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|a 10.1016/j.jcp.2021.110591
|2 doi
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|a eng
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| 100 |
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|a Kucherova, Anna
|e verfasserin
|4 aut
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| 245 |
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|a Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike
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|c 2021
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|a Date Revised 09.09.2024
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|a published: Print-Electronic
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|a Citation Status PubMed-not-MEDLINE
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|a © 2021 The Author(s).
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|a 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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|a Journal Article
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|a Covid-19
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|a Molecular trajectory
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|a Multiscale modeling
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| 650 |
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|a Poisson-Boltzmann
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| 650 |
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|a SARS-CoV-2
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| 650 |
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|a Spike protein
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| 700 |
1 |
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|a Strango, Selma
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Sukenik, Shahar
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Theillard, Maxime
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational physics
|d 1986
|g 444(2021) vom: 01. Nov., Seite 110591
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|x 0021-9991
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|g volume:444
|g year:2021
|g day:01
|g month:11
|g pages:110591
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|u http://dx.doi.org/10.1016/j.jcp.2021.110591
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