ArticleBioinformatics (Oxford, England)2020
Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Structural Features of a Tiny Viral Protein, ORF7b of SARS-CoV-2.International journal of molecular sciences · 2026Article
- Computation suggests that the cell adhesion sub-proteome is enriched for sites of pH-dependence and charge burial.PloS one · 2025Article
- Computational investigation of missense somatic mutations in cancer and potential links to pH-dependence and proteostasis.PloS one · 2024Article
- Computational Investigation of Mechanisms for pH Modulation of Human Chloride Channels.Molecules (Basel, Switzerland) · 2023Article
- The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2.Frontiers in molecular biosciences · 2022Review
- A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium.Briefings in bioinformatics · 2021Article
- Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups.Computational and structural biotechnology journal · 2021Article
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2 authors.
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Abstract
motivationEvolution couples differences in ambient pH to biological function through protonatable groups, in particular, those that switch from buried to exposed and alter protonation state in doing so. We present a tool focusing on structure-based discovery and display of these groups.
resultsSince prediction of buried group pKas is computationally intensive, solvent accessibility of ionizable groups is displayed, from which the user can iteratively select pKa calculation centers. Results are color-coded, with emphasis on buried groups. Utility is demonstrated with benchmarking against known pH sensing sites in influenza virus hemagglutinin and in variants of murine hepatitis virus, a coronavirus. A pair of histidine residues, which are conserved in coronavirus spike proteins, are predicted to be electrostatically frustrated at acidic pH in both pre- and post-fusion conformations. We suggest that an intermediate expanded conformation at endosomal pH could relax the frustration, allowing histidine protonation and facilitating conformational conversion of coronavirus spike protein. AVAILABILITY AND IMPLEMENTATION: This tool is available at http://www.protein-sol.manchester.ac.uk/pka/.
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