Understanding the Origins of Changing the Product Specificity Properties of Arginine Methyltransferase PRMT7 by E181→D and E181→D/Q329→A Mutations: A QM/MM Study

Arginine methylations can regulate important biological processes and affect many cellular activities, and the enzymes that catalyze the methylations are protein arginine methyltransferases (PRMTs). The biological consequences of arginine methylations depend on the methylation states of arginine that are determined by the PRMT’s product specificity. Although the product specificity is a very important property, it is still unknown concerning why different PRMTs may generate different methylation states for the target arginine residues on protein substrates. PRMT7 is the only known member of Type III PRMT that produces mono-methylarginine (MMA) product. Interestingly, its E181D and E181D/Q329A mutants can catalyze, respectively, the formation of asymmetrically di-methylated arginine (ω-NG, NG-dimethylarginine or ADMA) and symmetrically di-methylated arginine (ω-NG, N'G-dimethylarginine or SDMA). The exact reasons for such product specificity modification as a result of the mutations have been unclear. Here QM/MM molecular dynamics (MD) and potential of mean force (PMF) free-energy simulations are performed for the E181D and E181D/Q329A mutants to understand the catalytic mechanism and the origin of their different product specificities from that of the wild-type PRMT7 as well as between E181D and E181D/Q329A. The simulations show that while the free energy barriers of E181D and E181D/Q329A for the first methylation are higher than that of the wild type, E181D and E181D/Q329A have the ability to add the second methyl group to the target mono-methyl arginine and generate ADMA and SDMA, respectively. The free energy barriers for E181D and E181D/Q329A to produce ADMA and SDMA, respectively, are considerably lower than the corresponding barriers involving the wild-type enzyme. Moreover, the computational study identifies some important structural, electronic and dynamic features that lead to the different product specificities and activities of the wild-type PRMT7, E181D and E181D/Q329A. These factors may play important roles in controlling the activity and product specificity of other PRMTs as well.