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Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods.

ABSTRACT: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mechanism elucidating the transition from the closed state to the partially open state still remains unclear. In this study, we applied a series of computational methods, including Markov state model, transition path theory and random forest to analyze the S1 motion. Our results showed a promising complete conformational movement of the receptor-binding domain, from buried, partially open, to detached states. We also estimated the transition probability among these states. Based on the asymmetry in both the dynamics behavior and the accumulated alpha carbon (Cα) importance, we further suggested a relation among chains in the trimer spike protein, which leads to a deeper understanding on protein motions of the S1 subunit. Communicated by Ramaswamy H. Sarma.

SUBMITTER: Tian H

PROVIDER: S-EPMC7484573 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods.

Tian Hao H Tao Peng P

Journal of biomolecular structure & dynamics 20200804 17

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mechanism elucidating the transition from the closed state to the partially open state still remains unclear. In this study, we applied a series of computational methods, including Mark ...[more]

PMID: 32746720

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Project description:BackgroundThe intricacies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing acute lung injury (ALI) and modulating inflammatory factor dynamics in vivo remain poorly elucidated. The present study endeavors to explore the impact of the recombinant SARS-CoV-2 spike protein S1 subunit (S1SP) on ALI and inflammatory factor profiles in mice, aiming to uncover potential therapeutic targets and intervention strategies for the prevention and management of Coronavirus Disease 2019 (COVID-19).MethodsTo mimic COVID-19 infection, K18-hACE2 transgenic mice were intratracheally instilled with S1SP, while C57BL/6 mice were administered LPS to form a positive control group. This setup facilitated the examination of lung injury severity, inflammatory factor levels, and alterations in signaling pathways in mice mimicking COVID-19 infection. Histopathological assessment through HE staining, along with analysis of lung wet/dry ratio and ultrasound imaging, revealed severe lung injury.ResultsAfter molding, K18-hACE2 mice exhibited a pronounced reduction in body weight and showed more significant lung injury (P < 0.05). Notably, there was a significant elevation in vascular permeability, total protein, and total white blood cells in bronchoalveolar lavage fluid (BALF) (P < 0.05), indicative of tissue damage. Additionally, the tight junction of lung tissue was compromised (P < 0.05), accompanied by intense oxidative stress marked by decreased SOD activity and elevated MDA content (P < 0.05). Cytokine levels, including IL-6, IL-1β, TNF-α, and MIG, were significantly upregulated in both BALF and serum of S1SP + K18 mice (P < 0.05). Furthermore, S1SP prominently augmented the expression of p-p65/P65 and attenuated IκBα expression in the NF-κB signaling pathway of humanized mice (P < 0.05), corroborating a heightened inflammatory response at the tissue level (P < 0.05).ConclusionThe administration of S1SP to K18-hACE2 mice resulted in severe lung injury, enhanced vascular permeability, and compromised epithelial barrier function in vivo. This was accompanied by disruption of lung tight junctions, the manifestation of severe oxidative stress and a cytokine storm, as well as the activation of the NF-κB signaling pathway, highlighting key pathological processes underlying COVID-19-induced lung injury.

Dataset Information

Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods.

Publications

Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods.

Similar Datasets

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