Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant

Bayani, Fatemeh; Hashkavaei, Negin Safaei; Uversky, Vladimir N.; Mozaffari‐Jovin, Sina; Sefidbakht, Yahya

doi:10.1016/j.compbiomed.2022.105735

Cited by 14 publications

(12 citation statements)

References 59 publications

(65 reference statements)

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“…MD simulations of all three mutants and wild type spikes with 4A8 antibody investigated the influence of G142D, Arg158, Phe-157/del, and one amino acid mutation E156/G on binding with monoclonal antibodies and depicted the case of immune evasion. Delta-4A8, Omicron-4A8 and wildtype-4A8 RMSDs were 20.147 ± 0.526 Å, 24.845 ± 0.342 Å and 16.142 ± 0.453Å, respectively ( Figure 5 (A)), suggesting that both the variants (Dealt and Omicron) with antibody 4A8 have higher deviation than wildtype [2] . The plateau was attained for Delta-4A8 complex after 65 ns, and jumps were detected during the MD simulations.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants

Chaudhari

Joshi

Kumar

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Resultsmentioning

confidence: 99%

Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants

Chaudhari

Joshi

Kumar

et al. 2022

Computational and Structural Biotechnology Journal

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“…There is undoubtedly well-built support for the importance of electrostatic interactions for this process which is constantly confirmed for the latest variants, ACE2 polymorphisms, and new studied Abs. ,,,− Nevertheless, it is worth mentioning that Jawad and coauthors more recently added that the van der Waals interactions can also be critical to stabilizing the RBD-ACE2 complex even if the Coulombic interactions are the main driving force for the recognition process between the RBD and ACE2 . Some new all-atom MD works have shown that the presence of long glycans can enhance the RBD-ACE2 binding affinity . Although the main aspects are consistently reproduced, quantitative results for the predicted binding affinities can vary a lot as was critically discussed by Taka and colleagues …”

Section: Introductionmentioning

confidence: 96%

“…59 Some new all-atom MD works have shown that the presence of long glycans can enhance the RBD-ACE2 binding affinity. 63 Although the main aspects are consistently reproduced, quantitative results for the predicted binding affinities can vary a lot as was critically discussed by Taka and colleagues. 64 Despite an incredibly high and continuously growing number of works on this research topic that is evolving so fast, there are still open questions and preliminary results that need to be revisited particularly due to the lack of a systematic prediction of all of them on the same basis and by the same theoretical tools.…”

Section: Introductionmentioning

confidence: 96%

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

2022

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Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pK a s for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

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“…Why is SARS-CoV-2 so highly contagious that it became a pandemic? A popular answer is the affinity of the SARS-CoV-2 S protein to the human ACE-2, which is essential to viral entry [ 98 , 99 , 100 , 101 , 102 , 103 , 104 ]. Clinical studies show, however, that COVID-19 patients shed large amounts of viral particles [ 92 ].…”

Section: Discussionmentioning

confidence: 99%

A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation

Goh¹,

Dunker

Foster

et al. 2022

Biomolecules

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The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID—percentage of intrinsic disorder—of the membrane protein M, PIDM) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles in the lungs and bronchial tissues, respectively, as there is a greater level of mucus in the bronchi. The other observation revealed that there are lower viral loads in 2017-pangolin-CoV, which is predicted to have similarly low PIDN as Omicron. The abnormally hard M, which is very rarely seen in coronaviruses, arose from the fecal–oral behaviors of pangolins via exposure to buried feces. Pangolins provide an environment for coronavirus (CoV) attenuation, which is seen in Omicron. Phylogenetic study using M shows that COVID-19-related bat-CoVs from Laos and Omicron are clustered in close proximity to pangolin-CoVs, which suggests the recurrence of interspecies transmissions. Hard M may have implications for long COVID-19, with immune systems having difficulty degrading viral proteins/particles.

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Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant

Cited by 14 publications

References 59 publications

Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants

Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation

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