Conformational dynamics of amyloid-β (16–22) peptide in aqueous ionic liquids

Dasari, Sathish and Mallik, Bhabani S. (2020) Conformational dynamics of amyloid-β (16–22) peptide in aqueous ionic liquids. RSC Advances, 10 (55). pp. 33248-33260. ISSN 2046-2069

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Abstract

Molecular dynamics simulations of amyloid-β (16-22) peptide dimer in water as well as at two different experimentally studied concentrations of hydrated ionic liquids (ILs), ethylammonium mesylate (EAM), ethylammonium nitrate (EAN), and triethylammonium mesylate (TEAM), were carried out employing an umbrella sampling method. We used the average Ψ angle of the peptide backbone as the reaction coordinate to observe the conformational changes of a peptide dimer. Secondary structural element values were calculated for the peptide dimer along the reaction coordinate to see the transition of the peptide dimer between β-sheet and α-helix conformations. We observe the β-sheet conformation as the global minimum on the free energy surfaces in both EAM and EAN ILs at both the concentrations and at a low concentration of TEAM. However, we observe α-helix conformation as the global minimum at a high concentration of TEAM. Our results are in good correlation with the experimental findings. We calculated the average number of intramolecular and intermolecular hydrogen bonds of α-helix and β-sheet conformations in all solutions, and they are in correlation with the secondary structure element values. To understand the peptide-IL interactions, atom-atom radial distribution functions of cation, anion, and water around amide oxygen and hydrogen atoms were calculated. The solvent-accessible surface area of the peptide dimer was calculated to understand the exposure of the peptide towards the solvent during conformational changes. Finally, van der Waals (vdW) and Coulomb interaction energies were calculated between peptide-cation, peptide-anion, and peptide-water to understand the stability of conformations in different concentrations. We find that the TEA cation has more vdW interaction energy compared to Coulomb interaction energy with peptide in 70% (w/w) TEAM, which mimics a membrane-like environment to induce α-helix conformation rather than β-sheet conformation.

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IITH Creators:
IITH CreatorsORCiD
Dasari, SathishUNSPECIFIED
Mallik, Bhabani Shankarhttp://orcid.org/0000-0001-9657-1497
Item Type: Article
Uncontrolled Keywords: Conformational dynamics; Coulomb interaction energy; Intermolecular hydrogen bonds; Molecular dynamics simulations; Radial distribution functions; Secondary structural elements; Secondary structure elements; Solvent accessible surface areas,Amides; Atoms; Coulomb interactions; Dimers; Distribution functions; Free energy; Glycoproteins; Hydrogen bonds; Ionic liquids; Molecular dynamics; Positive ions; Reaction kinetics; Tea; Van der Waals forces
Subjects: Chemistry
Divisions: Department of Chemistry
Depositing User: . LibTrainee 2021
Date Deposited: 06 Jul 2021 05:28
Last Modified: 06 Jul 2021 05:28
URI: http://raiith.iith.ac.in/id/eprint/8123
Publisher URL: http://doi.org/10.1039/d0ra06609e
OA policy: https://v2.sherpa.ac.uk/id/publication/25266
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