ArticlePolymers2022
The Local Topological Free Energy of the SARS-CoV-2 Spike Protein.
Article in Polymers, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- Geometry based prediction of tau protein sites and motifs associated with misfolding and aggregation.Scientific reports · 2025Article
- Multi-scale Jones polynomial and persistent Jones polynomial for knot data analysis.AIMS mathematics · 2025Article
- Knot data analysis using multiscale Gauss link integral.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Mathematical topology and geometry-based classification of tauopathies.Scientific reports · 2024Article
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3 authors.
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Abstract
The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model.
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