scholarly journals Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

2012 ◽  
Vol 75 (1-2) ◽  
pp. 19-24 ◽  
Author(s):  
Paulo E. Brandão
Keyword(s):  
Amino Acids ◽  
Gallus Gallus ◽  
Spike Glycoprotein

scholarly journals Analisis In-Silico Struktur Tiga Dimensi Reseptor Trk A dan Trk B Protein Neurotrophin 3 Pada Gallus gallus (Chicken)

2020 ◽  
Vol 12 (2) ◽  
pp. 78-84
Author(s):  
Muhammad F. Rahman ◽  
Amiruddin Kasim ◽  
Muchlis L. Djirimu ◽  
I. Made Budiarsa
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Three Dimensional ◽  
Gallus Gallus ◽  
Dimensional Structure ◽  
Neurotrophin 3 ◽  
Trk A ◽  
And Function ◽  
Trk B ◽  
Ucsf Chimera

NT3 protein is expressed by Neurotrophin 3 (NTF-3) which plays a role in the process of differentiation, survival of peripheral and neuropathological of neurons. The information of structure and function of NT-3 proteins is still very limited, especially in Gallus gallus. This study aims to predict the three-dimensional structure of the Trk A and Trk B proteins in Gallus gallus. The target protein obtained from the UniProt server with access codes Q91009 (Trk A) and Q91987 (Trk B) using the 6kzc 1.A (PDB ID) template was analyzed in silico through a homology approach and describing the structural assessment using Chimera UCSF software. The analysis showed that the Trk A protein had a QMEAN value of -0.08, composed of 778 amino acids, mass 87334.30 Daltons, and Seq Identity 79.93%. Trk B had a QMEAN value of 0.16, consisting of 818 amino acids, mass 91732.05 Daltons, and Seq Identity 84.30%. Key words: NT3; homology; UCSF chimera; G. gallus

scholarly journals Identification of a Receptor-Binding Domain of the Spike Glycoprotein of Human Coronavirus HCoV-229E

2003 ◽  
Vol 77 (4) ◽  
pp. 2530-2538 ◽  
Author(s):  
Aurelio Bonavia ◽  
Bruce D. Zelus ◽  
David E. Wentworth ◽  
Pierre J. Talbot ◽  
Kathryn V. Holmes
Keyword(s):  
Amino Acids ◽  
Receptor Binding ◽  
Protein A ◽  
Binding Domain ◽  
Expression Vectors ◽  
Receptor Binding Domain ◽  
3T3 Cells ◽  
Spike Glycoprotein ◽  
Human Coronavirus ◽  
S Proteins

ABSTRACT Human coronavirus HCoV-229E uses human aminopeptidase N (hAPN) as its receptor (C. L. Yeager et al., Nature 357:420-422, 1992). To identify the receptor-binding domain of the viral spike glycoprotein (S), we expressed soluble truncated histidine-tagged S glycoproteins by using baculovirus expression vectors. Truncated S proteins purified by nickel affinity chromatography were shown to be glycosylated and to react with polyclonal anti-HCoV-229E antibodies and monoclonal antibodies to the viral S protein. A truncated protein (S547) that contains the N-terminal 547 amino acids bound to 3T3 mouse cells that express hAPN but not to mouse 3T3 cells transfected with empty vector. Binding of S547 to hAPN was blocked by an anti-hAPN monoclonal antibody that inhibits binding of virus to hAPN and blocks virus infection of human cells and was also blocked by polyclonal anti-HCoV-229E antibody. S proteins that contain the N-terminal 268 or 417 amino acids did not bind to hAPN-3T3 cells. Antibody to the region from amino acid 417 to the C terminus of S blocked binding of S547 to hAPN-3T3 cells. Thus, the data suggest that the domain of the spike protein between amino acids 417 and 547 is required for the binding of HCoV-229E to its hAPN receptor.

scholarly journals Analysis of Amino Acid Sequence of SARS-CoV, SARS-CoV-2, and MERS-CoV Spike Glycoproteins: Preliminary Study for Obtaining Universal Peptide Vaccine Candidates

2020 ◽  
Vol 8 (2) ◽  
pp. 185
Author(s):  
Yani Suryani ◽  
Opik Taupiqurrohman
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Peptide Vaccine ◽  
Peptide Vaccines ◽  
Spike Glycoprotein ◽  
Web Based ◽  
Vaccine Candidates ◽  
Preliminary Study

In the manufacture of universal peptide vaccines, it is necessary to analyze the amino acids of the various candidates. Therefore, this study aims to examine the amino acids of the spike glycoproteins of SARS-CoV, SARS-CoV-2, and MERS CoV. The method used is the alignment of the amino acid spike glycoprotein between SARS-CoV with SARS-CoV-2, MERS CoV with SARS-CoV-2, and SARS-CoV with MERS-CoV using web-based software water emboss. The analysis result showed that SARS and SARS CoV-2 were very similar with 87% similarity and 76.4% identity values. In contrast, SARS-CoV-2 with MERS and SARS with MERS were very different, having similarity and identity values of less than 70%. Therefore, it is reasonable to conclude that spike glycoprotein's peptide is only useful from attacks by the SARS-CoV and SARS-CoV-2 viruses.

scholarly journals Repositioning of ligands that target spike glycoprotein as potential drugs against SARS-CoV-2

2020 ◽  
Author(s):  
Gema Lizbeth Ramírez-Salinas ◽  
Marlet Martínez-Archundia ◽  
José Correa-Basurto ◽  
Jazmín García-Machorro
Keyword(s):  
Amino Acids ◽  
Viral Entry ◽  
Drug Repositioning ◽  
Specific Treatment ◽  
Binding Motif ◽  
Spike Glycoprotein ◽  
Docking Simulations ◽  
Approved Drugs ◽  
Virus Replication Cycle ◽  
Fda Approved Drugs

Abstract The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify FDA-approved drugs with the potential for binding to the spike structural glycoprotein at the hinge site, receptor binding motif (RBM), and fusion peptide (FP) using molecular docking simulations. It was identified drugs that binding to amino acids crucial for down to up conformational change, receptor recognition, and fusion of the viral membrane with the cell membrane. Results show some drugs that bind to hinge site amino acids (Varenicline, or even steroids as Betamethasone) while other drugs bind to crucial amino acids for RBM (Naldemedine, Atovaquone, Cefotetan) or FP (Edarbi, Maraviroc, Difluprednate); and highlights the Saquinavir that binds both the RBM and the FP. Therefore, these drugs could inhibit spike glycoprotein and prevent viral entry (possible anti-COVID-19 drugs). Several drugs are in clinical studies; focused on another pharmacological target (candesartan, Atovaquone, Losartan, Maviroc and Ritonavir) in this work we propose an additional target, the spike glycoprotein. These results can impact in the proposal of treatments that can inhibit the first steps virus replication cycle.

scholarly journals Murine Coronavirus Evolution In Vivo: Functional Compensation of a Detrimental Amino Acid Substitution in the Receptor Binding Domain of the Spike Glycoprotein

2005 ◽  
Vol 79 (12) ◽  
pp. 7629-7640 ◽  
Author(s):  
Sonia Navas-Martin ◽  
Susan T. Hingley ◽  
Susan R. Weiss
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Receptor Binding ◽  
Amino Acid Substitution ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Functional Compensation

ABSTRACT Murine coronavirus A59 strain causes mild to moderate hepatitis in mice. We have previously shown that mutants of A59, unable to induce hepatitis, may be selected by persistent infection of primary glial cells in vitro. These in vitro isolated mutants encoded two amino acids substitutions in the spike (S) gene: Q159L lies in the putative receptor binding domain of S, and H716D, within the cleavage signal of S. Here, we show that hepatotropic revertant variants may be selected from these in vitro isolated mutants (Q159L-H716D) by multiple passages in the mouse liver. One of these mutants, hr2, was chosen for more in-depth study based on a more hepatovirulent phenotype. The S gene of hr2 (Q159L- R654H -H716D- E1035D ) differed from the in vitro isolates (Q159L-H716D) in only 2 amino acids (R654H and E1035D). Using targeted RNA recombination, we have constructed isogenic recombinant MHV-A59 viruses differing only in these specific amino acids in S (Q159L-R654H-H716D-E1035D). We demonstrate that specific amino acid substitutions within the spike gene of the hr2 isolate determine the ability of the virus to cause lethal hepatitis and replicate to significantly higher titers in the liver compared to wild-type A59. Our results provide compelling evidence of the ability of coronaviruses to rapidly evolve in vivo to highly virulent phenotypes by functional compensation of a detrimental amino acid substitution in the receptor binding domain of the spike glycoprotein.

scholarly journals Preliminary Bioinformatic Analysis of Gallus gallus (Chicken) CD8a Gene

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Zhongling Gong
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Continuous Distribution ◽  
Water Extract ◽  
Gallus Gallus ◽  
Random Coil ◽  
Root Tip ◽  
Tip Cells ◽  
Root Tip Cells

The experimental object of this study is Gallus gallus (chicken) CD8a gene. In this study, we performed sequence analysis of CD8a gene and analyzed the primary structure, secondary structure and tertiary structure of CD8a encoded protein by using bioinformatics. Through the analysis, we concluded that the sequence length is 648bp with various restriction sites identified, which is similar to CD8a of other species in Galliformes order. The sequence encodes a total of 216 amino acids. The amino acids have low hydrophobicity, with 12 phosphorylation sites and a transmembrane region, and no signal peptide. The protein secondary structure mainly consists ofαspiral, accounting for 22.69%; extension chain, accounting for 15.74%; random coil, accounting for 61.57 %, in non-continuous distribution. The relationship between CD8a and other species homologous sequences is basically consistent with the establishment of the system tree by the establishment of three trees. n the root tip cells of Vicia faba and increase in micronucleus rate. The results showed that the water extract of Solidago canadensis had different degree of inhibition and damage to silkworm root tip cells; it also had some genetic toxicity and rapid diffusion ability.

scholarly journals Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Science ◽  
2021 ◽  
Vol 371 (6534) ◽  
pp. 1139-1142 ◽  
Author(s):  
Kevin R. McCarthy ◽  
Linda J. Rennick ◽  
Sham Nambulli ◽  
Lindsey R. Robinson-McCarthy ◽  
William G. Bain ◽  
...  
Keyword(s):  
Amino Acids ◽  
Neutralizing Antibodies ◽  
Rna Viruses ◽  
Human Populations ◽  
Spike Glycoprotein ◽  
Immune Pressure ◽  
Global Concern ◽  
Antigenic Evolution ◽  
Antibody Epitopes ◽  
Recurrent Deletion

Zoonotic pandemics, such as that caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can follow the spillover of animal viruses into highly susceptible human populations. The descendants of these viruses have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses. In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

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