Thermal-induced unfolding-refolding of a nucleocapsid COVN protein

Warin Rangubpit; Pornthep Sompornpisut; R.B. Pandey; Warin Rangubpit; Pornthep Sompornpisut; R.B. Pandey

doi:10.3934/biophy.2021007

AIMS Biophysics

2021, Volume 8, Issue 1: 103-110. doi: 10.3934/biophy.2021007

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Thermal-induced unfolding-refolding of a nucleocapsid COVN protein

1.
School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
2.
Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok 10330, Thailand

Received: 12 November 2020 Accepted: 23 December 2020 Published: 08 January 2021

Unfolding of a coarse-grained COVN protein from its native configuration shows a linear response with increasing temperature followed by non-monotonic double peaks in its radius of gyration. The protein conforms to a random coil of folded segments in native state with increasingly tenuous and globular structures in specific temperature regimes where the effective dimensions of corresponding structures D ≈ 1.6–2.4. Thermal agitation alone is not sufficient to fully eradicate its segmental folding as few local folds are found to persist around such residues as ⁶⁵L, ¹¹⁰Y, ²²⁴L, ³⁷⁴P even at high temperatures.
- protein folding,
- nucleocapsid COVN protein,
- coarse-grain model,
- Monte Carlo simulation,
- thermal-induced folding
Citation: Warin Rangubpit, Pornthep Sompornpisut, R.B. Pandey. Thermal-induced unfolding-refolding of a nucleocapsid COVN protein[J]. AIMS Biophysics, 2021, 8(1): 103-110. doi: 10.3934/biophy.2021007

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Abstract

Unfolding of a coarse-grained COVN protein from its native configuration shows a linear response with increasing temperature followed by non-monotonic double peaks in its radius of gyration. The protein conforms to a random coil of folded segments in native state with increasingly tenuous and globular structures in specific temperature regimes where the effective dimensions of corresponding structures D ≈ 1.6–2.4. Thermal agitation alone is not sufficient to fully eradicate its segmental folding as few local folds are found to persist around such residues as ⁶⁵L, ¹¹⁰Y, ²²⁴L, ³⁷⁴P even at high temperatures.

Acknowledgments

Support from the Chulalongkorn University Dusadi Phipat scholarship award to Warin Rangubpit has been instrumental for her visit to University of Southern Mississippi. We thank Brian Olson for helping with computer support. 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

All authors participated in discussion and agreed to investigate the protein folding of COVN. RBP proposed to use coarse-grain model in consultation with PS and WR. RBP and WR generated data. WR analyzed data. PS participated in results and discussion of the data.

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