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How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations

View ORCID ProfileSoumya Lipsa Rath, Madhusmita Tripathy, Nabanita Mandal
doi: https://doi.org/10.1101/2021.10.05.463008
Soumya Lipsa Rath
aDepartment of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, India, 506004
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  • ORCID record for Soumya Lipsa Rath
  • For correspondence: slrath@nitw.ac.in tripathy@cpc.tu-darmstadt.de
Madhusmita Tripathy
bEduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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  • For correspondence: slrath@nitw.ac.in tripathy@cpc.tu-darmstadt.de
Nabanita Mandal
aDepartment of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, India, 506004
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Abstract

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unravelling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature induced fluctuations should be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low temperature behaviour. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~30 to 40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 06, 2021.
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How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations
Soumya Lipsa Rath, Madhusmita Tripathy, Nabanita Mandal
bioRxiv 2021.10.05.463008; doi: https://doi.org/10.1101/2021.10.05.463008
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How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations
Soumya Lipsa Rath, Madhusmita Tripathy, Nabanita Mandal
bioRxiv 2021.10.05.463008; doi: https://doi.org/10.1101/2021.10.05.463008

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