Ab Initio Electronic Dielectric “Constant” of Proteins: A Baseline for Electrostatic Interaction in Biomolecular Systems
The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous ab initio quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the electronic component of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution..
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Preprint| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
chemRxiv.org - (2021) vom: 17. Nov. Zur Gesamtaufnahme - year:2021 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Adhikari, Puja [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.26434/chemrxiv.14403188 |
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| 520 | |a The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous ab initio quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the electronic component of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution. | ||
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| 700 | 1 | |a Jawad, Bahaa |e verfasserin |4 aut | |
| 700 | 1 | |a Ching, Wai-Yim |e verfasserin |4 aut | |
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