Kapsidmerupakan lapisan pembungkus tubuh virus, yang tersusun atas protein. Kapsid terdiri dari sejumlah kapsomer yang terikat satu sama lain dengan ikatan nonkovalen. Fungsi kapsid : Memberi bentuk virus ; Sebagai pelindung virus dari kondisi lingkungan yang merugikan dirinya ; Mempermudah proses penempelan pada proses penembusan ke dalam sel ; Untuk melindungi materi genetik ; 2. Materi genetik Integrated Methods in Protein Biochemistry Part AMax Meyrath, ... on behalf of the CON-VINCE Consortium, in Methods in Enzymology, 20222 Before you beginThis virus-free assay uses two cell lines expressing respectively the viral spike and host cell receptor ACE2 on their surface and builds on the principle that cell membranes merge upon spike-ACE2 interaction. Each cell line additionally expresses one part of the NanoLuc luciferase HiBiT or LgBiT that on their own do not emit light, but when brought together, quickly self-complement due to their high affinity for each other to reconstitute a fully functional NanoLuc HiBiT technology, Promega. When co-incubated, these two cell lines are able to form syncytia through their cell membrane fusion facilitated by the spike-ACE2 interaction, in turn allowing rapid and spontaneous complementation of the cytoplasmic NanoLuc fragments and giving rise to ultra-bright bioluminescence in the presence of a specific substrate Fig. 1. Similar to classical viral neutralization assays, pre-incubation with neutralizing antibodies blocking the spike-ACE2 interaction prevents syncytia formation, which can be titrated and quantified by measuring the reduced light emission in comparison to cells that were not treated with neutralizing antibodies Fig. 1A and C.Fig. 1. Cell fusion assay based on high-affinity NanoLuc complementation HiBiT A Schematic representation of the assay set-up. LgBiT and spike-expressing HEK293T cells are mixed with HiBiT- and ACE2-expressing Vero E6 cells and co-incubated overnight. Upon spike interaction with ACE2, cell membranes merge, forming a multinucleated syncytium and enabling complementation of both NanoLuc fragments, eventually leading to light emission upon substrate addition. Pre-incubation of spike-expressing cells with neutralizing antibodies will prevent the spike–ACE2 interaction and limit syncytia formation. Multiple sera can be tested simultaneously in 96- or 384-well format, enabling high-throughput screening of samples. B Representative microscopy pictures, illustrating syncytium formation between Vero E6 cells expressing an mKOrange-tagged membrane marker and HEK293T cells expressing a NeonGreen cytoplasmic marker. DAPI-stained nuclei are depicted in blue. C Representative picture of a 96-well plate after substrate addition taken with an ordinary mobile phone camera Huawei p20 Pro. The intense blue bioluminescent signal emitted by the NanoLuc is well visible even with the naked eye. No light is emitted from wells where cells did not efficiently form syncytia, indicative of the presence of neutralizing A Figure was created using the material, vectors and protocols described below, this “SARScytium” assay can easily and reproducibly be performed using transiently transfected cells, where one cell line is transfected with viral spike and LgBiT, whereas the other cell line is transfected with HiBiT and ACE2 Fig. 1A. The approach using transient transfections allows for high versatility and flexibility of the assay with easy and fast adaptability to spike variants. This can be of particular interest given that the antibody neutralization profile considerably varies between the different spike variants and the high probability of emergence of new variants Duarte et al., 2022; Harvey et al., 2021. Alternatively, cells stably expressing the required proteins can be used. This accounts especially for ACE2, where a variety of cells stably expressing ACE2 are commercially available, such as Vero E6 cells that endogenously express ACE2, or HEK or HeLa cells exogenously overexpressing ACE2 together or not with the protease TMPRSS2 that serves as a co-factor for SARS-CoV-2 infection and is implicated in spike priming on the full chapterURL coronavirus infections of the lower respiratory tract and their preventionN. Petrovsky, in The Microbiology of Respiratory System Infections, 20163 Recombinant spike protein vaccinesA major advance in vaccine development was the identification that the SARS virus spike S protein mediates cell entry via its ability to bind angiotensin-converting enzyme 2 and CD209L, thereby triggering virus endocytosis into target A human monoclonal antibody binding the S protein N-terminal domain was shown to be able to block infection, thereby identifying S protein as a major target of SARS virus neutralizing Consistent with this, monkeys could be protected against SARS infection by intranasal immunization with a S protein-encoding live parainfluenza S protein was also shown to be the target of CD4 and CD8 T cell responses suggesting these may also be important to SARS A recombinant S protein vaccine was manufactured using an insect cell expression system but was found to be considerably less immunogenic that inactivated whole virus vaccine, requiring ∼100 times more antigen to achieve the same level of Attempts to improve the immunogenicity of S protein vaccine by formulation with alum adjuvant again resulted in severe lung eosinophilic immunopathology in response to SARS virus infection, marking this as another potentially unsafe This confirmed that the problem of lung eosinophilic immunopathology was not just confined to inactivated or nucleocapsid protein vaccines but was a more general problem of vaccines made from any SARS virus full chapterURL VaccinesJaap W. Back, Johannes Langedijk, in Advances in Immunology, 20122 Stabilizing AntigensThe detailed structural knowledge on many neutralization sites, the location of some conserved exposed surfaces on the native viral spike, and the general architecture and dynamics of the labile structure reveals some clues of how to stabilize the spike in order to induce such broadly neutralizing way of using the structural knowledge for a recombinant protein-based vaccine is to engineer, modify, or stabilize the labile spike in such a way that the recombinant soluble protein mimics the prefusion native trimer that can cross-react with all the broadly neutralizing antibodies and remains stable in a vaccine adjuvant. Several approaches have been applied successfully to stabilize the case the immunogen is based on the soluble envelope protein, the deletion of the membrane anchor destabilizes the trimer which can be compensated by inclusion of heterologous trimerization domains Yang et al., 2000. Additionally, the prefusion conformation can be stabilized by preventing the FP from swinging out and the gp120 head to detach. A straightforward solution to fix the FP in its prefusion position and obstruct the refolding of gp41 into the stable postfusion conformation is to prevent the cleavage of the precursor gp160 into mature gp120–gp41 heterodimer Yang et al., 2000. Alternatively, to increase the chance of maintaining the FP in its native, probably buried, position, gp120 and gp41 can be covalently linked by the introduction of an intermolecular disulfide bridge Binley et al., 2000; Yang et al., 2000. Although it has been possible to engineer a disulfide with trial and error, high-resolution detail of the structure would permit rational introduction of stabilizing disulfide bonds that connect the heterodimer. Disulfide bridges have also been used for the intramolecular stabilization of the flexible regions within the subunits Dey et al., 2009; Zhou et al., 2007. Constructing a heat-stable foot-and-mouth disease vaccine by disulfide engineering came within reach when the crystal structure of the viral capsid was solved Mateo et al., 2008 and also the atomic-level resolution of the complete prefusion spike of HIV will undoubtedly contribute to structure-based design of inter- and intramolecular disulfides without going through the arduous path of trial and full chapterURL East Respiratory Syndrome-Coronavirus MERS-CoV InfectionJaffar A. Al-Tawfiq, Ziad A. Memish, in Emerging Infectious Diseases, 20144 Which Factors are Involved in Disease Pathogenesis? What are the Pathogenic Mechanisms?The pathogenesis of the disease has been elucidated in recent studies. MERS-CoV has spike glycoprotein S that targets the cellular receptor, dipeptidyl peptidase 4 DPP4.12,13 This viral spike has a putative receptor-binding domain RBD.13 MERS-CoV RBD has a core and a receptor-binding subdomain, which interacts with DPP4 β-propeller MERS-CoV MERS-CoV spike protein interacts with CD26 also known as DPP4 and causes viral attachment to host cells and virus-cell This is thought to be the first step in viral infection. The MERS-CoV infection results in profound apoptosis of infected respiratory cells within 24 full chapterURL Angel, ... Greenberg, in Encyclopedia of Virology Third Edition, 2008MorphologyRotaviruses were given their name because, when examined by classical electron microscopy, they appear as wheel rota-shaped, 70 nm particles. However, by cryoelectron microscopy a method that permits visualization of the viral spikes, the viral diameter is 100 nm Figure 1. Using this method, the virus particle has been shown to be formed by three concentric layers of proteins the core comprises viral structural protein 2 VP2, the RNA-dependent RNA polymerase VP1, guanyl tranferase VP3, and the viral genome Figure 1, the intermediate layer is formed by structural protein VP6, the most abundant and most antigenic viral protein, and the external layer comprises 780 copies of glycoprotein VP7 and 60 viral spikes formed by VP4. The surface of the virion has three types of pores that penetrate into the interior of the capsid. These channels seem to be important during viral replication, allowing exchange of compounds in aqueous solution to the inside of the capsid and the export of nascent RNA 1. An artist's reconstruction based on cryoelectron microscopy studies of an RV particle. Shown are the seven structural proteins, and the viral RNA. Reproduced with permission from Andrew Swift, Swift RV structural proteins and nonstructural proteins NSPs have been crystallized, permitting the initiation of detailed molecular studies of viral physiology. By this method, the viral spikes have been shown to consist of VP4 trimers, the structure of which rearranges upon trypsin cleavage a process that enhances viral infection and probably again on entry into the cell. These changes resemble the conformational transitions of membrane fusion proteins of enveloped viruses. The crystal structure of the viral hemaglutinin VP8 VP4 is cleaved by trypsin into VP8 and VP5 that contains several virus-neutralizing epitopes has also been determined. Details of the characteristics and function of the viral proteins are described elsewhere in this full chapterURL Angel, ... Greenberg, in Reference Module in Biomedical Sciences, 2014MorphologyRotaviruses were given their name because, when examined by classical electron microscopy, they appear as wheel rota-shaped, 70 nm particles. However, by cryoelectron microscopy a method that permits visualization of the viral spikes, the viral diameter is 100 nm, with an icosahedral structure T = 13 l Figure 1, and formed by three concentric layers of proteins. The core comprises three viral structural proteins VP and the 11 segments of dsRNA in the viral genome 120 copies of the scaffolding protein VP2, and anchored to each segment of dsRNA are the RNA-dependent RNA polymerase VP1 and the guanyl tranferase and methyltransferase VP3 Figure 1. The intermediate layer is made up of 260 trimers of the structural protein VP6, the most abundant and most antigenic viral protein. Particles with these protein layers are non-infectious but transcriptionally active and called double layered particles DLP. Their surface has 132 channels of three types that penetrate into the interior of the capsid. These channels are important during viral replication, allowing exchange of compounds in aqueous solution to the inside of the capsid and the export of nascent RNA transcripts. The external layer comprises 260 trimers of the glycoprotein VP7, which depend on bound calcium ions for stability, and 60 trimeric spikes formed by 1. An artist's reconstruction based on cryoelectron microscopy studies of an RV particle. Shown are the seven structural proteins, and the viral with permission from Andrew Swift, Swift RV structural proteins and nonstructural proteins NSPs have been crystallized, permitting detailed molecular studies of viral physiology. Using this method, the rearrangement of the viral spike protein VP4 upon trypsin cleavage a process that greatly enhances viral infection has been characterized The cleavage of VP4 by trypsin into VP8* and VP5*, which remain non-covalently associated with each other on the virion surface –VP5* being the proximal portion– generates a “rigidification” of the spike. These changes resemble the conformational transitions of membrane fusion proteins of enveloped viruses. Structure-based epitopes for neutralizing antibodies have been identified on the two RV outer layer proteins for VP7 two unique areas are targeted by neutralizing antibodies, some of which stabilize the capsid and prevent viral uncoating. The viral hemaglutinin VP8* contains at least four virus-neutralizing epitopes and antibodies directed against these epitopes probably block virus attachment. Antibodies directed at VP5* appear to neutralize the virus by inhibiting cell entry during capsid uncoating. Details of the characteristics and function of the viral proteins are described elsewhere in this full chapterURL Envelope Proteins of the BunyaviralesPablo Guardado-Calvo, Félix A. Rey, in Advances in Virus Research, 201710 Hantavirus Gn Is Homologous to Alphavirus E2Class II viral fusion proteins function together with an accompanying protein, which is released first from the same polyprotein precursor and can interact cotranslationally and in cis with the fusion protein, helping avoid premature activation in the secretory pathway. The evolution of both proteins is closely related because of structural and functional constraints. The glycoprotein complex in Alphaviruses is produced as an immature p62-E1 heterodimer, which trimerises to form the viral spikes. Furin maturation of immature p62 into mature E3-E2 proteins primes the viral spikes in the Golgi apparatus and renders E1 fusion competent. The structures of the immature p62-E1 heterodimer and mature E3–E2–E1 heterotrimers were described Voss et al., 2010, showing that E2 is folded in three distinct globular domains termed A, B, and C, organized around a central “β-ribbon” structure with characteristic “archs” Figs. 2D and 5B. The E1 TMIR is buried in between domains A and B of E2, and domain C contacts domain III of E1 near the viral membrane. Together with domain A, domain C is involved in threefold contacts stabilizing the trimeric 5. Comparison of the crystal structures of Puumala virus hGn A and Chikungunya virus E2 B. The structures are color-coded by domains domain A in blue, domain B in green, and domain C in cyan. The central domain is colored magenta for the region of the β-ribbon going from domain A to B, and yellow for the connection from domain B to C. C and D topology diagrams of domains A and B panels C and D, respectively. Chikungunya virus E2 domains are shown on the left and Hantavirus hGn on the right. Although there is an important insertion between strands at different locations between strands B and C in E2 and between C and D in hGn, the topological arrangement of the β-strands in the A domains in E2 and hGn is the same but the A strand in purple has switched β-sheets. In the case of domain B, the topology is identical. In hGn, domain A corresponds to residues 27–182, and domain B to residues 294–368. There is an insertion augmenting the region corresponding to the β-ribbon connector, which is represented in gray. The way the polypeptide chain exits domain A and enters the β-ribbon through an “arch” Voss et al., 2010 panels A and B is also conserved between E2 and hGn. The structure of hGn was obtained in the absence of hGc, and it is conceivable that domains A and B may have collapsed against each other without hGc. In the Chikungunya virus E2/E1 heterodimer, the domains are arranged around the rod-like E1, as represented in Fig. 2D. Only a structure of an hGn/hGc heterodimer can resolve this bunyaviruses, the mechanism to avoid premature fusion in the secretory pathway is not understood, and the lack of an internal cleavage site in Gn suggests that the maturation mechanism must be different to that reported for alphaviruses and flaviviruses. The structure of the N-terminal two-thirds of Gn from Puumala hantavirus hGn, the first structure of a bunyavirus Gn protein was recently determined using X-ray crystallography Li et al., 2016 and docked into a 16 Å resolution cryoelectron tomography cryo-ET map of Tula hantavirus, thereby providing the first partial glimpse of the hantavirus ultrastructural organization. The structure showed that hGn has two domains folded as a β-sandwich, which in spite of having insertions in different locations—which is the likely reason why current automated servers for structural comparisons do not detect the structural homology—exhibit the same topology of the corresponding domains termed A and B in alphavirus E2 Fig. 5. Moreover, the two β-sandwich domains are connected in a very similar way by a central β-ribbon structure with β-arches. Furthermore, secondary structure predictions for the absent C-terminal third domain of Gn suggest that it is also β-sheet-rich, with a size similar to that domain C of alphavirus E2 Fig. 5.In addition, the organization of the alphavirus and hantavirus spikes also shows similarities. The mature alphavirus particles are organized in an icosahedral capsid with triangulation number T = 4. They contain 80 trimeric spikes formed of E2 and E1 protomers. Docking the atomic model from the crystal structure of the E2/E1 heterodimer into cryo-EM reconstructions of alphavirus particles has shown that E2 forms homotrimers at the center of each spike, making all of the intraspike contacts, whereas E1 is peripheral and establishes quasi twofold homocontacts with E1 between adjacent spikes on the virion. The organization of the hantaviral particles is similar. The virions are pleomorphic in shape but are decorated by patches of spikes that form local high-order lattices with quasi fourfold symmetry. The cryo-ET reconstruction combined with docking the crystal structure of PUUV Gn into the segmented density has allowed to assign densities to Gn and Gc. The hantaviral spike is composed of two different regions, an elongated peripheral stalk that crosslinks diagonally different spikes and a central region located around the quasi fourfold axis of the tetrameric spikes. The model proposed suggests that Gn would be placed at the center of the spike, forming homotetramers, and accounting for most of the intraspike contacts and Gc would be placed peripherally, forming homodimers, and linking together adjacent spikes. This organization thus has important similarities with that of the alphaviruses, in spite of the differences between trimer vs tetramer full chapterURL Cellular and Molecular Biology of HIV-1 Broadly Neutralizing AntibodiesBarton F. Haynes, ... Gary J. Nabel, in Molecular Biology of B Cells Second Edition, 20152 Highly Conserved Structures on HIV-1 EnvHIV-1 Env is composed of three identical gp160 protomers. Surface gp160 precursor molecules are cleaved by cellular furin proteases, and the mature Env spike consists of a trimer of noncovalently associated gp120 and gp41 subunits Figure 1. HIV-1 Env mediates virus–cell fusion through three major steps. First, it engages host cell CD4, the primary HIV-1 receptor. This interaction results in an activated intermediate conformation that engages a secondary chemokine receptor, usually CCR5 and sometimes CXCR4. In the third step, the gp41 subunit rearranges into a six-helix bundle that causes hemifusion of the viral and cell surface membranes Figure 2 [41]. Antiviral neutralizing antibodies must bind either to the prefusion native viral spike or to an Env intermediate to block the virus–cell 1. Structure of the open conformation of trimeric envelope Env at subnanometer resolution.A Side view of the structure of trimeric Env bound to 17b Fab. The map was fitted with three copies of the X-ray structure for the gp120–17b portion of the 1GC1 coordinates with gp120 red and 17b Fv fragments light chain, yellow; heavy chain, green. One copy of the gp41 N-terminal helix cyan of 1AIK coordinates N34 was fitted individually into each of the three densities, which occupy the central region of the spike that is essentially a cavity in the unliganded state. B Side view of the density map from the unliganded native trimer, with the three gp41 N-terminal helices cyan superimposed to show that, in the open conformation, they occupy the solvent-filled cavity in the density map of the unliganded Ref. [41].FIGURE 2. Model for the mechanism of envelope Env CD4- or coreceptor-triggered activation of the Env spike forms an activated intermediate in which the N-terminal gp41 helices are vulnerable to neutralizing ligands. The prehairpin intermediate is formed upon insertion of the fusion peptide into the target cell membrane and dissociation of gp120, leading to the formation of the six-helix bundle state and subsequent fusion between viral and target cell Ref. [41].Numerous bnAbs have been isolated from individuals identified within cohorts with plasma neutralizing activity against diverse strains. BnAbs recognize one of at least four highly conserved yet vulnerable regions of Env the membrane proximal external region MPER of gp41 [18,20,42], a peptide-glycan epitope involving the V1V2 domain V1V2 glycan [16,22], a gp120 outer-domain glycan or peptide-glycan region V3 glycan [43,44], and the CD4 binding site CD4bs region of gp120 [19,23–25,45,46] Table 1. Recently, a fifth bnAb epitope composed of both the gp41 and gp120 subunits of Env has been defined [46a,46b,46c,46d]. Importantly, advances in cryoelectron microscopy and crystal structures have provided new insights into the native prefusion structure and the conformation of the HIV-1 Env spike [52–54]. Together with the detailed atomic level structures of bnAbs bound to their cognate epitopes, these Env trimeric structures provide tools that facilitate structure-based vaccine design [55–58].TABLE 1. Genetic Characteristics of HIV-1 Broadly Neutralizing Monoclonal AntibodiesViral EpitopeAntibody Binding CharacteristicsaAntibody Clonal FamilyIsotype and SubclassbHeavy Chain V-GeneLight Chain V-Gene κ or λCDRH3 Length Kabat AAcVH Mutation nt%dVH Mutation AA%dNeutralization BreadtheNeutralization PotencyfPolyreactivegReferencesMPER of gp41Contiguous sequence2F5IgG32–5κ1-13221415++++Yes[47]4E10IgG31–69κ3-20181420++++++Yes[48] PG16NR3–33λ2-142812–1317–20++++++No[12]CH01–04IgG13–20κ3-202414–1723–29+++Noh[16]PGT 141–145NR1–8κ2-2831–3212–1821–29++++++NR[43]Outer domain glycanGlycan only2G12IgG13–21κ1-5142132+++NR[44]V3-glycanPeptidoglycanPGT121–123NR4–59λ3-212417–2121–27++++++NR[43]PGT125–131NR4–39λ2-81915–2323–33++++++NR[43]PGT135–137NR4–39κ3-151817–2025–29+++NR[43]CD4 binding siteCDRH3 loopb12NR1–3κ3-20181320+++Noi[50]No liganded structureHJ16NR3–30κ4-1191537+++NR[45]CDRH3 loopCH103–106IgG14–59λ3-11314–1622++++Yesj[19]Mimics CD4 via CDRH2VRC01–03IgG11–2κ3-20m12–1430–3240–48+++++++No[23,51]VRC-PG04, 04bIgG11–2κ3-20143038–39++++++No[24]VRC-CH30–34IgG11–2κ1-331323–2436–40++++++No[24]No liganded structure3BNC117, 3BNC60lNR1–2κ1-33102737–40++++++Yesk[25]Mimics CD4 via CDRH2NIH45–46lIgG11–2κ3-20163041+++++++Yes[25]No liganded structure12A12, 12A21lNR1–2κ1-331323–2538–40+++++++Yes[25]8ANC131, 134lNR1–46κ3-20162737–38+++++Yes[25]1NC9, 1B2530lNR1–46λ1-4716–1924–2636–38+[25]gp120-gp41No liganded structure35O22NR1–18λ2-1416NR35+++++No[46a]No liganded structurePGT151∗NR3–30κ2D-292818–2227–31+++++No[46b,46c]Peptidoglycan8ANC195∗NR1–69κ1-5202447+++Yes[25,46d]NR, Not binding characteristics indicated by cocrystal structural analysis. mAb 2G12 utilizes unusual domain swap structure—see indicated references. mAb b12 was isolated from a phase display library, and the natural light chain pair was not retained; b12 displays heavy chain only binding in cocrystal structure with indicates the natural isotype and subclass of the isolated antibody. In some cases, this was not reported. In many cases, the PCR-amplified heavy and light chain genes are expressed in an IgG1 expression vector even if the natural antibody was a different CDRH3 lengths are often based on IMGT or Kabat nomenclature. The Kabat definition is generally used for structural studies and is often 2 AA residues shorter than the IMGT definition. For explanation of the differences in nomenclature, see percentage of mutations nt in an antibody heavy chain is based on comparison with the inferred germ-line gene. Percentage mutation is sometime also reported based on translated AA sequences AA.eNeutralization breadth is indicated for antibodies tested on large panels of >100 tier 2 Env pseudoviruses and the values shown are the percentage of viruses neutralized at an IC50 of <50 μg/ml. ++++ ≥ 90%; +++ = 75–90%; ++ = 50–74%; + ≤ 50%. If there are several members of a clonal family, the broadest clonal member was potency indicated by median or geometric mean IC50 μg/ml of neutralized viruses excluding nonneutralized viruses; ++++, IC50 < +++, IC50 = ++, IC50 = +, IC50 = or self-reactivity as assessed by a combination of common autoimmune assays, including cardiolipin ELISA, Hep2 cell IFA, and Athena assay for antinuclear antibody in this clonal lineage, CH03, is have found b12 polyreactive, but studies in b12 VHDJH + VLJL knock-in mice have demonstrated that the degree of polyreactivity for this antibody is not sufficient to predispose these antibodies to tolerance deletion [30].jCH103, CH104, CH106 are autoreactive, CH105 is not is reported to be polyreactive, but 3BNC60 is members of the clonal family also reported in the primary publication. NIH45-45 is same donor and clonal family as VRC01. For mAbs 1NC9 and 1B2530, neutralization data only available for and 02 were initially reported to derive from inferred VK3-11, but additional analysis of the antibody lineages strongly suggests VK3-20. Also, VRC03 was initially inferred to be from different clonal family than VRC01, but more detailed analysis suggests that VRC01, 02 and 03 are clonal relatives Mascola, J and Kwong, P, unpublished observations.Read full chapterURL 1Peter D. Kwong, in Handbook of Cell Signaling Second Edition, 2010Recognition in the Context of a Humoral Immune ResponseAn understanding of the parameters governing HIV-1 receptor interactions would be incomplete without an understanding of the context in which this recognition occurs. While all recognitions pit specific versus non-specific interactions, HIV-1 receptor recognition occurs in the context of a persistent infection. To bind receptor while simultaneously eluding neutralization by the humoral immune system, gp120 has evolved sophisticated strategies of evasion Figure [17, 36–38].Figure Mechanisms of humoral immune trimeric structure of gp120 is depicted in the orientation obtained by optimization of quantifiable surface parameters [40], which is in close agreement with placement based on electron tomogram characterization of HIV-1 viral spikes [41]. The orientation shown depicts the trimer from the viewpoint of the target cell membrane. Core gp120 is depicted with a black Cα worm for inner domain; light gray Cα worm for bridging sheet; gray Cα worm for outer domain; all atom representation for carbohydrate; and semitransparent surfaces for V1/V2-variable loop. Oligomeric shielding of the inner domain by neighboring protomers is apparent, as is the extensive carbohydrate masking of the outer domain surface. The potential shielding of the CD4 binding site by the V1/V2-variable loop is shown with primary mechanisms protect the envelope glycoprotein surface not involved in receptor recognition sequence variation, oligomerization, carbohydrate masking, variable loops, and conformational change. The small size of the HIV genome, coupled to high rates of replication error and recombination, facilitates rapid antigenic escape. Oligomerization uses protein–protein interfaces to block access to conserved epitopes. This protects protein surfaces in both the gp120–gp120 interface as well as the gp120–gp41 interface. Antibodies directed against these surfaces are usually non-neutralizing and recognize only separate gp120 or gp41 components, not the oligomeric gp120/gp41 viral masking involves covering exposed protein surfaces with a dense array of N-linked glycans. Because N-linked glycans are derived from host biochemical pathways, they are interpreted as “self” by the immune system and do not elicit antibodies. In addition, glycans sterically inhibit access to underlying protein surfaces. Epitopes protected by carbohydrate masking are thus immunologically “silent” [37].In terms of the potentially vulnerable receptor-binding surfaces, the virus must recognize receptor, while at the same time eluding an ever-adapting immune response. The surfaces on gp120 that interact with cellular receptors are not only larger than the typical antibody footprint 600 Å2, but also must be functionally conserved and receptor surfaces are partially protected by variable loops. These loops have little structural restraint, and sequence variation can occur at a rate roughly 1,000,000 times faster than the human genome [39]. The CD4 binding site is protected by the V1/V2-variable loop. This loop emanates from the bridging sheet, is approximately 70 amino acids in length, and contains several sites of N-linked glycosylation. Both by steric occlusion and by antigenic variation, the loop shields the CD4 binding site from antibody most conserved exposed surface on gp120 is the bridging sheet, which interacts with both CD4 and co-receptor [17, 23]. HIV hides the conserved bridging sheet through another innovative means, that of conformational change [38]. The bridging sheet is not formed until cell-surface CD4 induces the appropriate structural reorganization in gp120. Such conformational masking serves not only to reduce the elicitation of antibodies against the bridging sheet, but also to prevent neutralization. Within the oligomeric viral spike, quaternary interactions oppose the conformational changes induced by CD4. This opposition decreases the binding efficiency of antibodies that recognize surfaces formed only in the CD4-bound state of gp120. The degree of opposition is controlled by variable loop elements involved in quaternary contact [18]. Extensive variation within these loops allows this opposition to be modulated. With primary isolates, humoral pressures select the degree of opposition to permit only highly avid binding. Because such avidity is available for cell-surface receptors, but not for most antibodies, conformational masking allows HIV-1 to resist neutralization while simultaneously permitting receptor of the HIV-1 receptor interactions illustrates some of the unique features associated with viral receptor recognition. Not only is there the problem of specific binding to receptors; there is also the complementary problem of avoiding specific recognition by the immune system. Compressed into the 500 amino acids of the HIV-1 gp120 are complex mechanisms of evasion and recognition. HIV-1 receptor recognition thus provides an example of a system driven to an extraordinary level of sophistication by the incredible evolutionary speed of HIV-1 opposed by the equally remarkable adaptive capabilities of the immune full chapterURL Delivery System IIRoy Curtiss3rd, in Mucosal Immunology Fourth Edition, 2015New Developments in Antigen Delivery and DisplayGalen et al. 2004 have developed use of the S. Typhi cytolysin A hemolysin as a means to export protective antigens out of the vaccine cells into the supernatant. This was demonstrated using the B. anthracis PA antigen induction of a significantly higher level of immunity after immunization of mice than observed when the PA was not secreted. Baillie et al. 2008 compared delivery of the B. anthracis PA antigen using the HlyA hemolysin and ClyA export system from the licensed S. Typhi Ty21a vaccine using immunization of mice. Delivery of PA via the ClyA system was superior, and the investigators found that the recombinant Ty21a vaccine was very effective in priming a significant immune response to PA administered parenterally at a later and Schifferli 2003, 2007 compared delivery of TGEV spike epitopes as fusion to a subunit of the P987 fimbriae versus using the MisL autotransporter by several attenuated S. Typhimurium strains. Although antibody titers to the S epitopes were higher for the MisL display system, the neutralizing antibody titers were higher for the P987 fimbrial presentation system. Thus, the presentation must have influenced conformation since the MisL fusion construct was synthesized at a times higher level than the P987 fusion T5SS have been investigated for some time as a means to export and present antigens on the cell surface see Curtiss, 2005. All systems have a transmembrane β-barrel and an external domain that may or may not be cleaved for release by a protease such as OmpT. One can preclude this release by deleting some of the basic amino acids in the hinge region. The Hbp autotransporter studied by Jong et al. 2012 for secretion and display of heterologous antigens in attenuated S. Typhimurium such as ESAT-6 from M. tuberculosis only differs by two amino acids from the autotransporter Tsh that was the first autotransporter identified in the Enterobacteriaceae Provence and Curtiss, 1994. Both Hbp and Tsh bind heme and digest hemoglobin, thus contributing to septicemia caused by ExPEC full chapterURL ContohSoal Karbohidrat dan Kunci Jawaban beserta Pembahasan - Karbohidrat ('hidrat dari karbon'), hidrat arang, atau sakarida (dari bahasa Yunani σάκχαρον, sákcharon, berarti "gula") merupakan segolongan besar senyawa organik yang paling melimpah di bumi.Karbohidrat sendiri terdiri atas karbon, hidrogen, dan oksigen. membagikan berbagai Pertanyaan tentang The use of viral spike proteins derived directly from infected individuals would more accurately represent glycan heterogeneity and in vivo host-pathogen interactions for the design of Methods in Enzymology, 2023Natural Protein FibersC. Viney, in Encyclopedia of Materials Science and Technology, Viral Spike ProteinThe structural characteristics of virus coats capsids are highly relevant to virus propagation, and are therefore the subject of intensive study. The coat must contain and protect the nucleic acid genetic contents, be resilient against impact, be capable of broaching the outer wall of a target cell, and provide a secure pathway for conducting nucleic acid into the target. Hollow spikes on the capsid fulfill the latter two roles, from which it has been deduced that they must have unusually high strength and stiffness in axial compression. Because compressive strength and stiffness have been a long-term but elusive goal of polymer science, the hierarchical structure of spike proteins deserves careful attention.a Cross-β-sheetsViral spike protein contains several repeats of relatively short β-strand-forming amino acid sequences. The chain folds back and forth to assemble a β-sheet, stabilized by intramolecular hydrogen bonds Fig. 2. Because the long axis of the sheet is transverse rather than parallel to the molecular backbone, the structure in this case is known as a cross-β-sheet. Some silks, the egg stalks of green lacewing flies, are also reinforced by cross-β-sheet crystals.b Higher-order structureThe structure varies significantly between different virus types. For both rotavirus and human adenovirus, there is evidence that three cross-β-sheets interact to form a hollow trimeric box beam that resists buckling in compression. Structural characterization is hampered by the small size of individual spikes length⩽30 nm and width⩽5 nm. Hydrophobic bonding is presumed to be important in stabilizing their structure, since 70% of the amino acid residues are hydrophobic in representative engineered model polymers, based on multiple consecutive copies of the principal repeated sequence in native adenovirus spike protein, can self-assemble into a liquid crystalline phase in solution. However, trimeric box beams have not been found in the hierarchical microstructure of fibers spun from this phase. The spun fibers are formed under significantly off-equilibrium conditions, and should not be expected to have the same internal structure as the native spikes.c PropertiesIn tensile tests conducted on dry fiber, the breaking strength is ∼ GPa, the stiffness ∼4 GPa, and the elongation to failure ∼ 30%. Given the evidence that the native spikes rely on hydrophobic bonding to maintain their structure, the properties of analog fibers as measured in air are likely to be inferior compared to results obtained in water—even if the detailed microstructure of the native material could be reproduced. In other words, the natural material is designed to work in an aqueous medium, and attempts to mimic its properties must take this reality into full chapterURL Immunodeficiency Virus HIVThomas S. Alexander, Ken S. Rosenthal, in Encyclopedia of Infection and Immunity, 2022VirologyMontagnier and associates in Paris, and Gallo and colleagues in the United States, reported the isolation of the human immunodeficiency virus HIV-1 from patients with lymphadenopathy and AIDS Barre-Sinoussi et al., 1983; Gallo et al., 1983. A closely related, less virulent virus, designated HIV-2, was isolated later and is prevalent in West Africa. HIV appears to have been acquired by humans from chimpanzees as early as the 1800s and then spread through Africa and the world by an increasingly mobile population. Although a devastating disease that cannot be completely cured, the development of antiviral drug cocktails highly active antiretroviral therapy [HAART] has allowed many HIV patients to resume a normal like other retroviruses, is an enveloped positive-strand ribonucleic acid RNA virus with a unique morphology, encodes an RNA-dependent deoxyribonucleic acid DNA polymerase reverse transcriptase [RT] and replicates through a DNA intermediate Rosenthal, 2021. The DNA copy of the viral genome is then integrated into the host chromosome to become a cellular is a complex retrovirus based on its genome and mode of replication and within the lentivirus class, based on the nature of its disease. Retroviruses are roughly spherical, enveloped, RNA viruses with a diameter of 80–120 nm. The envelope contains the gp120/gp41 viral glycoprotein complex which is acquired by budding from the plasma membrane. The envelope surrounds a capsid that contains two identical copies of the positive-strand RNA genome inside an electron-dense core. The virion also contains 10 to 50 copies of the reverse transcriptase and integrase enzymes and two cellular transfer RNA tRNAs. These tRNAs are base-paired to each copy of the genome to be used as a primer for the RT. The morphology of the core for HIV resembles a truncated cone which differs from other retroviruses Fig. 1.Fig. 1. Cross section of human immunodeficiency virus. The enveloped virion contains two identical ribonucleic acid RNA strands, RNA polymerase, integrase, and two transfer RNAs tRNA base-paired to the genome within the protein core. This is surrounded by proteins and a lipid bilayer. The envelope spikes are the glycoprotein gp120 attachment protein and gp41 fusion protein. CA, Capsid; MA, matrix; NC, nucleocapsid; SU, surface component; TM, transmembrane component of envelope Rosenthal KS 2021 Retroviruses. In Murray PR, Rosenthal KS, Pfaller MA. Medical Microbiology 9th edn. pp. 533–549. genome of HIV includes the three major genes similar to all retroviruses which encode polyproteins for Gag group-specific antigen, capsid, matrix, and nucleic acid–binding proteins, Pol polymerase, protease, and integrase, and Env envelope, glycoproteins. These genes encode polyproteins which are subsequently cleaved into functional proteins by cellular and the viral protease. In addition to these genes, HIV also encodes the tat and rev regulatory proteins and the nef, vif, vpr and vpu HIV-1/vpx HIV-2 accessory proteins. The transcripts for these proteins require more complex transcriptional processing splicing. These proteins promote the processing or virulence of the virus and will be discussed later. At each end of the genome are long terminal repeat LTR sequences. The LTR sequences contain promoters, enhancers, and other gene sequences used for binding different cellular transcription factors. Some of the genes are expressed early in the replicative cycle and others, late in the infection starts with binding of the viral glycoprotein spikes on the surface of the envelope trimer of gp120 and gp41 molecules to the primary receptor, the CD4 protein, and then a second receptor, a 7-transmembrane G-protein–coupled chemokine receptor Fig. 2 Rosenthal, 2021. Binding to these receptors determines the tissue tropism and host range of HIV which includes CD4 T cells, myeloid and other cells. The co-receptor used upon initial infection by HIV is CCR5, which is expressed on myeloid and peripheral, activated, central memory, intestinal, and other subsets of CD4 T cells macrophages, [M]-tropic virus. Later, during chronic infection of a person, the env gene mutates so that the gp120 binds to a different chemokine receptor CXCR4, which is expressed primarily on T cells T-tropic virus. Binding to the chemokine receptor activates the cell and brings the viral envelope and cell plasma membrane close together, allowing the gp41 to interact with and promote fusion of the two membranes. Binding to CCR5 and gp41-mediated fusion are both targets for antiviral 2. The life cycle of human immunodeficiency virus HIV. HIV binds to CD4 and chemokine co-receptors and enters by fusion. The genome is reverse transcribed into deoxyribonucleic acid DNA in the cytoplasm, enters the nucleus, and is integrated into the nuclear DNA. Transcription and translation of the genome occur as a cellular gene in a fashion similar to that of human T-cell lymphotropic virus. The virus assembles at the plasma membrane and matures after budding from the cell. cDNA, Complementary DNA; mRNA, messenger ribonucleic Rosenthal KS 2021 Retroviruses. In Murray PR, Rosenthal KS, Pfaller MA. Medical Microbiology 9th edn. pp. 533–549. the nucleocapsid genome within the conic protein capsid is released into the cytoplasm, the early phase of replication begins. As the nucleocapsid traverses the cytoplasm to the nucleus, the RT, encoded by the pol gene, uses the tRNA in the virion as a primer and synthesizes a complementary negative-strand DNA cDNA. The RT also acts as a ribonuclease H, degrades the RNA genome, and then synthesizes the positive strand of DNA. The RT is a major target for antiviral drugs. During the synthesis of the virion DNA provirus, sequences from each end of the genome U3 and U5 are duplicated, thus attaching the LTRs to both ends. This process creates sequences necessary for integration and creates enhancer and promoter sequences within the LTR for regulation of transcription. This creates a DNA copy of the genome which is larger than the original genomic is very error prone. For example, the error rate for the RT from HIV is one error per 2000 bases, or approximately five errors per genome HIV, 9000 base pairs. This genetic instability of HIV is responsible for promoting the generation of new strains of virus during a person's disease, a property that switches the tropism of the virus see glycoprotein above, and can alter the pathogenicity of the virus and promote antiviral resistance or immune other retroviruses, the double-stranded cDNA of HIV can enter the nucleus through nuclear pores of resting T cells. However, the genome cannot be utilized until the cell is activated and undergoes division. The genome can remain in the nucleus and cytoplasm in a nonintegrated circular DNA form until the cell is activated. In an activated cell, the cDNA is spliced into the host chromosome with the aid of a virus-encoded, virion-carried enzyme, integrase. Integrase is also a major target for an anti-retroviral of the T cell or macrophages by cytokines, mitogens, in response to other infections, or certain virus infections EBV, CMV, HHV6 will generate transcription factors that bind to the LTR to activate the late phase of replication, the transcription of the integrated genome. The viral DNA is transcribed as a cellular gene by the host RNA polymerase II present in activated cells. Transcription of the genome produces a full-length RNA, which like for simple retroviruses is processed to produce several mRNAs that contain the gag, gag-pol, or env gene sequences. The accessory proteins require more complex processing. The full-length transcripts of the genome can also be assembled into new are four genotypes of HIV-1, designated M main, N, O, and P. Most HIV-1 is of the M group, and this group is divided into 11 subtypes, or clades, designated A to K for HIV-2, A to F. The designations are based on significant differences in the sequence of their env and gag genes and hence the antigenicity and immune recognition of the gp120 and capsid proteins of these viruses. Coinfection of a cell with HIV can allow the two pairs of genomes to recombine and produce hybrids between full chapterURL approaches in COVID-19 From infection to vaccinesLuiz Gustavo Gardinassi, ... Simone Gonçalves da Fonseca, in Omics approaches and technologies in COVID-19, Decoding SARS-CoV-2 infection biologyInteractions between SARS-CoV-2 and host cells are primarily driven by Spike viral glycoprotein, which forms trimers and bind to ACE2 receptor expressed in the cell membrane surface [52]. There is evidence for the priming of the S viral protein by the host protease TMPRSS2 [53]. Other binding or entry factors have also been implicated in facilitating ACE2-depedent SARS-CoV-2, including neutropilin-1 NRP1 [54] and heparan sulfate [55]. Notably, SARS-CoV-2 infection in vitro does not depend entirely on this system, whereby transcriptomic analysis revealed that H522 human lung adenocarcinoma cells do not express ACE2 neither TMPRSS2 and supported viral replication via heparan sulfate-mediated entry [56]. Furthermore, RNA-seq data revealed sustained modulation of the cell cycle and interferon related pathways throughout SARS-CoV-2 infection of H522 cells. A study with Calu-3 human airway epithelial cells showed that infection induces rapid gene expression of TMPRSS2, followed by immediate host response [57]. This response was marked by the upregulation of genes involved with cytokine production and antiviral responses, which was also faster when compared to infection by SARS-CoV or Middle East respiratory syndrome coronavirus MERS-CoV infection. Another study focused on the pathways regulated by ILRUN, identified previously as a pro-viral molecule. Inhibition of ILRUN expression in Caco-2 and Calu-3 cells and further RNA sequencing revealed downregulation of several pathways, but it upregulated ACE2 and TMPRSS2 expression, suggesting that ILRUN operates as an antiviral factor for SARS-CoV-2 [58].After cell entrance, gRNA is used as a template to produce nonstructural proteins, whereas several viral proteins interact with host cell machinery required for viral replication. Transcriptomic analysis of different cell lines infected with SARS-CoV-2 revealed a consistent differential transcriptional signature of 41 genes, including SERPINA3 [59]. The authors also predicted conserved interactions between viral RNA and host RNA binding proteins, whereas 31 are coexpressed with the ACE2 and TMPRSS2, among which included PABPC1 and EIF4B. Using a ribonucleoprotein capture protocol aided by transcriptomic analyses revealed ZC3HAV1, TRIM25, PARP12, and SHFL as RNA binding proteins, while EIF3D and CSDE1 function as proviral factors [60]. The N viral protein was the most significant, followed by nsp1, whereas gene ontology enrichment of SARS-CoV-2 RNAs interacting with host proteins revealed terms such as mRNA splicing, mRNA export, mRNA stability, and stress granule assembly, while JAK-STAT signaling pathway seems to regulate part of the SARS-CoV-2 RNA interactome. Transcriptomic analysis of HL-CZ human promonocytic cell line transfected with genes encoding SARS-CoV-2 spike S1 subunit revealed modulation of genes involved with topologically incorrect protein, virus receptor activity, heat shock protein binding, endoplasmic reticulum stress, antigen processing, and presentation [61]. Expression of S2 subunit induced downregulation of interferon-gamma-mediated signaling pathway, regulation of phosphatidylinositol 3-kinase activity, adipocytokine signaling, and insulin signaling pathways. NSP15 upregulated genes reflecting neutrophil degranulation, neutrophil-mediated immunity, oxidative phosphorylation, while NSP16 downregulated S-adenosylmethionine-dependent methyltransferase activity. Of interest, methylated RNA immunoprecipitation sequencing MeRIP-Seq and direct RNA sequencing demonstrated that SARS-CoV-2 RNA contained m6A modifications, whereas SARS-CoV-2 infection increased the expression of methyltransferase-like 3 METTL3 and altered its distribution. Furthermore, manipulation of METTL3 expression impacted SARS-CoV-2 replication [62].Transcriptomic analyses of organoids composed by primary human airway epithelial cells infected with SARS-CoV-2 showed rapid viral replication between 1 and 72 h with host ISG upregulation after 72 h postinfection, whereas previous rhinovirus exposure accelerated ISG induction upon SARS-CoV-2 infection [63]. This study highlights the timing between ISG expression and outcomes of SARS-CoV-2 infection. Analysis of transcriptomes from cell lines A549 and Calu3 infected with SARS-CoV-2, MERS-CoV, or IAV showed that perturbations in genes encoding proteins involved with mitochondrial and autophagy processes were specific for SARS-CoV-2, whereas upregulation of GSK3B could be a potential mechanism by which infection disrupts autophagic flux and contribute to viral replication [64]. Infection of human hepatocyte-derived cellular carcinoma cell line Huh7 with SARS-CoV-2 had a profound effect over transcriptional activity relative to several signaling pathways, whereas further assays confirmed the perturbations of Akt/mTOR/HIF-1 signaling [65]. An assessment of transcriptomes from A549 cells infected with SARS‐CoV‐2 revealed differential expression of genes involved with the mevalonate pathway, which was specific to SARS-CoV-2 infection when compared to infections with H3N2 influenza virus, H1N1 influenza virus, or respiratory syncytial virus [66]. Reanalysis of public transcriptome data from diverse cell lines and organoids infected with SARS-CoV-2 showed the differential expression of several genes involved in glycosylation processes, with significant impact in glycosyltransferases and lectins. This study implicate those molecules as potential factors affecting both viral replication and host response [67].COVID-19 causes more than respiratory symptoms and affects extrapulmonary sites causing intestinal and cardiac manifestations in patients. To understand potential implementation of intracellular pathways during infection of intestinal epithelium, human-induced pluripotent stem cell-derived intestinal organoids HIOs were infected with SARS-CoV-2, which replicated and shed viral particles. Transcriptomics data revealed a robust upregulation of ISGs that was conserved across different epithelial cell types [68]. Transcriptional profiling of primary human cardiac stromal cells derived from cardiospheres demonstrated their susceptibility to SARS-CoV-2 infection, which depended on the expression of ACE2 [69]. These cells also acquired hyperinflammatory and profibrotic phenotypes that could be involved in the pathogenesis of cardiac manifestations. Exposure of human-induced pluripotent stem cell iPSC-derived heart cells to SARS-CoV-2 confirmed productive infection, with concomitant transcriptional signs of damage, especially in cardiomyocytes [70]. Of note, alterations found in this model mimic cytopathic characteristics in hearts of COVID-19 reported studies have contributed to the understanding of processes such as SARS-CoV-2 entry, replication, and host-pathogen interactions. This information enabled the formulation of better models reflecting intracellular pathways activated and repressed upon SARS-CoV-2 infection, whereas tools have been created to facilitate the visualization and evaluation of such pathways. One such tool is the COVID-19 Disease Map, which was generated on previous knowledge from published work and represents a repository for molecular mechanisms of SARS-CoV-2 virus-host interactions [71] and can be used to interrogate transcriptomics data of cells infected with SARS-CoV-2 in vitro as well data obtained from COVID-19 full chapterURL and the Cardiovascular SystemSubramani Mani MBBS, PhD, Mark E. Garcia MD, in Textbook of SARS-CoV-2 and COVID-19, 2024Direct Infection of the MyocardiumDirect entry of SARS-CoV-2 into cells is facilitated by the affinity of the viral spike protein S to the host cell ACE2 receptor, with the host protease transmembrane protease serine 2 TMPRSS2, acting as the Many organs and tissues of the body express both ACE2 and TMPRSS2, including the lungs, heart, gut, liver, kidney, neurons, joints, and eye,39–42 and this explains the tropism and potential of the virus to cause injury to these organs and tissues. Moreover, Chen et showed that although the expression levels of ACE2 are lower in the heart compared with the gut and kidney, the levels were higher in the heart than in the lungs, which act as the primary targets for presents the ACE2 receptor expression profile in the cardiovascular studies and case reports have demonstrated the presence of SARS-CoV-2 genomic RNA or viral particles morphologically identified as SARS-CoV-2 in myocardial tissue obtained from biopsy-confirmed myocarditis Tavazzi et reported one of the earliest cases of biopsy-proven myocardial localization of viral particles with the morphology of a coronavirus in a COVID-19 patient who presented with cardiogenic shock. Escher et identified SARS-CoV-2 genomic RNA in 5 of 104 endomyocardial biopsy EMB samples of patients with suspected myocarditis or unexplained A more recent study by Bearse et looked at 41 consecutive autopsies of patients who died from COVID-19 to understand the relationship of myocardial injury to SARS-CoV-2 infection. Based on in situ hybridization ISH and NanoString transcriptomic NST profiling, the researchers determined that endomyocardial infection by SARS-CoV-2 was present in 30 of 41 cases 73%.20 Cellular targets for SARS-CoV-2 include cardiomyocytes, pericytes, fibroblasts, and resident macrophages of the provides additional details of the mechanism of SARS-CoV-2 entry into the heart and blood on ISH, NST profiling for virus positivity and histopathological findings of inflammatory infiltrates characteristic of myocyte injury for defining myocarditis, the researchers partitioned their study sample n = 41 in three groups—virus-positive with myocarditis n = 4, virus-positive without myocarditis n = 26, and virus-negative without myocarditis n = 11 to study the relationship between cardiac pathological changes and cardiac infection by the SARS-CoV-2 presents the details of the pathological findings in the various groups. Electrocardiographic ECG abnormalities in the form of atrial fibrillation, premature atrial complexes, prolongation of QTc, and nonspecific ST segment and T wave alterations were observed disproportionately in patients whose hearts were infected with et in their histopathological study of 40 patients hospitalized with COVID-19 who subsequently died, report that SARS-CoV-2 RNA was much more prevalent in the lung tissue 34/40 [85%] compared with cardiac tissue 8/40 [20%]45Read full chapterURL Cellular Phagocytosis and Its Impact on Pathogen ControlStefan S. Weber, Annette Oxenius, in Antibody Fc, 2014Targeting of Viruses to FcRsViral infection of target cells in the absence of virus-specific antibodies is in general dependent on the interaction between viral spike proteins and corresponding receptors on target cells, thereby conferring a specific tropism of individual viruses to their target cells. Antibody-opsonized virus particles, however, may gain access to additional FcR-expressing target cells. Uptake of opsonized virus particles into FcR-bearing phagocytes via FcR-dependent phagocytosis may have different outcomes for the infection process and for the ensuing spread and control of the virus infection. While very little is known about the exact intracellular fate of opsonized virus particles and how this relates to their infectivity in phagocytes, most available data indicate that FcR-mediated uptake into phagocytes does not interfere with intracellular viral replication. However, in situations when opsonizing antibodies have direct neutralizing effects on the fusion or uncoating process of the virus, and when this property is maintained under acidic conditions as present in late phagosomes/lysosomes,106–108 FcR-mediated uptake of opsonized viruses might restrict replication within phagocytes. In cases where the infected phagocyte does not support the requirements of a specific viral life cycle, FcR-mediated uptake of opsonized viruses may also lead to enhanced control of viral full chapterURL coronavirus disease COVID-19 Emergence, early infection rate, and deployment strategies for preventive solutionsMohona Munshi, ... Sourav Chakraborty, in Lessons from COVID-19, CurcuminIt is a natural polyphenolic compound that can be used as a potential treatment for COVID-19 patients. The preliminary for COVID infection is interaction with the human cell and viral spike protein. Angiotensin-converting enzyme 2 ACE-2 presents in the human respiratory tract which acts as the receptor is identified by the SARS-CoV-2 spike protein. Then the viral genome RNA is released in the cytoplasm which follows membrane fusion and the RNA codes for instant replication of proteins and transcription complex Jia et al., 2005. After entering the cell, the CoV enables the expression of gene and encoding of genome ensues. This will again in turn encode the accessory protein which allows the adaption of CoV to the human host. This curcumin can restrain the virus entry to the cell, prevent the virus encapsulation and viral protease, and modulate different cell signaling pathways. Curcumin has various antiviral activities and is a therapeutic choice for the management of COVID-19 infection. Curcumin can modulate several molecular targets that get attachment and internalization of SARS-CoV-2 in various organs including the kidney and liver. Curcumin can modulate cellular signals such as apoptosis, inflammation, and RNA replication. It also suppresses pulmonary edema and fibrosis associated with the pathway of COVID-19 infection. But the bioavailability of curcumin is less which can only be mitigated by the administration of nontoxic limits. Overall, the immunomodulatory and antiinflammatory effects show evidence of the antifibrotic and pulmonary protective nature of this phytochemical on lung tissue making it a potential way of COVID-19 treatment Zahedipour et al., 2020.Read full chapterURL Fenner's Veterinary Virology Fifth Edition, 2017Virus ReplicationArenaviruses replicate noncytolytically to high titer in many kinds of cells, including Vero African green monkey and BHK-21 baby hamster kidney cells. Virus replication occurs in the cytoplasm. The viral spike glycoprotein attaches to a cell receptor, which can be transferrin receptor 1 for several New World arenaviruses and alpha-dystroglycan for lymphocytic choriomeningitis virus. Entry and endosomal uptake occur via either clathrin-dependent or clathrin-independent pathways, perhaps depending on the individual species of arenavirus. Specifically, it is proposed that New World arenaviruses such as Junin virus utilize clathrin-mediated endocytosis, whereas Old World arenaviruses such as lymphocytic choriomeningitis and Lassa viruses utilize a clathrin-independent pathway. Because the genome of the single-stranded, negative-sense RNA viruses cannot be translated directly, the first step in replication is activation of the virion RNA polymerase transcriptase. The ambisense coding strategy of the arenavirus genome means that only the nucleoprotein N and polymerase L protein mRNAs are transcribed directly from genomic RNA before translation Fig. Newly synthesized polymerase and nucleocapsid proteins facilitate the synthesis of full-length, complementary-sense RNA, which then serves as template for the transcription of glycoprotein GP and zinc-binding protein Z mRNAs and the synthesis of more full-length, negative-sense RNA. Budding of virions occurs from the plasma membrane Fig. Arenaviruses have limited ability to lyse the cells in which they replicate, usually producing a carrier state in which defective-interfering particles are produced see Chapter 2 Virus Replication. After an initial period of active virus transcription, translation, genome replication, and production of progeny virions, viral gene expression is downregulated, and cells enter a state of persistent infection wherein virion production continues for an indefinite period but at a greatly reduced rate providing a mechanism for persistent nonlethal infection of potential reservoir hosts Table Budding of Lujo virus from the plasma membrane of an infected Vero of C. Goldsmith, C. Humphrey, B. Bird, Centers for Disease Properties of ArenavirusesTwo genera, Mammarenavirus and Reptarenavirus, with two historical subgroups of mammalian viruses, one for Old World and one for New World mammarenaviruses. Reptarenaviruses are associated with snakesVirions are pleomorphic, enveloped, 50–300 generally 110–130 nm in sizeVirion contains nonfunctional host-cell ribosomesVirions contain at least two circular helical nucleocapsids with associated RNA-dependent RNA polymerase transcriptaseGenome consists of two segments, large L, kb and small S, kb, of single-stranded RNA, both ambisenseViral proteins nucleoprotein N, RNA-dependent RNA polymerase L, two glycoproteins Gp1, Gp2, and a zinc-binding matrix protein ZReplication occurs in the cytoplasm; generally noncytocidal; persistent infectionsMaturation occurs by budding from the plasma membraneGenetic reassortment occurs between closely related virusesRead full chapterURL of Protein SynthesisHenry Wade, ... Qiaozhu Su, in Advances in Protein Chemistry and Structural Biology, 2022AbstractSevere acute respiratory syndrome coronavirus 2 Sars-CoV-2 has caused a global pandemic that has affected the lives of billions of individuals. Sars-CoV-2 primarily infects human cells by binding of the viral spike protein to angiotensin-converting enzyme 2 ACE2. In addition, novel means of viral entry are currently being investigated, including Neuropillin 1, toll-like receptors TLRs, cluster of differentiation 147 CD147, and integrin α5β1. Enriched expression of these proteins across metabolic regulatory organs/tissues, including the circulatory system, liver, pancreas, and intestine contributes to major clinical complications among COVID-19 patients, particularly the development of hypertension, myocardial injury, arrhythmia, acute coronary syndrome and increased coagulation in the circulatory system during and post-infection. Pre-existing metabolic disease, such as cardiovascular disease, obesity, diabetes, and non-alcoholic fatty liver disease, is associated with increased risk of hospitalization, persistent post-infection complications and worse outcomes in patients with COVID-19. This review overviews the biological features of Sars-CoV-2, highlights recent findings that delineate the pathological mechanisms of COVID-19 and the consequent clinical full chapterURL RhabdovirusesH. Bourhy, ... Boyle, in Encyclopedia of Virology Third Edition, 2008Virion PropertiesMorphologyRhabdovirus virions are 100–400 nm long and 50–100 nm in diameter Figure 1. Viruses appear bullet-shaped. From the outer to the inner side of the virion, one can distinguish the envelope covered with viral glycoprotein spikes and, internally, the nucleocapsid with helical symmetry consisting of the nucleoprotein tightly bound to genomic Organization and GeneticsAll rhabdoviruses contain a genome consisting of a nonsegmented single-stranded negative-sense RNA molecule with a size in the range of approximately kbp. This RNA molecule contains at least five open reading frames ORFs encoding five virion proteins in the order 3′–5′ nucleoprotein N; phosphoprotein P; matrix protein M; glycoprotein G; and polymerase L. Viruses in the genus Ephemerovirus contain several additional ORFs between the G and L genes, which encode a second glycoprotein GNS and several other nonstructural proteins. Similarly, in the genus Novirhabdovirus, a sixth functional cistron between the G and L genes encodes a nonstructural protein NV of unknown function. The unclassified rhabdoviruses, sigma virus infecting flies Drosophila spp. and plant rhabdoviruses in the genera Cytorhabdovirus and Nucleorhabdovirus also contain an additional ORF which is located between the P and M genes. Flanders virus from mosquitoes Culista melanura has a complex arrangement of genes and pseudogenes in the same genome region. Nucleotide sequence analysis of Tupaia virus from the tree shrew Tipiai belangeri has identified an additional gene encoding a small hydrophobic protein between the M and G genes, and genome sequence analysis of Wongabel virus, an unassigned rhabdovirus isolated from biting midges Culicoides austropalpalis, has revealed that it contains five additional genes that appear to be novel. The function of these other proteins including additional glycoproteins is not yet known. Therefore, despite preservation of a characteristic particle morphology, the Rhabdoviridae includes viruses that display a wide genetic diversity Figure 2.Figure 2. Genome organization of low sequence identities across the Rhabdoviridae prevent the construction of a family phylogeny. One approach to determining the phylogenetic relationships among the rhabdoviruses, as well as the identification of new viral species, is to utilize the conserved regions that have been identified in alignments of the N and L full chapterURL Methods in Protein Biochemistry Part CSabyasachi Baboo, ... John R. YatesIII, in Methods in Enzymology, N-glycosylated viral spike proteins as vaccine candidatesViruses account for at least one fifth of all communicable diseases Collaborators, 2018; Fauci, Touchette, & Folkers, 2005; Gaunt, Harvala, McIntyre, Templeton, & Simmonds, 2011; Jones et al., 2008; Wolfe, Dunavan, & Diamond, 2007; Woolhouse, Scott, Hudson, Howey, & Chase-Topping, 2012 and are responsible for vast economic losses Smith, Machalaba, Seifman, Feferholtz, & Karesh, 2019 and human suffering Mayer, Shisana, & Beyrer, 2016. For decades, scientists have studied the mechanisms of how viruses are recognized by hosts and how they escape host immune systems Chan & Gack, 2016; Dimitrov, 2004; Freed & Martin, 1995; Marsh & Helenius, 2006; Thompson, de Vries, & Paulson, 2019, and they have used this knowledge to guide the design of vaccines against viral pathogens Harvey et al., 2021; Seabright, Doores, Burton, & Crispin, 2019; VanBlargan, Goo, & Pierson, 2016. Because viral spike proteins or peplomers are responsible for viral anchorage and entry into host cells Dimitrov, 2004; Freed & Martin, 1995; Marsh & Helenius, 2006, they are the prime antigenic target for vaccines. However, these proteins help the virus evade the host immune system through heavy glycosylation Seabright et al., 2019 and heterogeneity of their glycoforms Rudd & Dwek, 1997; Zhang, Li, Lu, & Liu, 2017, so glycosylation patterns must be considered in vaccine design Burton & Hangartner, 2016; Seabright et al., 2019; Steichen et al., 2019; Thompson et al., 2019. What we know about glycosylation of viral spike proteins has come primarily from experiments in cultured cells and does not include information about the variations induced by proteotoxic stress in virus-infected cells Boyce & Yuan, 2006; Hirschberg et al., 1998; Hossler, Mulukutla, & Hu, 2007; Kaufman, 1999; Su, Liao, & Lin, 2002; Sun, Tie, Chen, & Lu, 2020; Wong et al., 2018; Yeo, Parent, Yeo, & Olden, 1985, phenotypic shifts in virus reproduction driven by interactions with the immune system Phillips, Doud, et al., 2018; Phillips, Ponomarenko, et al., 2018 or natural variations in glycosylation created by growth in different cell types Kong et al., 2010; Pritchard, Harvey, Bonomelli, Crispin, & Doores, 2015; Raska et al., 2010; Wang et al., 2020; Zhao, Song, Huang, Yu, & Mechref, 2021. The use of viral spike proteins derived directly from infected individuals would more accurately represent glycan heterogeneity and in vivo host-pathogen interactions for the design of vaccines. However, clinical samples are available in limited supply, and thus provide only very small quantities of viral spike glycoproteins. The sensitivity of existing approaches for analyzing site-specific glycan heterogeneity makes the analysis of such small quantities of glycoprotein full chapterURL

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Previewsoal lainnya: Kingdom dan Ekosistem - Biologi SMA Kelas 12. Sekelompok siswa diminta untuk mengamati ekosistem di lingkungan sekitar sekolah. Hal-hal berikut yang tidak termasuk komponen yang harus diamati adalah A. Komponen biotik. B. Kompenen abiotik. C. Relung atau niche. D. Interaksi antar komponen biotik
Proteinmerupakan senyawa utama penyusun capsid (ind: kapsid) yang membungkus asam nukleat pada tubuh virus. Kapsid yang tersusun dari protein ini bila terisi asam nukleat (DNA atau RNA) disebut dengan nukleokapsid (nucleocapsid) Lipid yang ada pada virus merupakan jenis fosfolipid, gikolipid, kolestrol dan beberapa lemak alami yang lain. Lemak merupakan komponen utama penyusun envelope (selubung). Senyawa-senyawa lain yang belum diketahui. Jenis-jenis virus | Photo by U.S. federal
Virusmerupakan partikel ultra mikroskopis yang hanya hidup di dalam sel. Hidup virus tersusun atas asam nukleat dan protein. Asam nukleat membawa informasi genetik virus dan protein berfungsi sebagai pelindung yang menyelubungi asam nukleat. Asam nukleat virus dapat berupa ADN (asam dioksiribounukleat) atau ARN (asam ribonukleat). Salahsatu struktur pada virus yang membedakannya dari kelompok makhluk hidup lainnya adalah adanya kapsid. Kapsid merupakan selubung yang membungkus asam nukleat (DNA atau RNA) sehingga disebut juga nukleokapsid. Kapsid ini tersusun atas subunit-subunit protein yang disebut kapsomer. Jumlah kapsomer yang dimiliki virus dapat menjadi salah satu Proteinkonjugasi merupakan senyawa protein yang mengikat (terikat dengan) molekul lain yang bukan protein. terdiri dari: Nukleoprotein, contohnya : protein pada inti sel dan kecamah biji-bijian. Glikoprotein, contohnya: pada musin kelenjar ludah, hati dan tendon. Fosfoprotein, contohnya: terdapat pada susu atau kuning telur. Contoh: Polivinil Klorida, Teflon, Polistirena, Polietena, Poliisoprena. Polimer kondensasi adalah polimer yang monomernya mempunyai dua gugus fungsi pada kedua ujung rantainya kemudian saling berikatan sambil melepas molekul kecil. Contoh : nilon, dakron (poliester), bakelit. 3. Hasil polimerisasi dari CH­ 2 = CHCl adalah . a.
Virustersusun dari asam nukleat, yaitu asam deoksiribonukleat (DNA) atau asam ribonukleat (RNA) yang dibungkus oleh selubung protein yang disebut kapsid. Bentuk virus bermacam-macam, ada yang berbentuk batang, bola atau bulat, berbentuk peluru, dan beberapa berbentuk huruf T seperti pada virus bakteriofage.
Proteindan karbohidrat akan menyatu membentuk komponen lipopolisakarida. Lipopolisakarida ini dapat menyusun spike virus dibawah tabung virus.
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Bahangenetik virus disimpan dalam struktur protein virus yang disebut kapsid. Kapsid adalah "pelindung" yang melindungi asam nukleat virus agar tidak terdegradasi oleh enzim inang. Struktur ini juga berfungsi untuk melampirkan virion ke inangnya, dan memungkinkan virion untuk menembus membran sel inang. Banyak salinan protein virus tunggal atau sejumlah protein virus berbeda membentuk kapsid, dan masing-masing protein virus ini dikodekan oleh satu gen dari genom virus. Kapsidadalah selubung yang berupa protein. Kapsid terdiri atas bagian-bagian yang disebut kapsomer. Misalnya, kapsid pada TMV terdiri atas satu rantai polipeptida yang tersusun atas 2100 kapsomer.Kapsid juga dapat terdiri atas protein monomer identik, yang masing-masing terdiri dari rantai polipeptida.
Proteinmembran tersusun atas glikoprotein atau protein yang bersenyawa dengan karbohidrat. Bergantung pada tipe sel dan organel tertentu dalam sel, membran memiliki 12 sampai lebih dari 50 macam protein berbeda. Protein ini tidak disusun secara acak tetapi setiap lokasi dan orientasinya disusun pada posisi relatif tertentu pada lipid bilayer.
Virusmerupakan partikel ultra mikroskopis yang hanya hidup di dalam sel. Virus tersusun dari asam nukleat dan protein. Asam nukleat berfungsi sebagai pembawa informasi genetik virus sedangkan protein berfungsi sebagai pelindung yang menyelubungi asam nukleat. Virus memiliki ukuran yang cukup bervariasi yaitu antara 20 nanometer hingga 300
Membransel tersusun atas lemak dan protein disebut dengan lipoprotein. Selain itu membran sel tersusun atas karbohidrat yang disebut dengan glikoprotein yaitu glikogen yang menempel pada protein dan berperan sebagai reseptor hormon dan neurotransmitter, glikolipid yaitu glikogen yang menempel pada fosfolipid berperan untuk menstabilkan membran.
Padabagian kepala virus diselubungi oleh kapsid, yaitu selubung protein yang tersusun oleh protein. Bentuk kapsid sangat bergantung pada jenis virusnya. Kapsid virus bisa berbentuk bulat, polihedral, heliks, atau bentuk lain yang lebih kompleks. Kapsid tersusun atas banyak kapsomer atau sub-unit protein. Kapsid adalah lapisan berupa rangkaian
17 Virus memiliki sifat-sifat berikut, kecuali . a. hanyamemiliki satu macam asam inti (DNA atau RNA) b. tidak memiliki sitoplasma, inti, danselaput plasma c. untuk reproduksinya hanya memerlukan bahan anorganik d. virus dapat aktif pada makhluk hidup spesifik e. bentuk dan ukuran virus bervariasi jawab. c 18. Pada virus, asam nukleat dibungkus oleh selaput protein yang dinamakan .
A Ciri-Ciri dan Struktur Virus. Virus merupakan partikel ultra mikroskopis yang hanya hidup di dalam sel. Hidup virus tersusun atas asam nukleat dan protein. Asam nukleat membawa informasi genetik virus dan protein berfungsi sebagai pelindung yang menyelubungi asam nukleat. Asam nukleat virus dapat berupa ADN (asam. Wqh43iv.