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First-Principles Simulation of Dielectric Function in Biomolecules
The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decompo...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510404/ https://www.ncbi.nlm.nih.gov/pubmed/34640170 http://dx.doi.org/10.3390/ma14195774 |
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author | Adhikari, Puja Podgornik, Rudolf Jawad, Bahaa Ching, Wai-Yim |
author_facet | Adhikari, Puja Podgornik, Rudolf Jawad, Bahaa Ching, Wai-Yim |
author_sort | Adhikari, Puja |
collection | PubMed |
description | The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2–5.7 eV and 14.4–15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models. |
format | Online Article Text |
id | pubmed-8510404 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-85104042021-10-13 First-Principles Simulation of Dielectric Function in Biomolecules Adhikari, Puja Podgornik, Rudolf Jawad, Bahaa Ching, Wai-Yim Materials (Basel) Article The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2–5.7 eV and 14.4–15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models. MDPI 2021-10-02 /pmc/articles/PMC8510404/ /pubmed/34640170 http://dx.doi.org/10.3390/ma14195774 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Adhikari, Puja Podgornik, Rudolf Jawad, Bahaa Ching, Wai-Yim First-Principles Simulation of Dielectric Function in Biomolecules |
title | First-Principles Simulation of Dielectric Function in Biomolecules |
title_full | First-Principles Simulation of Dielectric Function in Biomolecules |
title_fullStr | First-Principles Simulation of Dielectric Function in Biomolecules |
title_full_unstemmed | First-Principles Simulation of Dielectric Function in Biomolecules |
title_short | First-Principles Simulation of Dielectric Function in Biomolecules |
title_sort | first-principles simulation of dielectric function in biomolecules |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510404/ https://www.ncbi.nlm.nih.gov/pubmed/34640170 http://dx.doi.org/10.3390/ma14195774 |
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