN1 or MCFD2, which encode components of a cargo receptor complex for endoplasmic reticulum to Golgi transport of FV and FVIII, leading to defects in an intracellular transport pathway shared by these two coagulation factors. Congenital combined deficiency of FV and FVIII is characterized by decreased activities of both FV and FVIII in plasma, usually to 5 to 30% of normal. Clinical manifestations in most cases are represented by mild or moderate hemorrhagic syndrome. The simultaneous decreases of two coagulation factors present complications in the diagnosis and management of the disease. In female patients, the disease requires a special approach for family planning, pregnancy management, and parturition. This review summarizes recent progress in clinical, laboratory, and molecular understanding of this disorder.

Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport

ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.

Atomic visualization of flipped-back conformations of high mannose glycans interacting with cargo lectins: An MD simulation perspective

Protein-carbohydrate interactions play a crucial role in mediating several biomolecular recognition events. We attempt to unravel its intricacies by understanding how carbohydrate-binding proteins interpret the glycan code. We aim to decipher lectin-mediated recognition in the endoplasmic reticulum (ER), which plays a crucial role in ER-mediated quality control (ER-QC). The ER-QC functions in three phases-protein folding, transport, and degradation. Altered protein QC leads to ER-related storage disorders. Cargo transport proteins-Ergic53 and Vip36-necessary for maintaining cellular homeostasis-are our primary focus. They recognize monoglucosylated/high mannose N-glycans on the folded glycoproteins. This article reports on the first dynamic investigation of the ER cargo lectins in complex with the high mannose glycans using an advanced sampling technique-replica exchange molecular dynamics to decipher the inherent conformational heterogeneity and the binding mechanism. The study involves simulations for the proteins complexed with three high mannose glycans-Man8B, Man9, and mono-glucosylated glycan. The recognition process is captured using MD simulations to achieve mechanistic insights and characterize the dynamics of glycans in their native and bound states via dihedral angle analysis. Results indicate that the flipped conformation of the glycans was crucial in differentiating their interaction with the proteins. Similar conformers of the glycans are preferred for Ergic53 and Vip36 in their glycan recognition events. Ergic53 preferred Man8B while it was Man9 for Vip36, in coherence with the previous experimental reports. These simulations provide a computational microscopic purview of the mechanism at both spatial and temporal scales. The results correlate with the published experimental data on the specificities of these lectins.

Mammalian cargo receptors for endoplasmic reticulum-to-Golgi transport: mechanisms and interactions

Proteins that are destined to enter the secretory pathway are synthesized on the rough endoplasmic reticulum (ER) and then translocated into the ER lumen, where they undergo posttranslational modifications, folding, and assembly. After passing a quality control system, the cargo proteins are packaged into coat protein complex II (COPII) vesicles to exit the ER. In metazoans, most COPII subunits have multiple paralogs, enabling COPII vesicles the flexibility to transport a diverse range of cargo. The cytoplasmic domains of transmembrane proteins can interact with SEC24 subunits of COPII to enter the ER exit sites. Some transmembrane proteins may also act as cargo receptors that bind soluble secretory proteins within the ER lumen, enabling them to enter COPII vesicles. The cytoplasmic domains of cargo receptors also contain coat protein complex I binding motifs that allow for their cycling back to the ER after unloading their cargo in the ER-Golgi intermediate compartment and cis-Golgi. Once unloaded, the soluble cargo proteins continue maturation through the Golgi before reaching their final destinations. This review provides an overview of receptor-mediated transport of secretory proteins from the ER to the Golgi, with a focus on the current understanding of two mammalian cargo receptors: the LMAN1-MCFD2 complex and SURF4, and their roles in human health and disease.

Crystal structure of an L-type lectin domain from archaea

The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn²⁺ -binding site compared to the Ca²⁺ -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.

Mannosylated Polymeric Ligands for Targeted Delivery of Antibacterials and Their Adjuvants to Macrophages for the Enhancement of the Drug Efficiency

Bacterial infections and especially resistant strains of pathogens localized in macrophages and granulomas are intractable diseases that pose a threat to millions of people. In this paper, the theoretical and experimental foundations for solving this problem are proposed due to two key aspects. The first is the use of a three-component polymer system for delivering fluoroquinolones to macrophages due to high-affinity interaction with mannose receptors (CD206). Cytometry assay determined that 95.5% macrophage-like cells were FITC-positive after adding high-affine to CD206 trimannoside conjugate HPCD-PEI1.8-triMan, and 61.7% were FITC-positive after adding medium-affine ligand with linear mannose label HPCD-PEI1.8-Man. The second aspect is the use of adjuvants, which are synergists for antibiotics. Using FTIR and NMR spectroscopy, it was shown that molecular containers, namely mannosylated polyethyleneimines (PEIs) and cyclodextrins (CDs), load moxifloxacin (MF) with dissociation constants of the order of 10-4-10-6 M; moreover, due to prolonged release and adsorption on the cell membrane, they enhance the effect of MF. Using CLSM, it was shown that eugenol (EG) increases the penetration of doxorubicin (Dox) into cells by an order of magnitude due to the creation of defects in the bacterial wall and the inhibition of efflux proteins. Fluorescence spectroscopy showed that 0.5% EG penetrates into bacteria and inhibits efflux proteins, which makes it possible to increase the maximum concentration of the antibiotic by 60% and maintain it for several hours until the pathogens are completely neutralized. Regulation of efflux is a possible way to overcome multiple drug resistance of both pathogens and cancer cells.

Computer simulation of the Receptor-Ligand Interactions of Mannose Receptor CD206 in Comparison with the Lectin Concanavalin A Model

Computer modeling of complexation of mono- and oligosaccharide ligands with the main (fourth) carbohydrate-binding domain of the mannose receptor CD206 (CRD4), as well as with the model receptor concanavalin A (ConA), was carried out for the first time, using methods of molecular dynamics and neural network analysis. ConA was shown to be a relevant model of CD206 (CRD4) due to similarity of the structural organization of the binding sites and high correlation of the values of free energies of complexation between the literature data and computer modeling (r > 0.9). Role of the main factors affecting affinity of the ligand–receptor interactions is discussed: the number and nature of carbohydrate residues, presence of Me-group in the O1 position, type of the glycoside bond in dimannose. Complexation of ConA and CD206 with ligands is shown to be energetically caused by electrostatic interactions (E) of the charged residues (Asn, Asp, Arg) with oxygen and hydrogen atoms in carbohydrates; contributions of hydrophobic and van der Waals components is lower. Possibility of the additional stabilization of complexes due to the CH–π stacking interactions of Tyr with the Man plane is discussed. The role of calcium and manganese ions in binding ligands has been studied. The values of free energies of complexation calculated in the course of molecular dynamics simulation correlate with experimental data (published for the model ConA): correlation coefficient r = 0.68. The Pafnucy neural network was trained based on the set of PDBbind2020 ligand–receptor complexes, which significantly increased accuracy of the energy predictions to r = 0.8 and 0.82 for CD206 and ConA receptors, respectively. A model of normalization of the complexation energy values for calculating the relevant values of ΔG_bind, K_d is proposed. Based on the developed technique, values of the dissociation constants of a series of CD206 complexes with nine carbohydrate ligands of different structures were determined, which were not previously known. The obtained data open up possibilities for using computer modeling for the development of optimal drug carriers capable of active macrophage targeting, and also determine the limits of applicability of using ConA as a relevant model for studying parameters of the CD206 binding to various carbohydrate ligands.

Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport

The transmembrane intracellular lectin ER-Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein-protein and protein-sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD-MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53-CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.

Improved secretion of glycoproteins using an N-glycan-restricted passport sequence tag recognized by cargo receptor

MCFD2 and ERGIC-53, which are the products of causative genes of combined factor V and factor VIII deficiency, form a cargo receptor complex responsible for intracellular transport of these coagulation factors in the early secretory pathway. In this study, using an NMR technique, we successfully identified an MCFD2-binding segment from factor VIII composed of a 10 amino acid sequence that enhances its secretion. This prompted us to examine possible effects of attaching this sequence to recombinant glycoproteins on their secretion. We found that the secretion level of recombinant erythropoietin was significantly increased simply by tagging it with the passport sequence. Our findings not only provide molecular basis for the intracellular trafficking of coagulation factors and their genetic deficiency but also offer a potentially useful tool for increasing the production yields of recombinant glycoproteins of biopharmaceutical interest.

Recombinant Expression and Purification of Animal Intracellular L-Type Lectins

Animal leguminous-type (L-type) lectins, including ERGIC-53 and VIP36 are responsible for intracellular transport and quality control of N-linked glycoproteins in the early secretory pathway. These lectins possess the carbohydrate recognition domain (CRD), which recognizes high-mannose-type glycans in a Ca²⁺-dependent manner. Here we describe the procedures involved in bacterial overproduction and purification of the CRDs of the animal L-type lectins.

Mammalian sugar-binding receptors: known functions and unexplored roles

Mammalian glycan-binding receptors, sometimes known as lectins, interact with glycans, the oligosaccharide portions of endogenous mammalian glycoproteins and glycolipids as well as sugars on the surfaces of microbes. These receptors guide glycoproteins out of and back into cells, facilitate communication between cells through both adhesion and signaling, and allow the innate immune system to respond quickly to viral, fungal, bacterial, and parasitic pathogens. For many of the roughly 100 glycan-binding receptors that are known in humans, there are good descriptions of what types of glycans they bind and how selectivity for these ligands is achieved at the molecular level. In some cases, there is also comprehensive evidence for the roles that the receptors play at the cellular and organismal levels. In addition to highlighting these well-understood paradigms for glycan-binding receptors, this review will suggest where gaps remain in our understanding of the physiological functions that they can serve.

Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica

ERGIC-53-like proteins are type I membrane proteins that belong to the class of intracellular cargo receptors and are known to be indispensable for the intracellular transport of glycoproteins. They are implicated in transporting glycoproteins between the endoplasmic reticulum and the Golgi body. The crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica has been determined at 2.4 Å resolution. Although the overall structure of the domain resembles those of its mammalian and yeast orthologs (ERGIC-53 and Emp46, respectively), there are significant changes in the carbohydrate-binding site. A sequence-based search revealed the presence of several homologs of ERGIC-53 in different species of Entamoeba. This is the first report of the structural characterization of a member of this class of proteins from a protozoan and serves to further knowledge and understanding regarding the species-specific differences.

LMAN1 (ERGIC-53) promotes trafficking of neuroreceptors

The endoplasmic reticulum-Golgi intermediate compartment protein-53 (ERGIC-53, aka LMAN1), which cycles between the endoplasmic reticulum (ER) and Golgi, is a known cargo receptor for a number of soluble proteins. However, whether LMAN1 plays a role as a trafficking factor in the central nervous system is largely unknown. Here, we determined the role of LMAN1 on endogenous protein levels of the Cys-loop superfamily of neuroreceptors, including gamma-aminobutyric acid type A receptors (GABA_ARs), 5-hydroxytryptamine (serotonin) type 3 (5-HT₃) receptors, and nicotinic acetylcholine receptors (nAChRs). Knockdown of LMAN1 reduces the surface trafficking of endogenous β3 subunits of GABA_ARs in mouse hypothalamic GT1-7 neurons. Furthermore, Western blot analysis of brain homogenates from LMAN1 knockout mice demonstrated that loss of LMAN1 decreases the total protein levels of 5HT₃A receptors and γ2 subunits of GABA_ARs. LMAN1 knockout regulates the ER proteostasis network by upregulating ERP44 without changing calnexin levels. Interestingly, despite the critical role of the glycan-binding function of LMAN1 in its other known cargo clients, LMAN1 interacts with GABA_ARs in a glycan-independent manner. In summary, LMAN1 is a trafficking factor for certain neuroreceptors in the central nervous system. This is the first report of LMAN1 function in membrane protein trafficking.

Mimicking Complex Biological Membranes and Their Programmable Glycan Ligands with Dendrimersomes and Glycodendrimersomes

Synthetic vesicles have been assembled and coassembled from phospholipids, their modified versions, and other single amphiphiles into liposomes, and from block copolymers into polymersomes. Their time-consuming synthesis and preparation as stable, monodisperse, and biocompatible liposomes and polymersomes called for the elaboration of new synthetic methodologies. Amphiphilic Janus dendrimers (JDs) and glycodendrimers (JGDs) represent the most recent self-assembling amphiphiles capable of forming monodisperse, stable, and multifunctional unilamellar and multilamellar onion-like vesicles denoted dendrimersomes (DSs) and glycodendrimersomes (GDSs), dendrimercubosomes (DCs), glycodendrimercubosomes (GDCs), and other complex architectures. Amphiphilic JDs consist of hydrophobic dendrons connected to hydrophilic dendrons and can be thought of as monodisperse oligomers of a single amphiphile. They can be functionalized with a variety of molecules such as dyes, and, in the case of JGDs, with carbohydrates. Their iterative modular synthesis provides efficient access to sequence control at the molecular level, resulting in topologies with specific epitope sequence and density. DSs, GDSs, and other architectures from JDs and JGDs serve as powerful tools for mimicking biological membranes and for biomedical applications such as targeted drug and gene delivery and theranostics. This Review covers all aspects of the synthesis of JDs and JGDs and their biological activity and applications after assembly in aqueous media.

Sweet New Roles for Protein Glycosylation in Prokaryotes

Long-held to be a post-translational modification unique to Eukarya, it is now clear that both Bacteria and Archaea also perform protein glycosylation, namely the covalent attachment of mono- to polysaccharides to specific protein targets. At the same time, many of the roles assigned to this protein-processing event in eukaryotes, such as guiding protein folding/quality control, intracellular trafficking, dictating cellular recognition events and others, do not apply or are even irrelevant to prokaryotes. As such, protein glycosylation must serve novel functions in Bacteria and Archaea. Recent efforts have begun to elucidate some of these prokaryote-specific roles, which are addressed in this review.

Extrinsic Functions of Lectin Domains in O-N-Acetylgalactosamine Glycan Biosynthesis

Glycan biosynthesis occurs mainly in Golgi. Molecular organization and functional regulation of this process are not well understood. We evaluated the extrinsic effect of lectin domains (β-trefoil fold) of polypeptide GalNAc-transferases (ppGalNAc-Ts) on catalytic activity of glycosyltransferases during O-GalNAc glycan biosynthesis. The presence of lectin domain T3lec or T4lec during ppGalNAc-T2 and ppGalNAc-T3 catalytic reaction had a clear inhibitory effect on GalNAc-T activity. Interaction of T3lec or T4lec with ppGalNAc-T2 catalytic domain was not mediated by carbohydrate. T3lec, but not T2lec and T4lec, had a clear activating effect on Drosophila melanogaster core 1 galactosyltransferase enzyme activity and a predominant inhibitory effect on in vivo human core 1 glycan biosynthesis. The regulatory role of the β-trefoil fold of ppGalNAc-Ts in enzymatic activity of glycosyltransferases involved in the O-glycan biosynthesis pathway, described here for the first time, helps clarify the mechanism of biosynthesis of complex biopolymers (such as glycans) that is not template-driven.

Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control

The endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by series of intracellular lectins. Glucosidase II catalyzes two-step hydrolysis at α1,3-linked glucose–glucose and glucose–mannose residues of high-mannose-type glycans to generate a quality control protein tag that is transiently expressed on glycoproteins and recognized by ER chaperones. Here we determined the crystal structures of the catalytic α subunit of glucosidase II (GIIα) complexed with two different glucosyl ligands containing the scissile bonds of first- and second-step reactions. Our structural data revealed that the nonreducing terminal disaccharide moieties of the two kinds of substrates can be accommodated in a gourd-shaped bilocular pocket, thereby providing a structural basis for substrate-binding specificity in the two-step deglucosylation catalyzed by this enzyme.

Onion-like glycodendrimersomes from sequence-defined Janus glycodendrimers and influence of architecture on reactivity to a lectin

A library of eight amphiphilic Janus glycodendrimers (GDs) with d-mannose (Man) headgroups, a known routing signal for lectin-mediated transport processes, was constructed via an iterative modular methodology. Sequence-defined variations of the Janus GD modulate the surface density and sequence of Man after self-assembly into multilamellar glycodendrimersomes (GDSs). The spatial mode of Man presentation is decisive for formation of either unilamellar or onion-like GDS vesicles. Man presentation and Janus GD concentration determine GDS size and number of bilayers. Beyond vesicle architecture, Man topological display affects kinetics and plateau level of GDS aggregation by a tetravalent model lectin: the leguminous agglutinin Con A, which is structurally related to endogenous cargo transporters. The agglutination process was rapid, efficient, and readily reversible for onion-like GDSs, demonstrating their value as versatile tools to explore the nature of physiologically relevant glycan/lectin pairing.

Analysis of COPII Vesicles Indicates a Role for the Emp47-Ssp120 Complex in Transport of Cell Surface Glycoproteins

Coat protein complex II (COPII) vesicle formation at the endoplasmic reticulum (ER) transports nascent secretory proteins forward to the Golgi complex. To further define the machinery that packages secretory cargo and targets vesicles to Golgi membranes, we performed a comprehensive proteomic analysis of purified COPII vesicles. In addition to previously known proteins, we identified new vesicle proteins including Coy1, Sly41 and Ssp120, which were efficiently packaged into COPII vesicles for trafficking between the ER and Golgi compartments. Further characterization of the putative calcium-binding Ssp120 protein revealed a tight association with Emp47 and in emp47Δ cells Ssp120 was mislocalized and secreted. Genetic analyses demonstrated that EMP47 and SSP120 display identical synthetic positive interactions with IRE1 and synthetic negative interactions with genes involved in cell wall assembly. Our findings support a model in which the Emp47-Ssp120 complex functions in transport of plasma membrane glycoproteins through the early secretory pathway.

N-linked sugar-regulated protein folding and quality control in the ER

Asparagine-linked glycans (N-glycans) are displayed on the majority of proteins synthesized in the endoplasmic reticulum (ER). Removal of the outermost glucose residue recruits the lectin chaperone malectin possibly involved in a first triage of defective polypeptides. Removal of a second glucose promotes engagement of folding and quality control machineries built around the ER lectin chaperones calnexin (CNX) and calreticulin (CRT) and including oxidoreductases and peptidyl-prolyl isomerases. Deprivation of the last glucose residue dictates the release of N-glycosylated polypeptides from the lectin chaperones. Correctly folded proteins are authorized to leave the ER. Non-native polypeptides are recognized by the ER quality control key player UDP-glucose glycoprotein glucosyltransferase 1 (UGT1), re-glucosylated and re-addressed to the CNX/CRT chaperone binding cycle to provide additional opportunity for the protein to fold in the ER. Failure to attain the native structure determines the selection of the misfolded polypeptides for proteasome-mediated degradation.

Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum

In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc₃Man₉GlcNAc₂). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing.

Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins

Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.