Thermal denaturation of a coronavirus envelope (CoVE) protein by a coarse-grained Monte Carlo simulation

Panisak Boonamnaj; Pornthep Sompornpisut; Piyarat Nimmanpipug; R.B. Pandey; Panisak Boonamnaj; Pornthep Sompornpisut; Piyarat Nimmanpipug; R.B. Pandey

doi:10.3934/biophy.2022027

AIMS Biophysics

2022, Volume 9, Issue 4: 330-340. doi: 10.3934/biophy.2022027

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Thermal denaturation of a coronavirus envelope (CoVE) protein by a coarse-grained Monte Carlo simulation

1.
Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok 10330, Thailand
2.
Department of Chemistry and Cluster of Excellence on Biodiversity based Economic and Society (B.BES-CMU), Chiang Mai University, Chiang Mai 50200, Thailand
3.
School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA

Received: 26 July 2022 Revised: 01 November 2022 Accepted: 02 November 2022 Published: 09 November 2022

Thermal response of an envelope protein conformation from coronavirus-2 (CoVE) is studied by a coarse-grained Monte Carlo simulation. Three distinct segments, the N-terminal, Trans-membrane, and C-terminal are verified from its specific contact profile. The radius of gyration (R_g) reveals a non-monotonic sub-universal thermal response: R_g decays substantially on heating in native phase under low-temperature regime in contrast to a continuous increase on further raising the temperature prior to its saturation to a random-coil in denature phase. The globularity index which is a measure of effective dimension of the protein, decreases as the protein denatures from a globular to a random-coil conformation.
- envelope protein,
- coronavirus,
- coarse-grained model,
- Monte Carlo simulation
Citation: Panisak Boonamnaj, Pornthep Sompornpisut, Piyarat Nimmanpipug, R.B. Pandey. Thermal denaturation of a coronavirus envelope (CoVE) protein by a coarse-grained Monte Carlo simulation[J]. AIMS Biophysics, 2022, 9(4): 330-340. doi: 10.3934/biophy.2022027

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Abstract

Thermal response of an envelope protein conformation from coronavirus-2 (CoVE) is studied by a coarse-grained Monte Carlo simulation. Three distinct segments, the N-terminal, Trans-membrane, and C-terminal are verified from its specific contact profile. The radius of gyration (R_g) reveals a non-monotonic sub-universal thermal response: R_g decays substantially on heating in native phase under low-temperature regime in contrast to a continuous increase on further raising the temperature prior to its saturation to a random-coil in denature phase. The globularity index which is a measure of effective dimension of the protein, decreases as the protein denatures from a globular to a random-coil conformation.

Acknowledgments

The authors acknowledge HPC at The University of Southern Mississippi supported by the National Science Foundation under the Major Research Instrumentation (MRI) program via Grant # ACI 1626217.

Conflict of interest

The authors declare no conflict of interest.

Author contributions

Panisak Boonamnaj: Conceptualization, Pornthep Sompornpisut: Conceptualization, Writing-Review & Editing, Administration, Piyarat Nimmanpipug: Conceptualization, R.B. Pandey: Conceptualization, Methodology, Investigation, Formal Analysis, Writing-Original Draft, Review & Editing.

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