Catalytic Mechanism and Product Specificity of Protein Arginine Methyltransferase PRMT7: A Study from QM/MM Molecular Dynamics and Free Energy Simulations.

QM/MM molecular dynamics and potential of mean force (PMF) free-energy simulations are performed for wild-type PRMT7 and E172Q, E181Q, and Q329A mutants in this work, and the catalytic mechanism, product specificity, and the role of key residues for the PRMT7 activity are investigated. The main strategies of PRMT7 in reducing the activation barrier for methyl transfer that are found in this study include (1) formation of reactive (near attack) conformations for the substrate Arg, (2) strengthening the active-site interactions at the transition state, and (3) generation of more effective nucleophiles by changing charge distributions on the target Arg through active-site interactions. More importantly, it is shown that it is a combination of these different factors that determines the PRMT7 methylation activity and substrate/product specificity. By taking these factors into consideration, it is possible to provide explanations for the observed effects of some mutations. For E172Q, E181Q, and Q329A, the simulation results suggest that E172Q has the least activity among the three mutants. The free energy barrier increases by 7 and 3 kcal/mol, respectively, as a result of the E181 → Q and Q329 → A mutations. The results showed that PRMT7 has a preference of adding a methyl group to the ω-guanidino nitrogen Nη2 atom of the substrate Arg and that the second methylation reactions cannot occur, which are consistent with previous investigations.