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

@article{Yu2016TheEO,
  title={The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view},
  author={Yuqi Yu and Jinan Wang and Qiang Shao and Jiye Shi and Weiliang Zhu},
  journal={Scientific Reports},
  year={2016},
  volume={6}
}
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… 
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References

SHOWING 1-10 OF 65 REFERENCES
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study
TLDR
Two molecular dynamics simulation techniques have been used to investigate the effect of 2,2,2-trifluoroethanol as a cosolvent on the stability of three different secondary structure-forming peptides, suggesting that the stabilizing effect of TFE is induced by the preferential aggregation of T FE molecules around the peptides.
Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.
TLDR
The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics simulations and a common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing.
Stability and folding kinetics of a ubiquitin mutant with a strong propensity for nonnative beta-hairpin conformation in the unfolded state.
TLDR
It is concluded that even though nonnative states in the denatured ensemble are highly populated and their stability further enhanced in the presence of cosolvents, the simultaneous increase in the proportion of nativelike secondary structure (hairpin or helix), in rapid equilibrium with non native states, is sufficient to accelerate the folding process.
Folding dynamics and mechanism of β-hairpin formation
Protein chains coil into α-helices and β-sheet structures. Knowing the timescales and mechanism of formation of these basic structural elements is essential for understanding how proteins fold. For
Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues.
TLDR
The results suggest an intrinsic propensity of the peptide to form a native-like beta-hairpin structure, and that the organic co-solvent acts in lieu of the stabilizing influence of tertiary interactions which occur in the folding of the complete ferredoxin sequence.
How ionic liquids can help to stabilize native proteins.
The native state of a globular protein is essential for its biocatalytic function, but is marginally stable against unfolding. While unfolding equilibria are often reversible, folding intermediates
The Trp-cage: optimizing the stability of a globular miniprotein.
TLDR
Despite the initial hypothesis, specific Pro/Trp interactions are not essential for core formation and the Y3/P19 hydrophobic staple interaction defines the folding motif as an 18-residue unit.
Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin.
TLDR
Detailed characterization of the structure of this state of ubiquitin has been carried out by 2D NMR spectroscopy, showing that gross structural reorganization of the protein has not occurred and that the A-state contains a subset of the interactions present in the native state (N-state).
...
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