Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods

Dasari, Sathish and Mallik, Bhabani S. (2020) Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods. The Journal of Physical Chemistry B, 124 (31). pp. 6728-6737. ISSN 1520-6106

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Abstract

Understanding the interaction of the ionic liquid (IL) with protein is vital to find the origin of the conformational changes of proteins in these alternative solvents. Here, we performed biased molecular dynamics simulations of alanine dipeptide (ADP), a widely used model for protein backbone structure, in water and two hydrated ionic liquids (ILs): 80% (w/w) 1-ethyl-3-methylimidazolium acetate ([EMIm][Ac]) and 80% (w/w) choline dihydrogen phosphate ([Cho][DHP]). We employed three different biasing methods, metadynamics (metaD), well-tempered metadynamics (WT-metaD), and adaptive biasing force (ABF), to construct the free-energy landscapes of the ADP conformations using the backbone dihedral angles (φ and ψ) as the collective variables. The calculations were also performed in water; the free-energy landscapes of ADP in water obtained from three methods are similar and agree well with the previously reported results. In hydrated [EMIm][Ac], α-planar conformation emerges as a minimum, which is comparable to that of α and β conformations corresponding to α-helix and β-sheet-like conformations of proteins. Investigation of corresponding conformations suggests that the imidazolium ring of [EMIm] cation is stacked with the amide bonds of ADP. Acetate anion makes hydrogen bonds with the amide hydrogens of the ADP. The amide-πstacking interaction is the driving force for α-planar conformation to become one of the minimum energy conformations in this IL, which destabilizes the protein conformation. However, α and β conformations are more stable in hydrated [Cho][DHP] compared to α-planar and β-planar conformations; therefore, this IL stabilizes the protein conformation. These findings are in good correlation with the previous study of proteins in these ILs. Our study helps to understand the interaction of proteins with the ionic entities and their stability in ILs.

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IITH Creators:

IITH Creators	ORCiD
Dasari, Sathish	UNSPECIFIED
Mallik, Bhabani Shankar	http://orcid.org/0000-0001-9657-1497

Item Type:

Article

Uncontrolled Keywords:

Engineering uncontrolled terms 1-ethyl-3-methylimidazolium acetates; Adaptive biasing forces; Collective variables; Conformational change; Conformational free energy; Dihydrogen phosphate; Free energy landscape; Molecular dynamics simulations;Amides; Amino acids; Dihedral angle; Hydration; Hydrogen bonds; Ionic liquids; Molecular dynamics; Peptides

Subjects:

Chemistry

Divisions:

Department of Chemistry

Depositing User:

. LibTrainee 2021

Date Deposited:

06 Jul 2021 05:56

Last Modified:

02 Mar 2022 08:44

URI:

http://raiithold.iith.ac.in/id/eprint/8125