Structure Of Glycoprotein Research Articles

Probing structural dynamics by mass spectrometry provides new insights into HIV's structural and antigenic diversity

High-resolution cryo-EM and crystal structures of the HIV Env glycoprotein captured in the prefusion closed conformation have revealed a high degree of structural similarity across diverse strains of HIV. Biophysical data however indicate that Env is a highly dynamic assembly, and the level of dynamics and conformational sampling embodied in the trimeric complex can vary dramatically between HIV strains. Sequence, structural, and antigenic variation in HIV Env is a major barrier to development of an effective HIV vaccine.

Cryo-Em structures of novel arenviral fusion glycoproteins reveal conserved sites of vulnerability

Recognized as a priority emerging pathogen by the World Health Organization due to its pandemic potential and the absence of efficacious therapeutics or vaccines, Lassa fever affects an estimated 300,000 people per year and results in approximately 5000 deaths. Lassa virus (LASV)—a member of the Arenaviridae family—presents heavily glycosylated envelope glycoprotein complexes (GPC) which are the focus of many preclinical vaccine studies. The trimeric conformation of GPC is necessary to induce almost all known neutralizing antibody responses in immunization studies; however, the solubilized ectodomain disassembles into monomers after expression.

Evaluation of different expression systems for the heterologous production of sprivivirus glycoprotein

Glycoprotein mediated the entry of rhabdoviruses into the host cell and was the target of neutralizing antibodies. It was a prime tool for the study of the evolution and pathogenesis of viruses. Here, four different expression systems including cell-free synthesis system, Escherichia coli, Pichia pastoris and the baculovirus infected Spodoptera frugiperda were used to explore the recombinant expression of spring viraemia of carp virus glycoprotein. The results indicated that the recombinant glycoprotein could be detected in E. coli cell-free system after in vitro incubation for 16 h at 25 °C. E. coli was found to be the optimal expression system for the production of the largest amount of recombinant glycoprotein. Although robust yields were considerable in E. coli, the formation of insoluble aggregates and the removal of solubilizing labels were challenging for the expression and purification of glycoprotein. For this reason, the higher eukaryotic expression systems, yeast GS115 and insect Sf9 cells were used for the production of glycoprotein. The purity of the recombinant protein obtained from yeast culture was over 90% after purification by Ni-NTA. In insect cells, the target protein was expressed mainly in the intracellular environment, but secretory glycoprotein was also detected by western blotting. These findings provided a basis for further investigations into the structure and function of SVCV glycoprotein.

Middle East Respiratory Syndrome coronavirus vaccine development: updating clinical studies using platform technologies.

Middle East Respiratory Syndrome coronavirus (MERS-CoV), a contagious zoonotic virus, causes severe respiratory infection with a case fatality rate of approximately 35% in humans. Intermittent sporadic cases in communities and healthcare facility outbreaks have continued to occur since its first identification in 2012. The World Health Organization has declared MERS-CoV a priority pathogen for worldwide research and vaccine development due to its epidemic potential and the insufficient countermeasures available. The Coalition for Epidemic Preparedness Innovations is supporting vaccine development against emerging diseases, including MERS-CoV, based on platform technologies using DNA, mRNA, viral vector, and protein subunit vaccines. In this paper, we review the usefulness and structure of a spike glycoprotein as a MERS-CoV vaccine candidate molecule, and provide an update on the status of MERS-CoV vaccine development. Vaccine candidates based on both DNA and viral vectors coding MERS-CoV spike gene have completed early phase clinical trials. A harmonized approach is required to assess the immunogenicity of various candidate vaccine platforms. Platform technologies accelerated COVID-19 vaccine development and can also be applied to developing vaccines against other emerging viral diseases.

Fifty Shades of Erns: Innate Immune Evasion by the Viral Endonucleases of All Pestivirus Species.

The genus Pestivirus, family Flaviviridae, includes four historically accepted species, i.e., bovine viral diarrhea virus (BVDV)-1 and -2, classical swine fever virus (CSFV), and border disease virus (BDV). A large number of new pestivirus species were identified in recent years. A common feature of most members is the presence of two unique proteins, Npro and Erns, that pestiviruses evolved to regulate the host’s innate immune response. In addition to its function as a structural envelope glycoprotein, Erns is also released in the extracellular space, where it is endocytosed by neighboring cells. As an endoribonuclease, Erns is able to cleave viral ss- and dsRNAs, thus preventing the stimulation of the host’s interferon (IFN) response. Here, we characterize the basic features of soluble Erns of a large variety of classified and unassigned pestiviruses that have not yet been described. Its ability to form homodimers, its RNase activity, and the ability to inhibit dsRNA-induced IFN synthesis were investigated. Overall, we found large differences between the various Erns proteins that cannot be predicted solely based on their primary amino acid sequences, and that might be the consequence of different virus-host co-evolution histories. This provides valuable information to delineate the structure-function relationship of pestiviral endoribonucleases.

Cryo-EM structure of glycoprotein C from Crimean-Congo hemorrhagic fever virus.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a causative agent of serious hemorrhagic diseases in humans with high mortality rates. CCHFV glycoprotein Gc plays critical roles in mediating virus-host membrane fusion and has been studied extensively as an immunogen. However, the molecular mechanisms involved in membrane fusion and Gc-specific antibody-antigen interactions remain unresolved largely because structural information of this glycoprotein is missing. We designed a trimeric protein including most of the ectodomain region of Gc from the prototype CCHFV strain, IbAr10200, which enabled the cryo-electron microscopy structure to be solved at a resolution of 2.8 ​Å. The structure confirms that CCHFV Gc is a class II fusion protein. Unexpectedly, structural comparisons with other solved Gc trimers in the postfusion conformation revealed that CCHFV Gc adopted hybrid architectural features of the fusion loops from hantaviruses and domain III from phenuiviruses, suggesting a complex evolutionary pathway among these bunyaviruses. Antigenic sites on CCHFV Gc that protective neutralizing antibodies target were mapped onto the CCHFV Gc structure, providing valuable information that improved our understanding of potential neutralization mechanisms of various antibodies.

Structural Biology Illuminates Molecular Determinants of Broad Ebolavirus Neutralization by Human Antibodies for Pan-Ebolavirus Therapeutic Development.

Monoclonal antibodies (mAbs) have proven effective for the treatment of ebolavirus infection in humans, with two mAb-based drugs Inmazeb™ and Ebanga™ receiving FDA approval in 2020. While these drugs represent a major advance in the field of filoviral therapeutics, they are composed of antibodies with single-species specificity for Zaire ebolavirus. The Ebolavirus genus includes five additional species, two of which, Bundibugyo ebolavirus and Sudan ebolavirus, have caused severe disease and significant outbreaks in the past. There are several recently identified broadly neutralizing ebolavirus antibodies, including some in the clinical development pipeline, that have demonstrated broad protection in preclinical studies. In this review, we describe how structural biology has illuminated the molecular basis of broad ebolavirus neutralization, including details of common antigenic sites of vulnerability on the glycoprotein surface. We begin with a discussion outlining the history of monoclonal antibody therapeutics for ebolaviruses, with an emphasis on how structural biology has contributed to these efforts. Next, we highlight key structural studies that have advanced our understanding of ebolavirus glycoprotein structures and mechanisms of antibody-mediated neutralization. Finally, we offer examples of how structural biology has contributed to advances in anti-viral medicines and discuss what opportunities the future holds, including rationally designed next-generation therapeutics with increased potency, breadth, and specificity against ebolaviruses.

Topical use of Autologous Platelet Rich Fibrin in Tympanoplasty: A Prospective Interventional Study

Introduction: Tympanoplasty is the surgery performed in Chronic Otitis Media (COM) to improve the hearing function and prevent ear discharge. Platelet Rich Fibrin (PRF) is one of the materials that can be used to improve the graft uptake and hearing outcome. It is obtained by centrifugation of blood. The PRF contains leukocytes, cytokines, structural glycoproteins and growth factors which accelerates healing. It has been used in various surgical procedures to improve the outcome. Aim: To determine the efficacy of autologous PRF in closure of tympanic membrane perforation after tympanoplasty and to study the influence of PRF on the hearing outcome in the study population. Materials and Methods: This prospective interventional study was conducted in Department of Ear, Nose and Throat at SDM Medical College, Dharwad, Karnataka, India, from November 2018 to June 2020. The study included 60 patients with safe type of COM, who underwent tympanoplasty. Two group were made, group A consisted of 30 consecutive patients with safe type COM who underwent tympanoplasty with PRF application and group B, consisted of 30 patients who underwent tympanoplasty without PRF application. The outcome was assessed by endoscopic evaluation every month for 3 months to look for graft uptake. Hearing gain was evaluated by Pure Tone Audiometry (PTA) after 3 months of surgery. Statistical analysis was done using Chi-square test. Results: Group A had 29 cases with complete tympanic membrane closure and only one failure. However in group B, three out of 30 cases had failure. Thus, the overall the success rate was 96.66% in group A and 90% in group B. Postoperative PTA in group A showed that 18 cases (60%) had an improvement of >15 dB whereas in group B, 12 cases (40%) had hearing improvement of >15 dB. Conclusion: Considering the higher success rate of tympanoplasty with group A compared to group B and no noticeable side effects, it is recommended that tympanoplasty with autologous PRF should be preferred.

Development of multivalent vaccine targeting M segment of Crimean Congo Hemorrhagic Fever Virus (CCHFV) using immunoinformatic approaches

Crimean-Congo Hemorrhagic Fever (CCHF) is a tick-borne viral infection with no licensed vaccine or therapeutics available for its treatment. In the present study we have developed the first multi-epitope subunit vaccine effective against all the seven genotypes of CCHF virus (CCHFV). The vaccine contains five B-cell, two MHC-II (HTL), and three MHC-I (CTL) epitopes screened from two structural glycoproteins (Gc and Gn in M segment) of CCHFV with an N-terminus human β-defensin as an adjuvant, as well as an N-terminus EAAAK sequence. The epitopes were rigorously investigated for their antigenicity, allergenicity, IFN gamma induction, anti-inflammatory responses, stability, and toxicity. The three-dimensional structure of the vaccine was predicted and docked with TLR-3, TLR-8, and TLR-9 receptors to find the strength of the binding complexes via molecular dynamics simulation. After codon adaptation, the subunit vaccine construct was developed in a pDual-GC plasmid and has population coverage of 98.47% of the world's population (HLA-I & II combined). The immune simulation studies were carried out on the C-ImmSim in-silico interface showing a marked increase in the production of cellular and humoral response (B-cell and T-cell) as well as TGFβ, IL-2, IL-10, and IL-12 indicating that the proposed vaccine would be able to sufficiently provoke both humoral and cell-mediated immune responses. Thus, making it a new and promising vaccine candidate against CCHFV.

Glycan characterisation and antioxidant activity of a novel N-linked glycoprotein from okra

Glycoproteins are present in all living beings, and have many biological functions. The characterisation of glycan structures of plant glycoproteins has become increasingly important in biotechnology and agricultural applications. In the present work, the antioxidant activities of the okra glycoprotein were assessed. The glycan structures of the okra glycoprotein were analysed using lectin microarray combined with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The okra glycoprotein showed relatively strong 2,2-diphenyl-1-picrylhydrazyl-scavenging ability and reducing power. In addition, the glycan structures of the okra glycoprotein mainly contained N-acetylglucosamine, mannose, and galactose. Furthermore, complex-type N-glycans were the major type of glycan structures from the okra glycoprotein. Most of the complex N-glycans of the okra glycoprotein had terminal GalNAc and Gal N-glycan structures; the glycoprotein showed a high level of fucosylated complex-type glycans. Therefore, the okra glycoprotein is a promising antioxidant. Results of the present work might serve as a reference for a better understanding of the structural information and bioactivity of okra glycoprotein.

Role of metapneumoviral glycoproteins in the evasion of the host cell innate immune response.

Human metapneumovirus (HMPV), an unsegmented negative-strand RNA virus, is the second most detected respiratory pathogen and one of the leading causes of respiratory illness in infants and immunodeficient individuals. HMPV infection of permissive cells in culture triggers a transient IFN response, which is efficiently suppressed later in infection. We report that two structural glycoproteins of the virus - namely G (Glycoprotein) and SH (Small Hydrophobic) - suppress the type I interferon (IFN) response in cell culture. This is manifested by inhibition of diverse steps of IFN induction and response, such as phosphorylation and nuclear translocation of IFN regulatory factor-3 and -7 (IRF3, IRF7), major transcription factors of the IFN gene. Furthermore, HMPV suppresses the cellular response to IFN by inhibiting the phosphorylation of STAT1 (Signal Transducer and Activator of Transcription 1), required for the induction of IFN-stimulated genes that act as antivirals. Site-directed mutagenesis revealed an important role of critical cysteine (Cys) residues in the Cys-rich carboxy terminal region of the SH protein in IFN suppression, whereas for G, the ectodomain plays a role. These results shed light on the mechanism of IFN suppression by HMPV, and may also offer avenues for new antiviral approaches in the future.

A new insect cell line engineered to produce recombinant glycoproteins with cleavable N-glycans

Glycoproteins are difficult to crystallize because they have heterogeneous glycans composed of multiple monosaccharides with considerable rotational freedom about their O-glycosidic linkages. Crystallographers studying N-glycoproteins often circumvent this problem by using β1,2-N-acetylglucosaminyltransferase I (MGAT1)–deficient mammalian cell lines, which produce recombinant glycoproteins with immature N-glycans. These glycans support protein folding and quality control but can be removed using endo-β-N-acetylglucosaminidase H (Endo H). Many crystallographers also use the baculovirus-insect cell system (BICS) to produce recombinant proteins for their work but have no access to an MGAT1-deficient insect cell line to facilitate glycoprotein crystallization in this system. Thus, we used BICS-specific CRISPR–Cas9 vectors to edit the Mgat1 gene of a rhabdovirus-negative Spodoptera frugiperda cell line (Sf-RVN) and isolated a subclone with multiple Mgat1 deletions, which we named Sf-RVNLec1. We found that Sf-RVN and Sf-RVNLec1 cells had identical growth properties and served equally well as hosts for baculovirus-mediated recombinant glycoprotein production. N-glycan profiling showed that a total endogenous glycoprotein fraction isolated from Sf-RVNLec1 cells had only immature and high mannose-type N-glycans. Finally, N-glycan profiling and endoglycosidase analyses showed that the vast majority of the N-glycans on three recombinant glycoproteins produced by Sf-RVNLec1 cells were Endo H-cleavable Man5GlcNAc2 structures. Thus, this study yielded a new insect cell line for the BICS that can be used to produce recombinant glycoproteins with Endo H-cleavable N-glycans. This will enable researchers to combine the high productivity of the BICS with the ability to deglycosylate recombinant glycoproteins, which will facilitate efforts to determine glycoprotein structures by X-ray crystallography.

Expression profiles of venom components in some social hymenopteran species over different post-capture periods

To explore and compare the expression patterns of venom components depending on post-capture periods, venom gland-specific transcriptome and proteome analyses were conducted for five model hymenopteran species at a series of time points after capture. Venom gland-specific genes with signal sequences were considered as putative venom component genes. Expression patterns of venom gland-specific genes in all the social wasps and bees examined varied considerably depending on the post-capture period. Higher numbers of venom genes exhibited a decreasing expression pattern than an increasing pattern as the capture period increased. For example, genes encoding most of the allergens (dipeptidyl peptidase 4, endocuticle structural glycoprotein, odorant-binding protein, phospholipase A1, A2, B1, serine protease, serine protease inhibitor and venom allergen 5), pain-producing factor (mast cell degranulating peptide), and paralyzing factor (neprilysin) commonly exhibited decreasing expression patterns in all of the hymenopteran species tested, except for some of the major venom genes in Apis mellifera and Bombus ignitus, which showed an increasing pattern. These findings indicate species- or group-specific variations in the expression patterns of major venom genes. Taken together, flash freezing in liquid nitrogen immediately after capture was determined to be the best way to obtain the most natural expression profiles of venom components in social wasp species, thus, enabling a better understanding of the toxic potential of venom in wasp sting accidents. This study provides guidance for establishing optimal protocols for venom gland isolation and venom extraction from wasps and bees that can ensure the most naturally represented venom composition.

The Molecular Basis for Erns Dimerization in Classical Swine Fever Virus.

The pestivirus classical swine fever virus (CSFV) represents one of the most important pathogens of swine. Its virulence is dependent on the RNase activity of the essential structural glycoprotein Erns that uses an amphipathic helix as a membrane anchor and forms homodimers via disulfide bonds employing cysteine 171. Dimerization is not necessary for CSFV viability but for its virulence. Mutant Erns proteins lacking cysteine 171 are still able to interact transiently as shown in crosslink experiments. Deletion analysis did not reveal the presence of a primary sequence-defined contact surface essential for dimerization, but indicated a general importance of an intact ectodomain for efficient establishment of dimers. Pseudoreverted viruses reisolated in earlier experiments from pigs with mutations Cys171Ser/Ser209Cys exhibited partially restored virulence and restoration of the ability to form Erns homodimers. Dimer formation was also observed for experimentally mutated proteins, in which other amino acids at different positions of the membrane anchor region of Erns were replaced by cysteine. However, with one exception of two very closely located residues, the formation of disulfide-linked dimers was only observed for cysteine residues located at the same position of the helix.

Activity of the glycosidases β-galactosidase, α-l-fucosidase, β-N-acetyl-hexosaminidase, and sialidase in uterine tissues from female dogs in diestrus with and without pyometra

This study aimed to compare the activity of selected glycosidases (β-galactosidase, α-l-fucosidase, β-N-acetyl-hexosaminidase, and sialidase) in homogenates of uterine tissues obtained from female dogs with and without pyometra. In addition, it examined the availability of substrates for these glycosidases in the homogenates. The study was carried out on female dogs undergoing ovariohysterectomy for pyometra (n = 10) and clinically healthy dogs (n = 10) undergoing elective spaying. The activity of β-galactosidase, α-l-fucosidase, and β-N-acetyl-hexosaminidase was analyzed using a spectrofluorometer and that of sialidase using a colorimetric method. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis with Alcian Blue (AB) and Periodic Acid–Schiff (PAS) staining was performed to determine the presence of substrates for these glycosidases in the homogenates of uterine tissues. The results revealed that the activity of all the examined glycosidases was significantly higher (P < 0.05) in the uterine tissues isolated from dogs with pyometra in comparison to healthy dogs. The electrophoretic patterns of the selected samples showed several proteins, which contained different sugar moieties stained by AB and PAS and the profiles differed significantly between the pyometra group and the healthy group. Densitometric analysis of AB staining showed patterns between 233 and 148, 86 and 55, and 43 and 20 kDa, which differed markedly in sugar content between the examined groups of animals. Similarly, PAS staining analysis revealed patterns of different molecular weights, between 233 and 117 and between 55 and 32 kDa, which also differed in sugar content. These findings suggest that canine pyometra is accompanied by the increase in the activity of selected glycosidases in the uterus. This could potentially modify the glycan structures of uterine glycoproteins and in result their biological functions. Further studies are needed to elucidate the potential role of the increased activity of glycosidases in the pathogenesis of this disease.

A novel RHCE*cE allele identified in a Chinese individual, encodes weakened expression of c and E antigens

A novel RHCE*cE allele identified in a Chinese individual, encodes weakened expression of c and E antigens

The glycosylation status of MHC class I molecules impacts their interactions with TAPBPR

Glycosylation plays a crucial role in the folding, structure, quality control and trafficking of glycoproteins. Here, we explored whether the glycosylation status of MHC class I (MHC-I) molecules impacts their affinity for the peptide editor, TAPBPR. We demonstrate that the interaction between TAPBPR and MHC-I is stronger when MHC-I lacks a glycan. Subsequently, TAPBPR can dissociate peptides, even those of high affinity, more easily from non-glycosylated MHC-I compared to their glycosylated counterparts. In addition, TAPBPR is more resistant to peptide-mediated allosteric release from non-glycosylated MHC-I compared to species with a glycan attached. Consequently, we find the glycosylation status of HLA-A*68:02, -A*02:01 and –B*27:05 influences their ability to undergo TAPBPR-mediated peptide exchange. The discovery that the glycan attached to MHC-I significantly influences the affinity of their interactions with TAPBPR has important implications, on both an experimental level and in a biological context.

Determining structures in a native environment using single-particle cryoelectron microscopy images

Cryo-electron tomography is a powerful tool for structure determination in the native environment. However, this method requires the acquisition of tilt series, which is time-consuming and severely slows structure determination. By treating the densities of non-target protein as non-Gaussian noise, we developed a new target function that greatly improves the efficiency of recognizing the target protein in a single cryo-electron microscopy image. Moreover, we developed a sorting function that effectively eliminates the model dependence and improved the resolution during the subsequent structure refinement procedure. By eliminating model bias, our method allows using homolog proteins as models to recognize the target proteins in a complex context. Together, we developed an in situ single-particle analysis method. Our method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. Both data were collected within 24 h, thus allowing fast and simple structural determination.

The host range restriction of bat-associated no-known-vector flaviviruses occurs post-entry

Most flaviviruses are transmitted horizontally between vertebrate hosts by haematophagous arthropods. Others exhibit host ranges restricted to vertebrates or arthropods. Vertebrate-specific flaviviruses are commonly referred to as no-known-vector (NKV) flaviviruses and can be separated into bat- and rodent-associated NKV flaviviruses. Rio Bravo virus (RBV) is one of eight recognized bat-associated NKV (B-NKV) flaviviruses. Studies designed to identify the genetic determinants that condition the host range restriction of B-NKV flaviviruses have never been performed. To investigate whether the host range restriction occurs at the level of attachment or entry, chimeric flaviviruses were created by inserting the pre-membrane and envelope protein genes of RBV into the genetic backbones of yellow fever virus (YFV) and Zika virus (ZIKV), two mosquito-borne flaviviruses associated with human disease. The chimeric viruses infected both vertebrate and mosquito cells. In vertebrate cells, all viruses produced similar mean peak titres, but the chimeric viruses grew more slowly than their parental viruses during early infection. In mosquito cells, the chimeric virus of YFV and RBV grew more slowly than YFV at early post-inoculation time points, but reached a similar mean peak titre. In contrast, the chimeric virus of ZIKV and RBV produced a mean peak titre that was approximately 10-fold lower than ZIKV. The chimeric virus of YFV and RBV produced an intermediate plaque phenotype, while the chimeric virus of ZIKV and RBV produced smaller plaques than both parental viruses. To conclude, we provide evidence that the structural glycoproteins of RBV permit entry into both mosquito and vertebrate cells, indicating that the host range restriction of B-NKV flaviviruses is mediated by a post-attachment/entry event.

Abstract P472: Edil3 Autoantibodies Do Not Distinguish Kawasaki Disease (KD) From Febrile Controls, But Are Acutely Lower In Children With Cardiac Involvement.

Kawasaki Disease (KD) is a childhood vasculitis, marked by prolonged fevers and coronary artery inflammation/aneurysms. Epidemiologic and demographic data support that a single preceding infectious agent may lead to KD, however, the cause remains unknown. The leading theory on pathogenesis is a post-infectious self-limiting autoimmune response, but this is still controversial. A recent study of individuals with KD demonstrated an association with autoantibody response to EDIL3 (also known as DEL-1). EDIL3 is a structural glycoprotein expressed by both macrophages and vascular endothelium. This presents an attractive potential target for investigation, as EDIL3 is known to modulate inflammation via leukocyte binding and infiltration through vessel walls. Additionally, EDIL3 is highly expressed in aortic and coronary artery tissue samples, showing some of the highest non-neural expression. Genetic variants of Del-1 have been associated with risk of intracranial aneurysms. Due to this burgeoning literature, we interrogated our cohort of plasma samples from febrile children, including Kawasaki disease, to confirm specificity of targeting to EDIL3. Plasma samples from febrile children and children with KD, including timecourse samples, were interrogated with ELISA assays using full-length recombinant EDIL3 (LSBio). In contrary to the published report, EDIL3 binding does not appear to be specific to KD when compared to febrile controls inclusive of a variety of disease etiologies (viral, bacterial, etc.). On serial samples (pre-IVIG, post-IVIG and convalescent) from the two different patient cohorts, antibodies binding EDIL3 are elevated in post-IVIG samples. This further supports general autoantibody reactivity against EDIL3 as IVIG is a pooled blood product from thousands of individuals typically. Intriguingly, in comparison of samples from children with or without any coronary artery Z scores above 2.5, EDIL3 autoantibody responses were actually lower in those with dilated coronary arteries. Current efforts are focused on identify specific human autoantibodies against EDIL3. Implications of these findings will be explored.