Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike
© 2021 The Author(s).
| Publié dans: | Journal of computational physics. - 1986. - 444(2021) vom: 01. Nov., Seite 110591 |
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| Auteur principal: | |
| Autres auteurs: | , , |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2021
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| Accès à la collection: | Journal of computational physics |
| Sujets: | Journal Article Covid-19 Molecular trajectory Multiscale modeling Poisson-Boltzmann SARS-CoV-2 Spike protein |
| Résumé: | © 2021 The Author(s). We present a new approach to compute and analyze the dynamical electro-geometric properties of proteins undergoing conformational changes. The molecular trajectory is obtained from Markov state models, and the electrostatic potential is calculated using the continuum Poisson-Boltzmann equation. The numerical electric potential is constructed using a parallel sharp numerical solver implemented on adaptive Octree grids. We introduce novel a posteriori error estimates to quantify the solution's accuracy on the molecular surface. To illustrate the approach, we consider the opening of the SARS-CoV-2 spike protein using the recent molecular trajectory simulated through the Foldinghome initiative. We analyze our results, focusing on the characteristics of the receptor-binding domain and its vicinity. This work lays the foundation for a new class of hybrid computational approaches, producing high-fidelity dynamical computational measurements serving as a basis for protein bio-mechanism investigations |
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| Description: | Date Revised 14.01.2025 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 0021-9991 |
| DOI: | 10.1016/j.jcp.2021.110591 |