This manuscript determines the factors by which the water-miscible ionic liquid (IL), 1-alkyl-3-methylimidazolium chloride [Rmim]Cl affects the thermodynamic stability and CO association dynamics of horse ferrocytochrome c (Cyt cII) at pH 7. Investigation of rate constant and activation thermodynamic parameters for CO-association reaction of Cyt cII measured at different concentrations of [Rmim]Cl (1-Ethyl-3-methylimidazolium chloride [Emim]Cl, 1-butyl-3-methylimidazolium chloride [Bmim]Cl, 1-hexyl-3-methylimidazolium chloride [Hmim]Cl) revealed that the hydrophobicity of alkyl group of [Rmim]Cl modulates the CO-association dynamics of Cyt cII. The CO-association association kinetic results were further supported by intermolecular docking studies between the Cyt cII and [Rmim]+ ([Hmim]Cl, [Bmim]Cl, [Emim]Cl). Analysis of thermodynamic parameters calculated from thermal denaturation transitions of Cyt cII at different concentrations of [Rmim]Cl ([Hmim]Cl, [Bmim]Cl, [Emim]Cl) revealed that the [Rmim]Cl decreases the denaturation free energy in the order: [Hmim]Cl > [Bmim]Cl > [Emim]Cl, which suggests that the hydrophobicity of alkyl group of [Rmim]Cl modulates the [Rmim]Cl-induced decrease in thermodynamic stability of Cyt cII. Analysis of entropy − enthalpy plots showed that in addition to the hydrophobic effect, the enthalpic effect of [Rmim]Cl also decreases the thermodynamic stability of the protein. The dependence of unfolding free energy on [Rmim]Clconcentration was also translated into preferential interaction coefficients, Γ23. Experimental and theoretical estimations of Γ23 for Cyt cII provided the positive values of Γ23 at all across the [Rmim]Cl concentrations, indicating a robust and favorable interaction between the [Rmim]Cl and Cyt cII. Furthermore, the [Rmim]Cl-mediated increase in Γ23 typically follows the order: [Hmim]Cl > [Bmim]Cl > [Emim]Cl. Molecular dynamics (MD) simulation studies of Cyt cII performed at different concentrations of [Rmim]Cl ([Emim]Cl, [Bmim]Cl, and [Hmim]Cl) further showed that the hydrophobicity of the alkyl group modulates the structural stability and conformational-fluctuations of the Cyt cII.
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