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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinM (47)

ProteinS (26)

ProteinN (21)

ProteinE (17)

ORF3a (5)


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SARS-CoV-2 Proteins
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    A Study on Non-Synonymous Mutational Patterns in Structural Proteins of SARS-COV-2

    Authors: Jayanta Das; Swarup Roy

    id:10.20944/preprints202008.0621.v2 Date: 2021-03-04 Source: Preprints.org

    SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitution in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution pattern (type and location), and major substitution changes. The majority of the substitutions are distinct, occurred mostly in a particular location, and leads to a change in amino acid's biochemical properties. In terms of mutational changes, Envelope (E) and Membrane ( M) proteins PROTEIN are relatively stable than Nucleocapsid (N PROTEIN) and Spike (S) proteins PROTEIN. Several co-occurrence substitutions are observed, particularly in S and N proteins PROTEIN. Substitution specific to active sub-domains reveals that Heptapeptide Repeat, Fusion peptides, Transmembrane in S protein PROTEIN, and N-terminal and C-terminal domains in N protein PROTEIN are remarkably mutated, and also found few deleterious mutations in these domains.

    The E3 Ubiquitin Ligase RNF5 Facilitates SARS-CoV-2 Membrane Protein-Mediated Virion Release

    Authors: Zhen Yuan; Binbin Ding

    doi:10.1101/2021.02.28.433287 Date: 2021-03-01 Source: bioRxiv

    As enveloped virus, SARS-CoV-2 membrane protein (M PROTEIN) mediates viral release from cellular membranes, but the molecular mechanisms of SARS-CoV-2 virions release remain poorly understood. Here, we performed RNAi screening and identified the E3 ligase RNF5 HGNC which mediates ubiquitination of SARS-CoV-2 M at residue K15 to enhance the interaction of viral envelope (E) with M. M-E complex ensures the uniform size of viral particles for viral maturation and mediates viral release. Moreover, overexpression of M induces complete autophagy which is dependent on RNF5 HGNC-mediated ubiquitin modification. M inhibits the activity of lysosome protease, and uses autolysosomes for virion release. Consequently, all these results demonstrate that RNF5 HGNC mediates ubiquitin modification of SARS-CoV-2 M to stabilize the M-E complex and induce autophagy for virion release.

    The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

    Authors:

    doi:10.1101/2021.02.23.432450 Date: 2021-02-23 Source: bioRxiv

    Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 MESHD severity, including the TRIM4 HGNC interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein PROTEIN. Viral NSP1 HGNC protein adjacency to the EIF3 HGNC complex was associated with inhibited host protein translation whereas ORF6 PROTEIN localization with MAVS HGNC was associated with inhibited RIG-I HGNC 2CARD-mediated IFNB1 HGNC promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 HGNC NSP5 PROTEIN protease, with specific functional cleavage sequences in host proteins CWC22 HGNC and FANCD2 HGNC. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2. Author SummarySARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 HGNC is proximal to the EIF3 HGNC translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 PROTEIN antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5 HGNC NSP5 PROTEIN, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.

    SARS-CoV2 envelop proteins reshape the serological responses of COVID-19 MESHD patients

    Authors: Sophie Martin; Christopher Heslan; Gwenaele Jegou; Leif A. Eriksson; Matthieu Le Gallo; Vincent Thibault; Eric Chevet; Tony Avril

    doi:10.1101/2021.02.15.431237 Date: 2021-02-15 Source: bioRxiv

    The SARS-CoV-2 pandemic has elicited a unique international mobilization of the scientific community to better understand this coronavirus and its associated disease and to develop efficient tools to combat infection. Similar to other coronavirae, SARS-CoV-2 hijacks the host cell complex secretory machinery to produce properly folded viral proteins that will compose the nascent virions; including Spike, Envelope and Membrane proteins, the most exposed membrane viral proteins to the host immune system. Antibody response is part of the anti-viral immune arsenal that infected MESHD patients develop to fight viral particles in the body. Herein, we investigate the immunogenic potential of Spike (S), Envelope (E) and Membrane ( M) proteins PROTEIN using a human cell-based system to mimic membrane insertion and N-glycosylation MESHD. We show that both S and M proteins PROTEIN elicit the production of specific IgG, IgM and IgA in SARS-CoV-2 infected MESHD patients. Elevated Ig responses were observed in COVID+ patients with moderate and severe forms of the disease. Finally, when SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN D614 and G614 variants were compared, reduced Ig binding was observed with the Spike G614 variant. Altogether, this study underlines the needs for including topological features in envelop proteins to better characterize the serological status of COVID+ patients, points towards an unexpected immune response against the M protein PROTEIN and shows that our assay could represent a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.

    Vaccine Design, Adaptation, and Cloning Design for Multiple Epitope-Based Vaccine Derived From SARS-CoV-2 Surface Glycoprotein (S PROTEIN), Membrane Protein (M PROTEIN) and Envelope Protein (E PROTEIN): In silico approach

    Authors: Peter T. Habib

    doi:10.21203/rs.3.rs-241638/v1 Date: 2021-02-14 Source: ResearchSquare

    The SARS Coronavirus-2 (SARS-CoV-2) pandemic has become a global epidemic that has increased the scientific community's concern about developing and finding a counteraction against this lethal virus. So far, hundreds of thousands of people have been infected by the pandemic due to contamination and spread. This research was therefore carried out to develop potential epitope-based vaccines against the SARS-CoV-2 virus using reverse vaccinology and immunoinformatics approaches. Three potential vaccine constructs were designed after intensive computational experimentation, and one vaccine model was chosen as the best vaccine based on a molecular docking analysis that is intended to work efficiently against SARS-CoV-2. In order to verify biological stability and find an appropriate mass production technique for the chosen vaccine, molecular dynamics simulation, and silico codon adaptation studies were subsequently carried out. This study should help to maintain current research efforts to secure a definitive preventive measure against this contagious disease.

    Unbiased interrogation of memory B cells from convalescent COVID-19 MESHD patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein PROTEIN

    Authors: Jillian M DiMuzio; Baron C Heimbach; Raymond J Howanski; John P Dowling; Nirja B Patel; Noeleya Henriquez; Chris Nicolescu; Mitchell Nath; Antonio Polley; Jamie L Bingaman; Todd Smith; Benjamin C Harman; Matthew K Robinson; Michael J Morin; Pavel A Nikitin; Karen M Ridge; Bria M Coates; Janet M. Lord; Claire J. Steves

    doi:10.1101/2021.01.27.428534 Date: 2021-01-28 Source: bioRxiv

    Patients who recover from SARS-CoV-2 infections MESHD produce antibodies and antigen-specific T cells against multiple viral proteins. Here, an unbiased interrogation of the anti-viral memory B cell repertoire of convalescent patients has been performed by generating large, stable hybridoma libraries and screening thousands of monoclonal antibodies to identify specific, high-affinity immunoglobulins (Igs) directed at distinct viral components. As expected, a significant number of antibodies were directed at the Spike (S) protein PROTEIN, a majority of which recognized the full-length protein. These full-length Spike specific antibodies included a group of somatically hypermutated IgMs. Further, all but one of the six COVID-19 MESHD convalescent patients produced class-switched antibodies to a soluble form of the receptor-binding domain (RBD) of S protein PROTEIN. Functional properties of anti-Spike antibodies were confirmed in a pseudovirus neutralization assay. Importantly, more than half of all of the antibodies generated were directed at non-S viral proteins, including structural nucleocapsid (N PROTEIN) and membrane ( M) proteins PROTEIN, as well as auxiliary open reading frame-encoded (ORF) proteins. The antibodies were generally characterized as having variable levels of somatic hypermutations (SHM) in all Ig classes and sub-types, and a diversity of VL and VH gene usage. These findings demonstrated that an unbiased, function-based approach towards interrogating the COVID-19 MESHD patient memory B cell response may have distinct advantages relative to genomics-based approaches when identifying highly effective anti-viral antibodies directed at SARS-CoV-2.

    Distinct Patterns of Emergence of SARS-CoV-2 Spike PROTEIN Variants including N501Y in Clinical Samples in Columbus Ohio

    Authors: Huolin Tu; Matthew R Avenarius; Laura Kubatko; Matthew Hunt; Xiaokang Pan; Peng Ru; Jason Garee; Keelie Thomas; Peter Mohler; Preeti Pancholi; Dan Jones; Rongjuan Pei; Shihai Zhang; Minbo Su; Yi Zhang; Jia Li; Laura Esparcia; Ana Marcos-Jimenez; Santiago Sanchez-Alonso; Irene Llorente; Joan B. Soriano; Carmen Suarez Fernandez; Rosario Garcia-Vicuna; Julio Ancochea; Jesus Sanz; Cecilia Munoz-Calleja; Rafael de la Camara; Alfonso Canabal Berlanga; Isidoro Gonzalez-Alvaro; Laura Cardenoso; John R Bradley

    doi:10.1101/2021.01.12.426407 Date: 2021-01-15 Source: bioRxiv

    Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct variants (first identified in the United Kingdom and South Africa, respectively) that illustrate multiple changes in the S gene, particularly p.Asn501Tyr (N501Y), that likely have clinical impact. We report here the emergence in Columbus, Ohio in December 2020 of two novel SARS-CoV-2 clade 20C/G variants. One isolate, that has become the predominant virus found in nasopharyngeal swabs in the December 2020-January 2021 period, harbors S p.Gln677His, membrane glycoprotein (M PROTEIN) p.Ala85Ser (Q677H) and nucleocapsid (N PROTEIN) p.Asp377Tyr (D377Y) mutations. The other isolate contains S N501Y and ORF8 PROTEIN Arg52Ile (R52I), which are two markers of the UK-B.1.1.7 (clade 20I/501Y.V1) strain, but lacks all other mutations from that virus. It is also from a different clade and shares multiple mutations with the clade 20C/G viruses circulating in Ohio prior to December 2020. These two SARS-CoV-2 viruses emerging now in the United States add to the diversity of S gene shifts occurring worldwide and support multiple independent acquisition of S N501Y (in likely contrast to the unitary S D614G shift) occurring first during this period of the pandemic.

    Diverse Humoral Immune Responses in Younger and Older Adult COVID-19 MESHD Patients

    Authors: Jennifer M Sasson; Joseph J Campo; Rebecca M Carpenter; Mary K Young; Arlo Z Randall; Krista Trappl-Kimmons; Amit Oberai; Christopher Hung; Joshua Edgar; Andy A Teng; Jozelyn V Pablo; Xiaowu Liang; Angela Yee; William A Petri Jr.; David Camerini

    doi:10.1101/2021.01.12.21249702 Date: 2021-01-13 Source: medRxiv

    We sought to discover links between antibody responses to SARS-CoV-2 and patient clinical variables, cytokine profiles and antibodies to endemic coronaviruses. Serum from patients of varying ages and clinical severity were collected and used to probe a novel multi-coronavirus protein microarray containing SARS-CoV-2 proteins and overlapping protein fragments of varying length as well as SARS-CoV, MERS-CoV, HCoV-OC43 and HCoV-NL63 proteins. IgG, IgA and IgM antibody responses to specific epitopes within the spike (S), nucleocapsid (N PROTEIN) and membrane proteins (M PROTEIN) were higher in older adult patients. Moreover, the older age group displayed more consistent correlations of antibody reactivity with systemic cytokine and chemokine responses when compared to the younger adult group. A subset of patients, however, had little or no response to SARS-CoV-2 antigens and disproportionately severe clinical outcomes. Further characterization of these serosilent individuals with cytokine analysis revealed significant differences in IL-10 HGNC, IL-15 HGNC, IP-10 HGNC, EGF HGNC and sCD40L levels when compared to seroreactive patients in the cohort.

    Microsecond simulation unravel the structural dynamics of SARS-CoV-2 Spike PROTEIN-C-terminal cytoplasmic tail (residues 1242-1273)

    Authors: Prateek Kumar; Taniya Bhardwaj; Rajanish Giri; Neha Garg; Ivet Bahar; Aaron Carmody; Julia Port; Kwe Claude Yinda; Atsushi Okumura; Greg Saturday; Fatima Amanat; Florian Krammer; Patrick Hanley; Brian Smith; Jamie Lovaglio; Sarah Anzick; Kent Barbian; Craig Martens; Sarah C Gilbert; Teresa Lambe; Vincent Munster; Michael Seilmaier; Clemens Wendtner; Reinhold Foerster; Bart Haagmans; Stephan Becker; Gerd Sutter; Asisa Volz

    doi:10.1101/2021.01.11.426227 Date: 2021-01-11 Source: bioRxiv

    Spike protein PROTEIN of human coronaviruses has been a vital drug and vaccine target. The multifunctionality of this protein including host receptor binding and apoptosis has been proved in several coronaviruses. It also interacts with other viral proteins such as membrane ( M) protein PROTEIN through its C-terminal domain. The specific dibasic motif signal present in cytosolic region at C-terminal of spike protein PROTEIN helps it to localize within the endoplasmic reticulum (ER). However, the structural conformation of cytosolic region is not known in SARS-CoV-2 using which it interacts with other proteins and transporting vesicles. Therefore, we have demonstrated the conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region (residues 1242-1273). Also, in temperature dependent replica-exchange molecular dynamics simulations it has shown to form secondary structures. We believe that our findings will surely help us understand the structure-function relationship of the spike protein's PROTEIN cytosolic region.

    Adaptive immune responses to SARS-CoV-2 in recovered severe COVID-19 MESHD patients

    Authors: Beatriz Olea; Eliseo Albert Vicent Sr.; Ignacio Torres Sr.; Paula Amat; Maria Jose Remigia; Roberto Gozalbo Sr.; Jesus Rodriguez Sr.; Javier Buesa Sr.; Maria Luisa Blasco Sr.; Josep Redon Sr.; Jaime Signes Sr.; David Navarro Sr.

    doi:10.1101/2021.01.05.20249027 Date: 2021-01-06 Source: medRxiv

    Objectives: There is an imperative need to determine the durability of adaptive immunity to SARS-CoV-2. We enumerated SARS-CoV-2-reactive CD4+ and CD8+ T cells targeting S1 and M proteins PROTEIN and measured RBD-specific serum IgG over a period of 2-6 months after symptoms onset in a cohort of subjects who had recovered from severe clinical forms of COVID-19 MESHD. Methods: We recruited 58 patients (38 males and 20 females; median age, 62.5 years), who had been hospitalized with bilateral pneumonia MESHD, 60% with one or more comorbidities. IgG antibodies binding to SARS-CoV-2 RBD were measured by ELISA. SARSCoV-2-reactive CD69+ -expressing- IFN{gamma HGNC}-producing-CD4+ and CD8+ T cells were enumerated in heparinized whole blood by flow cytometry for ICS. Results: Detectable SARS-CoV-2-S1/M-reactive CD69+ -IFN-{gamma} CD4+ and CD8+ T cells were displayed in 17 (29.3%) and 6 (10.3%) subjects respectively, at a median of 84 days after onset of symptoms (range, 58-191 days). Concurrent comorbidities increased the risk (OR, 3.15; 95% CI, 1.03-9.61; P=0.04) of undetectable T-cell responses in models adjusted for age, sex and hospitalization ward. Twenty-one out of the 35 patients (60%) had detectable RBD-specific serum IgGs at a median of 118 days (range, 60 to 145 days) after symptoms onset. SARS-CoV-2 RBD specific IgG serum levels were found to drop significantly over time. Conclusion: A relatively limited number of subjects who developed severe forms of COVID-19 MESHD had detectable SARS-CoV-2-S1/M IFN{gamma HGNC} CD4+ and CD8+ T cells at midterm after clinical diagnosis. Our data also indicated that serum levels of RBD specific IgGs decline over time, becoming undetectable in some patients.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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