Open AccessVariations in Proteins Dielectric Constants
Author(s) -
Amin Muhamed,
Küpper Jochen
Publication year - 2020
Publication title -
chemistryopen
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.644
H-Index - 29
ISSN - 2191-1363
DOI - 10.1002/open.202000108
Subject(s) - dielectric , polarizability , protonation , chemistry , protein data bank (rcsb pdb) , molecule , anisotropy , amino acid , protein data bank , computational chemistry , protein structure , analytical chemistry (journal) , crystallography , chemical physics , ion , materials science , stereochemistry , organic chemistry , physics , biochemistry , optics , optoelectronics
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 isϵ r = 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.