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Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving?

Inês Gomes1, Nuno Galamba1

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Deep eutectic solvents (DESs) stabilize proteins by kinetically hindering fluctuations, not through traditional hydration mechanisms. This study explores ubiquitin stability in a betaine-glycerol-water DES, revealing suppressed dynamics and enhanced thermal stability.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Materials Science

Background:

  • Deep eutectic solvents (DESs) are emerging as promising alternatives for biomolecular applications, including cryopreservation.
  • Understanding protein behavior in DESs is crucial for optimizing their use in stabilizing biological molecules.
  • Traditional models of protein stabilization often rely on hydration layer dynamics, which may differ in DES environments.

Purpose of the Study:

  • To investigate the stability and dynamics of ubiquitin, a small protein, in a betaine-glycerol-water (B:G:W) DES across varying water concentrations.
  • To elucidate the underlying mechanisms of protein stabilization within DESs using molecular dynamics simulations.
  • To develop and validate an AMBER-based model for accurately simulating DES properties like density and viscosity.

Main Methods:

  • Molecular dynamics (MD) simulations were employed to study ubiquitin in water and B:G:W DES mixtures (1:2:ζ; ζ = 0, 1, 2, 5, 10).
  • An AMBER-based force field model was developed and validated against experimental density and shear viscosity data.
  • Analysis focused on protein structural fluctuations, hydration patterns, and backbone dynamics to understand stabilization effects.

Main Results:

  • Water molecules in the B:G:W DES were found to be largely trapped, limiting the formation of complete protein hydration layers.
  • Ubiquitin remained stable in the DES, exhibiting suppressed structural fluctuations that recovered with increased hydration.
  • A significant enhancement in the protein's thermal stability was observed in the DES, attributed to slowed backbone torsional dynamics.

Conclusions:

  • The study supports kinetic stabilization of proteins in DESs, driven by suppressed dynamics rather than preferential hydration.
  • A solvent-slaving mechanism involving beta-fluctuations and non-monotonic amino acid hydration explains protein behavior in aqueous DESs.
  • The findings challenge conventional stabilization mechanisms and highlight the unique role of DESs in biomolecular preservation.