scholarly journals Crystal structure of the classical MHC-I molecule: insights into the MHC-I system in antiviral diseases in dogs

2021 ◽  
Author(s):  
Yujiao Sun ◽  
Lizhen Ma ◽  
Shen Li ◽  
Yawen Wang ◽  
Ruiqi Xiao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Vaccine Development ◽  
3D Structure ◽  
Binding Motif ◽  
Mhc I ◽  
Viral Epitope ◽  
First Category ◽  
Viral Vaccine ◽  
Epitope Vaccines

AbstractOnly one classical MHC-I locus (aka DLA-88) evolved in dogs, and thus far, a total of 76 DLA-88 alleles can be divided into two categories. The first category consists of 60 alleles, and the second category consists of 16 alleles. The main difference between the two categories is the insertion of an amino acid in the α2 region of DLA-88 alleles. To elucidate the structure of the first category, in this study, the crystal structure of pDLA-88*001:01 was determined for the first time. The 3D structure and topological characteristics of the ABG of pDLA-88*001:01 with a CDV peptide were analyzed. The viral presentation profile and the binding motif of viruses presented by pDLA-88*001:01 were determined. Most importantly, there were no amino acid insertions in the α2 region of the first category, which changed the conformation of the D pocket and the docking of the TCR. The results suggest obvious differences between the two categories. Because of the variation in the α2 region, pDLA-88*001:01 showed distinctive features in the two categories. Due to the peptide-binding motif of pDLA-88*001:01, more than 320 high-affinity viral peptides were predicted from dog H7N9, CPV, CMV, CMV, and CDV strains. The results reveal that there are two kinds of structural MHC-I systems in dogs that are responsible for CTL immunity against viral diseases. The results provide knowledge for designing viral epitope vaccines in canines.ImportanceDLA plays an important role in the acquired immunity of organism. In previous study, the pMHC-I structure of dog was analyzed with DLA-88 self-peptide. In this study, we screened several viral peptides which can bind to DLA-88 and resolved the structure of the DLA-88 complex binding the CDV peptide. This study enriches the study of canine MHC-I molecular-presenting polypeptide-activated TCR, which is of great significance for the study of canine cellular immunity and anti-viral vaccine development.

scholarly journals Structure ofStreptococcus agalactiaeglyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface

2014 ◽  
Vol 70 (10) ◽  
pp. 1333-1339 ◽  
Author(s):  
Chapelle A. Ayres ◽  
Norbert Schormann ◽  
Olga Senkovich ◽  
Alexandra Fry ◽  
Surajit Banerjee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Vaccine Development ◽  
Vaccine Candidate ◽  
Group B Streptococcus ◽  
Bacterial Pathogenesis ◽  
Bacterial Virulence ◽  
Significant Difference ◽  
Potential Vaccine ◽  
Group B

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH fromStreptococcus agalactiaein complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294–307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.

T-cell Epitope-based Vaccine Design for Nipah Virus by Reverse Vaccinology Approach

2020 ◽  
Vol 23 (8) ◽  
pp. 788-796
Author(s):  
Praveen K.P. Krishnamoorthy ◽  
Sekar Subasree ◽  
Udhayachandran Arthi ◽  
Mohammad Mobashir ◽  
Chirag Gowda ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class Ii ◽  
Vaccine Development ◽  
Nipah Virus ◽  
3D Structure ◽  
Cell Epitope ◽  
Class Ii ◽  
Class I ◽  
Reverse Vaccinology ◽  
Stable Complex

Aim and Objective: Nipah virus (NiV) is a zoonotic virus of the paramyxovirus family that sporadically breaks out from livestock and spreads in humans through breathing resulting in an indication of encephalitis syndrome. In the current study, T cell epitopes with the NiV W protein antigens were predicted. Materials and Methods: Modelling of unavailable 3D structure of W protein followed by docking studies of respective Human MHC - class I and MHC - class II alleles predicted was carried out for the highest binding rates. In the computational analysis, epitopes were assessed for immunogenicity, conservation, and toxicity analysis. T – cell-based vaccine development against NiV was screened for eight epitopes of Indian - Asian origin. Results: Two epitopes, SPVIAEHYY and LVNDGLNII, have been screened and selected for further docking study based on toxicity and conservancy analyses. These epitopes showed a significant score of -1.19 kcal/mol and 0.15 kcal/mol with HLA- B*35:03 and HLA- DRB1 * 07:03, respectively by using allele - Class I and Class II from AutoDock. These two peptides predicted by the reverse vaccinology approach are likely to induce immune response mediated by T – cells. Conclusion: Simulation using GROMACS has revealed that LVNDGLNII epitope forms a more stable complex with HLA molecule and will be useful in developing the epitope-based Nipah virus vaccine.

scholarly journals S-Acylation of Proteins of Coronavirus and Influenza Virus: Conservation of Acylation Sites in Animal Viruses and DHHC Acyltransferases in Their Animal Reservoirs

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 669
Author(s):  
Dina A. Abdulrahman ◽  
Xiaorong Meng ◽  
Michael Veit
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Ion Channels ◽  
Substrate Specificity ◽  
Influenza A ◽  
3D Structure ◽  
Viral Fitness ◽  
Amino Acid Substitutions ◽  
Essential Function ◽  
Animal Reservoirs

Recent pandemics of zoonotic origin were caused by members of coronavirus (CoV) and influenza A (Flu A) viruses. Their glycoproteins (S in CoV, HA in Flu A) and ion channels (E in CoV, M2 in Flu A) are S-acylated. We show that viruses of all genera and from all hosts contain clusters of acylated cysteines in HA, S and E, consistent with the essential function of the modification. In contrast, some Flu viruses lost the acylated cysteine in M2 during evolution, suggesting that it does not affect viral fitness. Members of the DHHC family catalyze palmitoylation. Twenty-three DHHCs exist in humans, but the number varies between vertebrates. SARS-CoV-2 and Flu A proteins are acylated by an overlapping set of DHHCs in human cells. We show that these DHHC genes also exist in other virus hosts. Localization of amino acid substitutions in the 3D structure of DHHCs provided no evidence that their activity or substrate specificity is disturbed. We speculate that newly emerged CoVs or Flu viruses also depend on S-acylation for replication and will use the human DHHCs for that purpose. This feature makes these DHHCs attractive targets for pan-antiviral drugs.

scholarly journals Crystal structure of Aspergillus fumigatus AroH , an aromatic amino acid aminotransferase

2021 ◽  
Author(s):  
Sharon Spizzichino ◽  
Gioena Pampalone ◽  
Mirco Dindo ◽  
Agostino Bruno ◽  
Luigina Romani ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Aspergillus Fumigatus ◽  
Aromatic Amino Acid ◽  
Aromatic Amino Acid Aminotransferase

scholarly journals Crystal Structure of an Aquabirnavirus Particle: Insights into Antigenic Diversity and Virulence Determinism

2009 ◽  
Vol 84 (4) ◽  
pp. 1792-1799 ◽  
Author(s):  
Fasséli Coulibaly ◽  
Christophe Chevalier ◽  
Bernard Delmas ◽  
Félix A. Rey
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Salient Feature ◽  
Infectious Pancreatic Necrosis Virus ◽  
Antigenic Determinants ◽  
Binding Motif ◽  
Icosahedral Symmetry ◽  
Fold Axis ◽  
Cell Internalization ◽  
Pancreatic Necrosis Virus

ABSTRACT Infectious pancreatic necrosis virus (IPNV), a pathogen of salmon and trout, imposes a severe toll on the aquaculture and sea farming industries. IPNV belongs to the Aquabirnavirus genus in the Birnaviridae family of bisegmented double-stranded RNA viruses. The virions are nonenveloped with a T=13l icosahedral capsid made by the coat protein VP2, the three-dimensional (3D) organization of which is known in detail for the family prototype, the infectious bursal disease virus (IBDV) of poultry. A salient feature of the birnavirus architecture is the presence of 260 trimeric spikes formed by VP2, projecting radially from the capsid. The spikes carry the principal antigenic sites as well as virulence and cell adaptation determinants. We report here the 3.4-Å resolution crystal structure of a subviral particle (SVP) of IPNV, containing 20 VP2 trimers organized with icosahedral symmetry. We show that, as expected, the SVPs have a very similar organization to the IBDV counterparts, with VP2 exhibiting the same overall 3D fold. However, the spikes are significantly different, displaying a more compact organization with tighter packing about the molecular 3-fold axis. Amino acids controlling virulence and cell culture adaptation cluster differently at the top of the spike, i.e., in a central bowl in IBDV and at the periphery in IPNV. In contrast, the spike base features an exposed groove, conserved across birnavirus genera, which contains an integrin-binding motif. Thus, in addition to revealing the viral antigenic determinants, the structure suggests that birnaviruses interact with different receptors for attachment and for cell internalization during entry.

scholarly journals Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Patamalai Boonserm ◽  
Songchan Puthong ◽  
Thanaporn Wichai ◽  
Sajee Noitang ◽  
Pongsak Khunrae ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
3D Structure ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Amino Acid Residues ◽  
Variable Regions ◽  
Complementarity Determining Regions ◽  
Crucial Part ◽  
Major Amino Acid

AbstractIt is important to understand the amino acid residues that govern the properties of the binding between antibodies and ligands. We studied the binding of two anti-norfloxacins, anti-nor 132 and anti-nor 155, and the fluoroquinolones norfloxacin, enrofloxacin, ciprofloxacin, and ofloxacin. Binding cross-reactivities tested by an indirect competitive enzyme-linked immunosorbent assay indicated that anti-nor 132 (22–100%) had a broader range of cross-reactivity than anti-nor 155 (62–100%). These cross-reactivities correlated with variations in the numbers of interacting amino acid residues and their positions. Molecular docking was employed to investigate the molecular interactions between the fluoroquinolones and the monoclonal antibodies. Homology models of the heavy chain and light chain variable regions of each mAb 3D structure were docked with the fluoroquinolones targeting the crucial part of the complementarity-determining regions. The fluoroquinolone binding site of anti-nor 155 was a region of the HCDR3 and LCDR3 loops in which hydrogen bonds were formed with TYR (H:35), ASN (H:101), LYS (H:106), ASN (L:92), and ASN (L:93). These regions were further away in anti-nor 132 and could not contact the fluoroquinolones. Another binding region consisting of HIS (L:38) and ASP (H:100) was found for norfloxacin, enrofloxacin, and ciprofloxacin, whereas only ASP (H:100) was found for ofloxacin.

Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif

2021 ◽  
Author(s):  
Blake M. Hauser ◽  
Maya Sangesland ◽  
Kerri St. Denis ◽  
Jared Feldman ◽  
Evan C. Lam ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Viral Escape ◽  
Binding Motif ◽  
Design Strategies ◽  
Viral Epitope ◽  
Viral Glycoproteins ◽  
Immunogen Design ◽  
Humoral Responses ◽  
Serum Response

Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV and WIV1-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins.

In silico and in vitro analysis of a multiepitope L1-E7 fusion construct for vaccine development against human papillomaviruses

2021 ◽  
Vol 18 ◽  
Author(s):  
Elnaz Abbasifarid ◽  
Azam Bolhassani ◽  
Shiva Irani ◽  
Fattah Sotoodehnejadnematalahi
Keyword(s):  
Western Blotting ◽  
Vaccine Development ◽  
Fluorescent Microscopy ◽  
Therapeutic Vaccine ◽  
Human Papillomaviruses ◽  
Mhc I ◽  
Fusion Construct ◽  
Mhc Ii ◽  
Hpv Types

Background: Human papillomavirus (HPV) infection is the major risk factor for cervical cancer. Current prophylactic HPV vaccines provide immunity against most genital and carcinogenic HPV types. However, these vaccines failed to produce immune responses against already established HPV infections. Methods: For the design of a therapeutic vaccine candidate, we utilized immunoinformatics tools to design a potential multiepitope fusion construct based on L1 and E7 genes from different high- and low-risk HPV types. After determination of CD4+ and CD8+ T cell epitopes, the allergenicity, toxicity, immunogenicity, conservancy, and population coverage were analyzed for epitope selection. Then, the hemolytic probability of the selected epitopes, and molecular docking between major histocompatibility complex (MHC) and the chosen epitopes were performed by different web servers. Next, a multiepitope peptide construct consisting of 12 epitopes linked by the AAY proteasomal sequence was designed. After that, physicochemical properties, solubility, secondary and tertiary structures of this construct were evaluated by bioinformatics tools. Finally, after amino acid reverse translation of the multiepitope peptide construct, expression of the L1-E7 DNA construct (pEGFP-L1-E7) was investigated in HEK-293T cells using fluorescent microscopy, flow cytometry, and western blotting. Results: Considering various parameters, the immunodominant peptides such as L1(MHC-I)-DLDQFPLGRKFLLQ, L1(MHC-II)-NQLFVTVVDTTRSTN, E7-HPV16(MHC-I)-AEPDRAHYNIVTF, E7-HPV18(MHC-I)-HGPKATVQDIVLHL, E7-HPV31(MHC-I)-KPDTSNYNIVTF, E7-HPV33(MHC-I)-RPDGQAQPATADYYI, E7-HPV45(MHC-I)- RTLQQLFLSFV, E7-HPV16(MHC-II)-TLHEYMLDLQPETTD, E7-HPV18(MHC-II)-LRAFQQLFLNTLSFV, E7-HPV31(MHC-II)-PTLQDYVLDLQPEAT, E7-HPV33(MHC-II)-LKEYVLDLYPEPTDL and E7-HPV45(MHC-II)-LQQLFLSTLSFVCPW were determined to design the vaccine construct. The results indicated efficient expression of the L1-E7 DNA construct (74 ± 2.19%) in vitro. Moreover, the polyepitope peptide generated in the cells was detected as a clear band of ~ 50 kDa in western blotting. Conclusion: Regarding the favorable transfection efficiency of the designed L1-E7 multiepitope construct, in vivo validation study on its therapeutic potential is underway.

scholarly journals Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes

2018 ◽  
Vol 115 (47) ◽  
pp. 11958-11963 ◽  
Author(s):  
Christian Kubitza ◽  
Florian Bittner ◽  
Carsten Ginsel ◽  
Antje Havemeyer ◽  
Bernd Clement ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Full Range ◽  
3D Structure ◽  
Cytochrome P450 Enzymes ◽  
Oxygenated Compounds ◽  
Online Databases ◽  
Starting Point ◽  
Wide Range ◽  
Nitrogen Containing Compounds

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.

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