scholarly journals Identifying Distinct Structural Features of the SARS-CoV-2 Spike Protein Fusion Domain Essential for Membrane Interaction

Biochemistry ◽  
2021 ◽  
Vol 60 (40) ◽  
pp. 2978-2986
Author(s):  
Daniel Birtles ◽  
Jinwoo Lee
Keyword(s):  
Structural Features ◽  
Spike Protein ◽  
Protein Fusion ◽  
Membrane Interaction ◽  
Fusion Domain

scholarly journals Spike Protein Fusion Peptide and Feline Coronavirus Virulence

2012 ◽  
Vol 18 (7) ◽  
pp. 1089-1095 ◽  
Author(s):  
Hui-Wen Chang ◽  
Herman F. Egberink ◽  
Rebecca Halpin ◽  
David J. Spiro ◽  
Peter J.M. Rottier
Keyword(s):  
Fusion Peptide ◽  
Spike Protein ◽  
Protein Fusion ◽  
Feline Coronavirus

scholarly journals Structural Biology of Nanobodies against the Spike Protein of SARS-CoV-2

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2214
Author(s):  
Qilong Tang ◽  
Raymond J. Owens ◽  
James H. Naismith
Keyword(s):  
Structural Biology ◽  
Molecular Size ◽  
Structural Features ◽  
Spike Protein ◽  
Biomedical Sciences ◽  
Blood Disorder ◽  
Animal Trials ◽  
Short Period ◽  
Single Domain Antibodies ◽  
Scientific Endeavour

Nanobodies are 130 amino acid single‑domain antibodies (VHH) derived from the unique heavy-chain-only subclass of Camelid immunogloblins. Their small molecular size, facile expression, high affinity and stability have combined to make them unique targeting reagents with numerous applications in the biomedical sciences. The first nanobody agent has now entered the clinic as a treatment against a blood disorder. The spread of the SARS-CoV-2 virus has seen the global scientific endeavour work to accelerate the development of technologies to try to defeat a pandemic that has now killed over four million people. In a remarkably short period of time, multiple studies have reported nanobodies directed against the viral Spike protein. Several agents have been tested in culture and demonstrate potent neutralisation of the virus or pseudovirus. A few agents have completed animal trials with very encouraging results showing their potential for treating infection. Here, we discuss the structural features that guide the nanobody recognition of the receptor binding domain of the Spike protein of SARS-CoV-2.

scholarly journals A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features

2021 ◽  
Author(s):  
Saman Fatihi ◽  
Surabhi Rathore ◽  
Ankit Pathak ◽  
Deepanshi Gahlot ◽  
Mitali Mukerji ◽  
...  
Keyword(s):  
Genomic Data ◽  
Structural Features ◽  
Antigenic Drift ◽  
Spike Protein ◽  
Wild Type ◽  
Genome Sequences ◽  
Host Interactions ◽  
Rigorous Framework ◽  
Dynamics Simulations ◽  
Viral Host Interactions

AbstractThe recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viral-host interactions. Here we dynamically track 3,11,795 genome sequences of spike protein, which comprises 2,584 protein mutations. We reveal mutational genomic ensemble at different timing and geographies, that evolves on four distinct residues. In addition to the well-established N501 mutational cluster, we detect the presence of three novel clusters, namely A222, N439, and S477. The robust examination of structural features from 44 known cryo-EM structures showed that the virus is deploying many mutations within these clusters on structurally heterogeneous regions. One such dominant variant D614G was also simulated using molecular dynamics simulations and, as compared to wild-type, we found higher stability with human ACE2 receptor. There is also a significant overlap of mutational clusters on known epitopes, indicating putative interference with antibody binding. Thus, we propose that the resulting coaxility of mutational clusters is the most efficient feature of SARS-CoV-2 evolution and provides precise mutant combinations that can enable future vaccine re-positioning.

scholarly journals HCoV-229E spike protein fusion activation by trypsin-like serine proteases is mediated by proteolytic processing in the S2′ region

2018 ◽  
Vol 99 (7) ◽  
pp. 908-912 ◽  
Author(s):  
Ariane Bonnin ◽  
Adeline Danneels ◽  
Jean Dubuisson ◽  
Anne Goffard ◽  
Sandrine Belouzard
Keyword(s):  
Serine Proteases ◽  
Proteolytic Processing ◽  
Spike Protein ◽  
Protein Fusion

scholarly journals Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study

2021 ◽  
Vol 31 (2) ◽  
Author(s):  
Hadi Sedigh Ebrahim-Saraie ◽  
Behzad Dehghani ◽  
Ali Mojtahedi ◽  
Mohammad Shenagari ◽  
Meysam Hasannejad-Bibalan
Keyword(s):  
B Cell ◽  
In Silico ◽  
Disulfide Bonds ◽  
Deep Understanding ◽  
Structural Features ◽  
Spike Protein ◽  
Tertiary Structures ◽  
In Silico Study ◽  
High Prevalence

BACKGROUND፡ Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools.METHOD: We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed.RESULTS: Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen.CONCLUSION: In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS CoV-2 infections and design of new vaccines.

scholarly journals A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features

2021 ◽  
Author(s):  
Saman Fatihi ◽  
Surabhi Rathore ◽  
Ankit K. Pathak ◽  
Deepanshi Gahlot ◽  
Mitali Mukerji ◽  
...  
Keyword(s):  
Structural Features ◽  
Spike Protein ◽  
Rigorous Framework
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