Structural Insight into Wild Type of Arginine Deiminase Protein and its Three Mutated Versions in Complex with Arginine Molecule: A Computational Approach

Abstract

Aims: This study aims to analyze the wild type of arginine deiminase and three mutant forms of it (G320L, A303R, and E304L) in complex with arginine molecule using Molecular Dynamics (MD) simulation to find the best enzyme form with a lower level of energy and more stability. Background: Arginine Deiminase (ADI) is an arginine-degrading enzyme that has an anticancer effect on some cancers, such as Hepatocellular Carcinoma (HCC) and melanoma. Methods: Homology models of native and mutant forms of ADI were generated and evaluated using the I-TASSER and other databases and prediction algorithms. All prepared enzyme structures via homology modeling were used as receptors in the molecular docking and MD simulation steps. Results: MD simulation results demonstrated that the G302L structure has the lowest value of Rg over MD simulation time, indicating its more appropriate intramolecular interactions than other structures. G302L has also established the most desirable interactions with arginine molecules during 80 ns MD simulation so that the G302L/ arginine complex has the maximum intermolecular hydrogen bonds. Arginine molecule in complex with G302L has the best position in the active site of ADI protein. Conclusion: The G302L mutant ADI from Mycoplasma hominis can be a good candidate for better stability in arginine deprivation therapy in arginine auxotrophic cancers.