Modeling stability and flexibility of α-Chymotrypsin in room temperature ionic liquids

Abstract

We investigate the structure and dynamics of α-Chymotrypsin in five room temperature ionic liquids (RTILs) sharing a common cation, hydrated with different water percentages (w/w) (weight of water over protein). Results from molecular dynamics simulations are correlated with experimental evidences from studies on the activity of enzymes in RTILs. α-Chymotrypsin protein structure is closer to its native crystallographic structure in RTILs than in aqueous environment. We show that the structural properties of α-Chymotrypsin were affected by the water concentration assayed in a typical bell-shaped profile, which is also frequently reported for organic solvents. The protein structure was more native like at 10–20% of water (w/w) for all RTILs except for [BMIM][Cl]. We found that the fluctuations of the main chain in [BMIM][BF₄] and [BMIM][TfO] were not significantly affected by the increasing amount of water. However, we were able to show that the flexible regions were the ones more hydrated, indicating that water is responsible for the flexibility of the protein. The solvation of the enzyme in water-immiscible RTILs, such as [BMIM][PF₆] and [BMIM][Tf₂N] lead to higher enzyme flexibility at increased water content. Enzyme solvation by [BMIM][Cl] resulted in ion penetration in the core enzyme structure, causing incremented flexibility and destabilization at low water percentages. All RTILs stripped water molecules from the protein surface, following a similar behavior also found in organic solvents. Anions formed structured arrangements around the protein, which allowed non-stripped water molecules to localize on the protein surface.

Keywords:

• ionic liquids
• molecular dynamics
• protein hydration
• protein structure

Acknowledgments

This work was in part financially supported by FCT (SFRH/BD/79195/2011), (PEst-C/QUI/UI0686/2011) and (FCOMP-01-0124-FEDER-022716). The authors thank the access to the Minho University GRIUM cluster and for contract research grant C2008-UMINHO-CQ-03. Muhammad A.M. Latif acknowledges the National Science Fellowship, MOSTI. Mohd B. Abdul Rahman acknowledges Genetic and Molecular Biology Iniative, MGI.