Flexibility of serine protease in nonaqueous solvent

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Publisher Summary The protease family of enzymes has long generated considerable interest because of their role in peptide degradation and possibly peptide synthesis. Although many distinct families of serine proteases seem to exist, the two best studied ones are chymotrypsin and subtilisin. In organic solvents, serine proteases are promising catalysts for organic synthesis and the preparation of unusual polymers. Several studies have been reported on serine proteases in aqueous media but only little is known about the dynamics of serine proteases in on-aqueous solvents. This chapter reports the results from a molecular dynamics simulation of the serine protease γ-chymotrypsin (γ-CT) in hexane. The active site of chymotrypsin contains the “catalytic triad” that consists of Ser-His-Asp. γ-CT suspended in nearly anhydrous solvents has been found to be catalytically active. For proteins to retain their activity in anhydrous solvents, some water molecules are required to be present. These “essential waters” have been suggested to function as a molecular lubricant for the protein. Hexane, having a dielectric constant of 1.89, is a suitable nonaqueous solvent for enzymatic reactions. The low dielectric constant of hexane allows it to not compete with the protein for the essential water and allows enzymes to retain their catalytic activity. γ-CT in hexane is thus an ideal system to further explore the effect of non-aqueous solution on protein structure, function, and dynamics. Studies have shown that both hydration and the placement of “essential” water molecules affect the root-mean-square (RMS) deviation, but not RMS fluctuation, of the protein when placed in a non-aqueous environment. As hydration increases, the structural similarities of the protein to the crystal structure increases.