Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity

Biophys J. 2004 Aug;87(2):812-21. doi: 10.1529/biophysj.104.041269.


Water plays an important role in enzyme structure and function in aqueous media. That role becomes even more important when one focuses on enzymes in low water media. Here we present results from molecular dynamics simulations of surfactant-solubilized subtilisin BPN' in three organic solvents (octane, tetrahydrofuran, and acetonitrile) and in pure water. Trajectories from simulations are analyzed with a focus on enzyme structure, flexibility, and the details of enzyme hydration. The overall enzyme and backbone structures, as well as individual residue flexibility, do not show significant differences between water and the three organic solvents over a timescale of several nanoseconds currently accessible to large-scale molecular dynamics simulations. The key factor that distinguishes molecular-level details in different media is the partitioning of hydration water between the enzyme and the bulk solvent. The enzyme surface and the active site region are well hydrated in aqueous medium, whereas with increasing polarity of the organic solvent (octane --> tetrahydrofuran --> acetonitrile) the hydration water is stripped from the enzyme surface. Water stripping is accompanied by the penetration of tetrahydrofuran and acetonitrile molecules into crevices on the enzyme surface and especially into the active site. More polar organic solvents (tetrahydrofuran and acetonitrile) replace mobile and weakly bound water molecules in the active site and leave primarily the tightly bound water in that region. In contrast, the lack of water stripping in octane allows efficient hydration of the active site uniformly by mobile and weakly bound water and some structural water similar to that in aqueous solution. These differences in the active site hydration are consistent with the inverse dependence of enzymatic activity on organic solvent polarity and indicate that the behavior of hydration water on the enzyme surface and in the active site is an important determinant of biological function especially in low water media.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetonitriles / chemistry*
  • Binding Sites
  • Computer Simulation
  • Enzyme Activation
  • Furans / chemistry*
  • Models, Chemical*
  • Models, Molecular*
  • Motion
  • Octanes / chemistry*
  • Protein Binding
  • Protein Conformation
  • Solvents / chemistry
  • Subtilisins / chemistry*
  • Surface Properties
  • Water / chemistry*


  • Acetonitriles
  • Furans
  • Octanes
  • Solvents
  • Water
  • tetrahydrofuran
  • Subtilisins
  • octane
  • acetonitrile