Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins

Barozi, Victor; Edkins, Adrienne L.; Bishop, Özlem Taştan

doi:10.1016/j.csbj.2022.08.015

Cited by 3 publications

(5 citation statements)

References 137 publications

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“…At the same time, a comparison of computed binding energies and the flexibility of the receptor-binding motif led to the conclusion that the latter factor was indeed the main cause of a favored interaction between the spike receptor-binding domain and the host receptor. In agreement with a number of additional studies, − the computational results in ref showed how the evolutionary Omicron sublineages progressively underwent specific mutations in a trade-off between binding affinity for ACE2 (lower than previous variants) and antibody escape capacity (higher than previous variants). From a different biophysical perspective, the present Raman study supported the hypothesis that the main path in the evolutionary behavior of the Omicron sublineages consisted of a trade-off among binding affinity with the receptor, immune escape attitude, and viral replication/budding.…”

Section: Results and Discussionsupporting

confidence: 85%

“…The large numbers of Omicron sublineages that continue to emerge during the COVID-19 pandemic represent a potential threat for vaccine breakthrough infections and reinfections. While it is now clear that α and Delta variants developed distinct paths of infectivity and immunological escape profiles as compared to ancestral SARS-CoV-2, the evolutionary direction of the Omicron sublineages yet remains a matter of discussion. − Notwithstanding the fact that surveillance and timely sequencing of novel Omicron subvariants remain the main tools to unfold the “strategy” of current and future Omicron sublineages, Raman spectroscopy could contribute to this task by providing an agile and fast approach to analyze sublineage multiplications. The present study provides some evidence in support of this assertion.…”

Section: Results and Discussionmentioning

confidence: 99%

“…Barozi et al 150 used a combined approach of post molecular dynamics and dynamic residue network analyses to characterize the Omicron sublineages BA.1.18, BA.2, BA.3, and BA.4. Those researchers focused their analyses on the interaction between the spike protein and the human angiotensin-converting enzyme 2, essential for infection and, at the same time, a target for neutralizing antibodies.…”

Section: Results and Discussionmentioning

confidence: 99%

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Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

Pezzotti,

Ohgitani,

Fujita

et al. 2023

ACS Infect. Dis.

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The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman “metabolomic snapshot”, which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

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Section: Results and Discussionsupporting

confidence: 85%

Section: Results and Discussionmentioning

confidence: 99%

Section: Results and Discussionmentioning

confidence: 99%

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Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

Pezzotti,

Ohgitani,

Fujita

et al. 2023

ACS Infect. Dis.

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“…The Betweenness Centrality (B)C estimates show how many shortest paths go through a given node, thereby revealing its important role in signal transmission throughout the network. Recently, Barozi and coworkers applied these centrality metrics to analyse the Molecular Dynamics of the Omicron S-protein by identifying a specific evolutionary pattern towards an increased allosteric regulation of the S-protein RBD-hACE2 binding 55 .…”

Section: Resultsmentioning

confidence: 99%

Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks

Guzzi

Paola

Puccio

et al. 2023

Sci Rep

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The structure of proteins impacts directly on the function they perform. Mutations in the primary sequence can provoke structural changes with consequent modification of functional properties. SARS-CoV-2 proteins have been extensively studied during the pandemic. This wide dataset, related to sequence and structure, has enabled joint sequence-structure analysis. In this work, we focus on the SARS-CoV-2 S (Spike) protein and the relations between sequence mutations and structure variations, in order to shed light on the structural changes stemming from the position of mutated amino acid residues in three different SARS-CoV-2 strains. We propose the use of protein contact network (PCN) formalism to: (i) obtain a global metric space and compare various molecular entities, (ii) give a structural explanation of the observed phenotype, and (iii) provide context dependent descriptors of single mutations. PCNs have been used to compare sequence and structure of the Alpha, Delta, and Omicron SARS-CoV-2 variants, and we found that omicron has a unique mutational pattern leading to different structural consequences from mutations of other strains. The non-random distribution of changes in network centrality along the chain has allowed to shed light on the structural (and functional) consequences of mutations.

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“…4 It seems that progressive mutational evolution of the spike in Omicron sub-lineages leads to increased transmissibility. 5 To evaluate the fusogenicity of SARS-CoV-2 variants, we established a SARS-CoV-2 spike-mediated cell-cell fusion system using HEK293FT cells transiently expressing spike-GFP fusion protein (Supplementary Fig. 1a) as effector cells and Vero-E6 naturally expressing ACE2 as target cells.…”

Section: Dear Editormentioning

confidence: 99%

Mutation N856K in spike reduces fusogenicity and infectivity of Omicron BA.1

Sun

Wang

Yang

et al. 2023

Sig Transduct Target Ther

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Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins

Cited by 3 publications

References 137 publications

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks

Mutation N856K in spike reduces fusogenicity and infectivity of Omicron BA.1

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