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- Title
Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants.
- Authors
Balupuri, Anand; Kim, Jeong-Min; Choi, Kwang-Eun; No, Jin Sun; Kim, Il-Hwan; Rhee, Jee Eun; Kim, Eun-Jin; Kang, Nam Sook
- Abstract
The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein–ACE2 complexes instead of only RBD–ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.
- Subjects
SARS-CoV-2; SARS-CoV-2 Omicron variant; STRUCTURAL stability; PROTEIN stability; COVID-19; PROTEIN analysis
- Publication
International Journal of Molecular Sciences, 2023, Vol 24, Issue 22, p16069
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms242216069