Effect of osmolytes on the EcoRI endonuclease: Insights into hydration and protein dynamics from molecular dynamics simulations

Osmolytes play an important role in cellular physiology by modulating the properties of proteins, including their molecular specificity. EcoRI is a model restriction enzyme whose specificity to DNA is altered in the presence of osmolytes. Here, we investigate the effect of two different osmolytes, glycerol and DMSO, on the dynamics and hydration of the EcoRI enzyme using molecular dynamics simulations. Our results show that the osmolytes, alter the essential dynamics of EcoRI. Particularly, we observe that the dynamics of the arm region of EcoRI which is involved in DNA binding is significantly altered. In addition, conformational free energy analyses reveals that the osmolytes bring about a change in the landscape similar to that of EcoRI bound to cognate DNA. We further observe that the hydration of the enzyme for each of the osmolyte is different, indicating that the mechanism of action of each of these osmolytes could be different. Further analyses of interfacial water dynamics using rotational autocorrelation function reveals that while the protein surface contributes to a slower tumbling motion of water, osmolytes, additionally contribute to the slowing of the angular motion of the water molecules. Entropy analysis also corroborates with this finding. We also find that the slowed rotational motion of interfacial waters in the presence of osmolytes contributes to a slowed relaxation of the hydrogen bonds between the interfacial waters and the functionally important residues in the protein. Taken together, our results show that osmolytes alter the dynamics of the protein by altering the dynamics of water. This altered dynamics, mediated by the changes in the water dynamics and hydrogen bonds with functionally important residues, may contribute to the altered specificity of EcoRI in the presence of osmolytes.

Different Hydrogen Bond Changes Driven by Surface Segregation Behavior of Imidazolium-Based Ionic Liquid Mixture at the Liquid-Vacuum Interface

In this work, molecular dynamics (MD) simulations were carried out to study the behaviors of a binary ionic liquid (IL) mixture consisting of equimolar [C₂C₁Im][BF₄] and [C₄C₁Im][BF₄], as well as two corresponding pure ILs, at the liquid-vacuum interface. Our simulation results show that the competition of nonpolar interactions between different alkyl chains of two cations results in an obvious surface segregation behavior of the IL mixture at the interface, indicating an enhanced aggregation of the [C₄C₁Im]⁺ cations but a weakened aggregation of the [C₂C₁Im]⁺ cations at the outermost surface. More interestingly, different hydrogen bond (HB) changes between two imidazolium cations at the interface can be driven by such surface segregation behavior, where the [C₂C₁Im]⁺ cations rather than the [C₄C₁Im]⁺ ones have more and stronger HBs with the [BF₄]^- anions by comparison with the corresponding pure ILs at the interface. Meanwhile, it is interesting to find that such a stronger HB would lower the rotations of the imidazolium rings of interfacial [C₂C₁Im]⁺ cations. By contrast, the [C₄C₁Im]⁺ cations at the outermost surface rotate faster owing to their weaker HB. In addition, the orientation analysis uncovers that there is a major decrease for the orderliness of interfacial [C₂C₁Im]⁺ cations, but a minor decrease for that of interfacial [C₄C₁Im]⁺ cations, from the pure IL to the IL mixture. Such distinct results are closely related to the surface segregation between the [C₂C₁Im]⁺ and [C₄C₁Im]⁺ cations in the IL mixture and their interfacial HB properties. Thus, our simulation results afford a deep insight into the surface segregation effect on the HB behavior of the imidazolium-based IL mixture at liquid-vacuum interface.

Unique orientations and rotational dynamics of a 1-butyl-3-methyl-imidazolium hexafluorophosphate ionic liquid at the gas–liquid interface: the effects of the hydrogen bond and hydrophobic interactions

Two-stage rotational motions of the interfacial [BMIM]⁺ cations are essentially determined by both hydrophobic and hydrogen-bonding interactions.