2020
DOI: 10.1002/cphc.201901078
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Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

Abstract: Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all‐atom molecular dynamics simulations on a model protein, HP‐36. Based on our calculation of Kirkwood‐Buff integrals, we analyze the relative accumulation of… Show more

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Cited by 31 publications
(48 citation statements)
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References 99 publications
(190 reference statements)
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“…75 OPLS-AA 76 force field is used to collect the topological parameters for the ammonium-based protein secondary structure stabilizer choline chloride and the protein denaturant urea, which is consistent with our recent works. 40,41,77 OPLS-AA performs quite well to reproduce experimentally verified physical properties. For example, in a very recent study, Doherty and Acevedo could reproduce physical properties like density, viscosity, surface tension and heat capacity of ChCl based DES that included urea too, for a wide range of temperature using the OPLS force field.…”
Section: Simulation Detailsmentioning
confidence: 82%
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“…75 OPLS-AA 76 force field is used to collect the topological parameters for the ammonium-based protein secondary structure stabilizer choline chloride and the protein denaturant urea, which is consistent with our recent works. 40,41,77 OPLS-AA performs quite well to reproduce experimentally verified physical properties. For example, in a very recent study, Doherty and Acevedo could reproduce physical properties like density, viscosity, surface tension and heat capacity of ChCl based DES that included urea too, for a wide range of temperature using the OPLS force field.…”
Section: Simulation Detailsmentioning
confidence: 82%
“…We have calculated the relative number fraction ( ( )) of Ow/Urea/Choline around Ow to account for how the environment around Ow is being occupied by these constituents as we did in our earlier work. 40 ( ) is formulated as-…”
Section: Radial Distribution Functionmentioning
confidence: 99%
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“…Due to its water free storage capacity the mixture can be used as reaction medium for different biocatalytic reactions and as long-term storage medium at high temperature also [33] . It can act as a nano-crowder to protect protein structure from denaturation [34] . It helps the cell membranes to connect and communicate within the whole body.…”
Section: Methodsmentioning
confidence: 99%
“…Although several other collective variables can be used to form this kind of conformational energy surface [54][55][56] RMSD and R g has been found useful in understanding the conformational transition in many cases. [57][58][59] The major energy minimum points in the energy landscape have been labeled with the uppercase alphabet and the conformation of the corresponding 9 . CC-BY 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”
Section: Stapling Agent Reduces Conformation Flexibilitymentioning
confidence: 99%