Understanding the mechanism of how ionic liquids stabilize and activate enzymes is crucial for researchers and engineers to optimize enzymatic reactions as well as synthesize the enzyme compatible ionic liquids. Many efforts with different tech­niques such as spectroscopy, molecular dynamics simulation have been paid to explore the dynamic structure and conformation of protein in ionic liquid in recent years [109—121]. In general, the ionic liquids that have strong interaction with protein such as halide containing ionic liquids tend to change the conformation of proteins and therefore inactivate enzymes while other ionic liquids such as [Tf2N]_ based ionic liquids strengthen the protein conformation resulting in enhanced enzyme stability. For example, Sasmal et al. by using fluorescence correlation spectroscopy studied the conformation dynamics of human serum albumin (HSA) protein in [Pmim][Br] and observed the denaturant effect of ionic liquids [121]. De Diego et al. used fluorescence and circular dichroism (CD) spectroscopy to analysis the a-chymotrypsin stabilization of [Emim][Tf2N] and found out that this ionic liquids shows ability to compact the native conformation of protein by great enhancement of the p-strand of protein. In our recent studies, molecular dynamics (MD) simulation was employed to investigate the structure of CALB enzyme in different ionic liquids and organic solvents and their corresponding enzyme activ­ities. The MD simulations indicate that the structure and dynamics of the cavity that holds the catalytic triad are solvent dependent: the cavity can be opened or closed in water; the cavity is open in [Bmim][TfO] and tert-butanol; the cavity is closed in [Bmim][Cl]. The closed or narrow cavity conformation observed in our simulations obstructs passage for substrates, thus lowering their probability of reaching the catalytic triad (Fig. 10.2). In addition, we observed that two isoleucines, ILE-189 and ILE-285, play a pivotal role in the open-close dynamics of cavity. Specifically, ILE-285 situated on a helix (a-10) that can significantly change conformation in different solvents. This change is acutely evident in [Bmim][Cl] where interactions of LYS-290 with chlorine anions induces a conformational switch from an a-helix into a turn (Fig. 10.3). Disruption of the a-10 helix structure results in a narrower entrance to the catalytic triad site and this change is responsible for reduced activity of CALB in [Bmim][Cl]. Moreover, the cavity profile’s size is well agreed with the enzyme activity for the synthesis of butyl acetate. The activity of the enzyme decreases with the size of the cavity in the following order: [Bmim][TfO] > tert — butanol > [Bmim][Cl].