The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid

Upfold, Nicole; Ross, Caroline; Tastan Bishop, Özlem; Knox, Caroline

doi:10.3390/v12040387

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The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid

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Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa

Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa

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Viruses 2020, 12(4), 387; https://doi.org/10.3390/v12040387

Received: 4 March 2020 / Revised: 26 March 2020 / Accepted: 28 March 2020 / Published: 31 March 2020

(This article belongs to the Special Issue Virus Bioinformatics 2020)

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Abstract

The assembly of picornavirus capsids proceeds through the stepwise oligomerization of capsid protein subunits and depends on interactions between critical residues known as hotspots. Few studies have described the identification of hotspot residues at the protein subunit interfaces of the picornavirus capsid, some of which could represent novel drug targets. Using a combination of accessible web servers for hotspot prediction, we performed a comprehensive bioinformatic analysis of the hotspot residues at the intraprotomer, interprotomer and interpentamer interfaces of the Theiler’s murine encephalomyelitis virus (TMEV) capsid. Significantly, many of the predicted hotspot residues were found to be conserved in representative viruses from different genera, suggesting that the molecular determinants of capsid assembly are conserved across the family. The analysis presented here can be applied to any icosahedral structure and provides a platform for in vitro mutagenesis studies to further investigate the significance of these hotspots in critical stages of the virus life cycle with a view to identify potential targets for antiviral drug design. View Full-Text

Keywords: assembly; axis of symmetry; capsid; cardiovirus; hotspot; pentamer; protomer; protein–protein interaction

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MDPI and ACS Style

Upfold, N.; Ross, C.; Tastan Bishop, Ö.; Knox, C. The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid. Viruses 2020, 12, 387. https://doi.org/10.3390/v12040387

AMA Style

Upfold N, Ross C, Tastan Bishop Ö, Knox C. The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid. Viruses. 2020; 12(4):387. https://doi.org/10.3390/v12040387

Chicago/Turabian Style

Upfold, Nicole, Caroline Ross, Özlem Tastan Bishop, and Caroline Knox. 2020. "The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid" Viruses 12, no. 4: 387. https://doi.org/10.3390/v12040387

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The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid

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