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“Omics” Technologies in Vaccine Research
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
Maione et al. (2005) performed comparative genome analysis of eight GBS isolates and identified 312 surface proteins. These proteins were produced recombinantly and used to immunize the mice. Four of the proteins conferred protective potential, and the combination of these proteins provided high protection against various strains. Similarly, Moriel et al. (2013) compared the ten complete and 33 draft genomes of Acinetobacter baumannii, and identified 62 antigens as vaccine candidates. Of these, 20 proteins were predicted to have a beta-barrel structure causing a problem for protein solubility. The remaining 42 proteins were identified as 18 outer membrane lipoproteins, ten haemagglutinins and adhesins, nine toxins and enzymes, two solenoid repeat proteins, and three hypothetical proteins.
Mite Allergens
Published in Richard F. Lockey, Dennis K. Ledford, Allergens and Allergen Immunotherapy, 2014
Enrique Fernández-Caldas, S.L. Inmunotek, Leonardo Puerta, Luis Caraballo, Richard F. Lockey
Group 13 allergens belong to the fatty acid-binding protein (FABP) family and have been cloned and characterized from several mite species [63–65]. Der f 13 shares a medium to high-sequence homology with human FABPs, with the closest one being the human brain FABP, having 39.1% aa identity and 58.6% similarity. A solution structure study reveals that Der f 13 adopts the typical beta barrel fold of an FABP very similar to that of other human FABPs [66]. ELISA inhibition assays with monoclonal antibody specific for Blo t 13 suggest that the homologous allergen Der s 13 is also present in D. siboney [67]. In Colombia, 11% of patients with asthma showed IgE reactivity to Blo t 13 [14]. In the mite-allergic population from Cuba, the frequency of IgE reactivity to this allergen was 53%. Blo t 13 had approximately 35.3% sequence identity with FABP of human, bovine, mouse, and rat [68]. In 2005, Tyr p 13 was isolated from a cDNA library of the mite Tyrophagus putrescentiae, showing 62.3% of identity in the aa sequence with Blo t 13. The recombinant allergen showed 6.4% of reactivity in allergic individuals from Korea [69]. In the sheep scab mite, Psoroptes ovis, a genomic sequence encoding for an FABP with 55% similarity with Blo t 13 was identified [70].
Tick-Borne Encephalitis
Published in Sunit K. Singh, Daniel Růžek, Neuroviral Infections, 2013
Daniel Růžek, Bartosz Bilski, Göran Günther
The domain III has a typical fold of an IgC molecule (Heinz 2003). It contains a beta barrel composed of seven antiparallel beta sheets. It is supposed that the lateral part of the domain III is responsible for binding to a specific cellular receptor (Rey et al. 1995).
Enteroviruses and coronaviruses: similarities and therapeutic targets
Published in Expert Opinion on Therapeutic Targets, 2021
Varpu Marjomäki, Kerttu Kalander, Maarit Hellman, Perttu Permi
Quite strikingly, at the time of writing this review article, there exist almost 300 (297) high resolution 3D structures of SARS-CoV-2 main protease in the protein data bank, PDB, either determined as a free enzyme or as complexes with non-inhibitory fragments or together with numerous inhibitors developed by the scientific community. Recent crystal structures of SARS-CoV-2 Mpro highlight a homodimeric structure, yet, the homodimerization is elemental for the catalytic activity of coronavirus Mpro [42,44,45]. Each monomer comprises three domains. The domains I (residues 8–101) and II (residues 102–184) participate in the catalytic activity with a typical beta-barrel chymotrypsin fold. The domain III (res. 201–303) is composed of five α-helices and is essential for the dimerization. The domain III interacts mostly with the domain II as well as with the so-called N-finger from the other protomer. The dimerization of SARS-CoV-2 Mpro is mainly driven by the salt-bridge established between the negatively charged Glu290 from one protomer and positively charged Arg4 from the other [46]. Dimerization is a prerequisite for the catalytic activity of SARS-CoV-2 Mpro. Indeed, the so-called N-finger, composed of the most N-terminal residues of one protomer, makes contacts with the Glu166 of the other protomer to complete the active site.
Envelope proteins as antiviral drug target
Published in Journal of Drug Targeting, 2020
Jyoti Verma, Naidu Subbarao, Maitreyi S. Rajala
Envelope glycoproteins of Flaviviruses and Alphaviruses are class II fusion proteins. Unlike class I fusion proteins, class II proteins form a dimer in their pre-fusion conformation. These proteins primarily consist of beta sheets forming three structural domains termed I, II and III [25]. Domain I is the central domain having a beta barrel form with two long insertions connecting adjacent beta strands forming elongated domain II at one end. Domain II consists of highly conserved fusion loop. At the C-terminal of domain I, a linker region extends to connect domain III which has an immunoglobulin superfamily fold and a stem region connecting the protein to the transmembrane anchor [26]. Class II fusion proteins undergo a re-arrangement converting from a pre-fusion dimer (homo- or hetero-) to a homotrimer conformation. Domain I and II form the core of the homotrimer with three fusion loops at the tip of the trimer and domain III folds back against the core trimer moving towards the fusion loop. This trimeric hairpin is analogous to the six-helix bundle in the class I proteins [27].
Dengue virus 4: the ‘black sheep’ of the family?
Published in Expert Review of Vaccines, 2020
The replicative capacity of DENV as well as its virulence depends, among many other things, on structural characteristics of the virion, specifically on the viral envelope protein (E). Taking into account its localization in the virion and its proved immunogenicity, Dengue virus E protein has been broadly used as antigen in several vaccine candidates [53]. This protein is composed of three structurally different domains: domain I, a central beta barrel; domain II, a region of elongated dimerization and domain III, an immunoglobulin-like domain. For flaviviruses, the last one is considered a putative receptor-binding domain and a target of neutralizing antibodies [54]. The identity percentages between E proteins of DENV serotypes range in 63–78% at the amino acid level [55,56]. Serotypes 1 and 3 showed the highest percentage of identical amino acids (78.4%) whereas the lowest percentage was observed between DENV-2 and DENV-4 (62.8%) [56].