Variations in Proteins Dielectric Constants
Abstract Using a new semi‐empirical method for calculating molecular polarizabilities and the Clausius−Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean dielectric constant of more than 150,000 proteins is ϵr=...
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2020-06-01
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Online Access: | https://doi.org/10.1002/open.202000108 |
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doaj-a5370fd367bf4b278f53fb7df0d7be6d2021-04-02T14:19:44ZengWiley-VCHChemistryOpen2191-13632020-06-019669169410.1002/open.202000108Variations in Proteins Dielectric ConstantsMuhamed Amin0Jochen Küpper1Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY Notkestrasse 85 22607 Hamburg GermanyCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY Notkestrasse 85 22607 Hamburg GermanyAbstract Using a new semi‐empirical method for calculating molecular polarizabilities and the Clausius−Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean dielectric constant of more than 150,000 proteins is ϵr=3.23 with a standard deviation of 0.04, which agrees well with previous measurement for dry proteins. The small standard deviation results from the strong correlation between the molecular polarizability and the volume of the proteins. We note that non‐amino acid cofactors such as Chlorophyll may alter the dielectric environment significantly. Furthermore, our model shows anisotropies of the dielectric constant within the same molecule according to the constituents amino acids and cofactors. Finally, by changing the amino acid protonation states, we show that a change of pH does not have a significant effect on the dielectric constants of proteins.https://doi.org/10.1002/open.202000108proteinsdielectric constantssemi-empirical methodselectrostatic interactionsmolecular polarizabilities |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Muhamed Amin Jochen Küpper |
spellingShingle |
Muhamed Amin Jochen Küpper Variations in Proteins Dielectric Constants ChemistryOpen proteins dielectric constants semi-empirical methods electrostatic interactions molecular polarizabilities |
author_facet |
Muhamed Amin Jochen Küpper |
author_sort |
Muhamed Amin |
title |
Variations in Proteins Dielectric Constants |
title_short |
Variations in Proteins Dielectric Constants |
title_full |
Variations in Proteins Dielectric Constants |
title_fullStr |
Variations in Proteins Dielectric Constants |
title_full_unstemmed |
Variations in Proteins Dielectric Constants |
title_sort |
variations in proteins dielectric constants |
publisher |
Wiley-VCH |
series |
ChemistryOpen |
issn |
2191-1363 |
publishDate |
2020-06-01 |
description |
Abstract Using a new semi‐empirical method for calculating molecular polarizabilities and the Clausius−Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean dielectric constant of more than 150,000 proteins is ϵr=3.23 with a standard deviation of 0.04, which agrees well with previous measurement for dry proteins. The small standard deviation results from the strong correlation between the molecular polarizability and the volume of the proteins. We note that non‐amino acid cofactors such as Chlorophyll may alter the dielectric environment significantly. Furthermore, our model shows anisotropies of the dielectric constant within the same molecule according to the constituents amino acids and cofactors. Finally, by changing the amino acid protonation states, we show that a change of pH does not have a significant effect on the dielectric constants of proteins. |
topic |
proteins dielectric constants semi-empirical methods electrostatic interactions molecular polarizabilities |
url |
https://doi.org/10.1002/open.202000108 |
work_keys_str_mv |
AT muhamedamin variationsinproteinsdielectricconstants AT jochenkupper variationsinproteinsdielectricconstants |
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