The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view

Scientific Reports
Yuqi YuWeiliang Zhu

Abstract

Protein folding is subject to the effects of solvation environment. A variety of organic solvents are used as additives for in vitro refolding of denatured proteins. Examination of the solvent effects on protein folding could be of fundamental importance to understand the molecular interactions in determining protein structure. This article investigated the folding of α-helix and β-hairpin structures in water and the solutions of two representative refolding additives (methanol (MeOH) and 1-Ethyl-3-methylimidazolium chloride (EMIM-Cl) ionic liquid) using REMD simulations. For both α-helix and β-hairpin in MeOH/water solution or α-helix in EMIM-Cl/water solution, the transient structures along the folding pathway are consistent with the counterparts in water but the relative statistical weights are changed, leading to the decrease in the overall folding free energy barrier. Accordingly, MeOH promotes the folding of both α-helix and β-hairpin but EMIM-Cl ionic liquid only promotes the folding of α-helix, consistent with experimental observations. The present study reveals for the first time the trivial effects on folding route but significant effects on folding thermodynamics from MeOH and EMIM-Cl, explaining the function of prot...Continue Reading

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Citations

Jan 27, 2017·Chemical Reviews·Ksenia S EgorovaValentine P Ananikov
Nov 16, 2019·Astrobiology·Kyle P MartinF Marty Ytreberg
Apr 8, 2020·Biotechnology and Bioengineering·Adam A CaparcoJulie A Champion
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Aug 2, 2017·Journal of Chemical Theory and Computation·Qiang Shao, Weiliang Zhu
Dec 3, 2021·Chembiochem : a European Journal of Chemical Biology·Vesna StanojlovicChiara Cabrele

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Methods Mentioned

BETA
protein folding
NMR
circular

Software Mentioned

MMTSM Toolset
AMBER11
FF94
ILDN
AMBER
REMD
FF99SB
AMBER FF94

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