Methanol and sorbitol affect the molecular dynamics of arginine deiminase: insights for improving its stability

Arginine deiminase enzyme of Mycoplasma arginini (MaADI) is a potential anti-cancer agent for treating arginine-auxotrophic cancers. Investigating the protein stability in the presence of osmolytes can help to increase protein stability under various stressed conditions. In this study, the stability and dynamics of MaADI were investigated in pure water and solutions of 1 M sorbitol, 10% (v/v) methanol, and 50% (v/v) methanol using molecular dynamics simulation. Sorbitol was found to stabilize the protein, whereas high-concentrated methanol destabilized it. Sorbitol molecules interacted with the protein through hydrogen bonding and reduced the protein fluctuations as well. At 50% methanol, the flexibility of regions 4-8, 195-201, 314-324, and 332-337 in the MaADI was increased; whereas residues 195-201 showed the highest variations. Thus, these regions of MaADI, especially 195-201, are the most sensitive regions in the presence of denaturing agents and can be subjected to protein engineering toward improving the stability of MaADI.