Journal article
Intrinsic Conformational Dynamics of Alanine in Water/Ethanol Mixtures: An Experiment-Driven Molecular Dynamics Study
The journal of physical chemistry. B, Vol.124(51), pp.11600-11616
24 Dec 2020
PMID: 33300341
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
In vitro, cationic glycylalanylglycine (GAG) forms a hydrogel in binary mixtures of water and ethanol. In water, alanine residue is known for its high polyproline II (pPII) content. Spectroscopic data, including three J-coupling constants and amide I' profiles, indicate that addition of 42% ethanol to water significantly reduces the pPII content of alanine residue in GAG. Here, experiment-based Gaussian Ramachandran distributions of alanine in GAG at different ethanol fractions are examined and three MD force fields are evaluated with respect to their ability to capture these ethanol-induced conformational changes. MD simulations on monomeric GAG in eight different water/ethanol mixtures within Amber ff14SB, OPLS-AA/M, and CHARMM36m reveal that only Amber ff14SB partially captures the ethanol-induced conformational changes of alanine residue in monomeric GAG when 42% ethanol is added to water. MD simulations of 200 mM GAG ensembles in pure water and in the aqueous solution with 42% ethanol showcase the ability of CHARMM36m to capture the effect of ethanol on the average pPII content of alanine in GAG and provide a plausible explanation for this effect, which may stem from an increased propensity of GAG to form oligomers in the presence of ethanol.
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Details
- Title
- Intrinsic Conformational Dynamics of Alanine in Water/Ethanol Mixtures: An Experiment-Driven Molecular Dynamics Study
- Creators
- Shuting Zhang - Drexel UniversityBrian Andrews - Drexel UniversityReinhard Schweitzer-Stenner - Drexel UniversityBrigita Urbanc - Drexel University
- Publication Details
- The journal of physical chemistry. B, Vol.124(51), pp.11600-11616
- Publisher
- American Chemical Society; Washington, DC
- Number of pages
- 17
- Grant note
- DMR-1707770; MCB-1817650 / National Science Foundation; National Science Foundation (NSF)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics
- Identifiers
- 991019167864904721
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- Chemistry, Physical