A molecular simulation and spectroscopic approach to the binding affinity between trypsin and 2-propanol and protein conformation

Abstract

Increasing the stability and activity of enzymes is one of the most popular ideas in biochemistry studies. The current study focused on the interactions between 2-propanol as an osmolyte and trypsin to increase the enzyme thermal stability by the modification of the solvent environment. To determine the binding mechanism of 2-propanol with trypsin, fluorescence emission quenching was observed as a static mode of quenching upon the binding of 2-propanol to trypsin. With the formation of hydrogen bonds and lower hydrophobicity levels after the addition of 2-propanol, Tm of complexes were increased. Also, the α-helix content of trypsin was increased as obtained by far-UV CD. CD results analysis showed that there was no significant perturbation in the structure of trypsin upon an increase in the concentration of 2-propanol. Molecular docking results also indicated that 2-propanol could bind to trypsin and hydrophobic interactions and hydrogen bond contributions played the major role in this binding. Consequently, the results of the molecular dynamics simulation showed that the stability of trypsin-2 propanol was obtained to be about 2.5 nm in the equilibrium state, indicating the stability and rigidity of the trypsin-2 propanol complex. Upon 2-propanol conjugation, the residual activity of the enzyme was increased. 2-propanol, therefore, acted as a stabilizer and activator for trypsin.

Keywords: Circular dichroism; Fluorescence quenching; Molecular docking; Molecular simulation; Thermal stability; Trypsin.