eal System, was described with AmberParm99 force field. Considering that the DFT method usually underestimates the energy barriers of methyl transfer, we also used the MP2 method with 6-31G basis set to calculate single-point potential energy of the reactant and the transient. The ONIOM energy was obtained from the following equation: EONIOM = E MM,R +E QM,SM -E MM,SM Linked hydrogen atoms were employed to saturate heavy atoms of the Real System, which bonded to Model System. Electronic embedding was applied in ONIOM calculation, which incorporates the partial charges of the MM region into 3 Catalytic Mechanism of PRMT1 quantum mechanical Hamiltonian, so that the electrostatic interaction EW-7197 cost between QM and MM region as well as the polarization of QM wave function can be better described. Results and Discussion Structure of the Initial Model As depicted in the Materials and Methods, the PRMT1-RGGAdoMet complex model was initially constructed. Structurally, PRMT1 is composed of four parts, namely, N-terminal, AdoMet-binding domain, barrel, and dimerization arm, as shown in the MD simulation progress. The hydrogen bond between E144 carboxyl oxygen and Sub_R N2 orients the guanidino group in a direction that faces the AdoMet methyl group, as shown in Stability and Rationality of Complex Models Although the monomer enzyme was employed in the simulation, the active cavity was presumed steady during computational time scale. Therefore, a 30-ns MD simulation was performed on PRMT1-RGG-AdoMet and PRMT1-meRGGAdoMet complex to verify the stability of the catalytic center. The root-mean-square deviations of the backbone atoms in the entire system and the distinct domains were calculated based on the initial position. The overall structure of PRMT1-RGG-AdoMet was moderately stable during the simulation, with an RMSD at approximately 4.5, as shown in Structure Parameters of Snapshots from MD trajectory The atoms involved in the QM region of PRMT1-RGGAdoMet and PRMT1-meRGG-AdoMet are shown in Microenvironment of Catalysis Center The hydrogen bond microenvironment is crucial in PRMT enzymatic activity. The orientations of the key residues in the 
active site were further analyzed in detail. The hydrogen bonds among AdoMet, Sub_R, and PRMT1 remained stable during 4 Catalytic Mechanism of PRMT1 8901831 title=’View abstract’ target=’resource_window’>14557281 that PRMT1 catalyzes substrate dimethylation in a partially processive manner. In PRMT1-meRGG-AdoMet, the methyl group on Sub_R-NH2 adopted a “downward” conformation to avoid hindrance with other parts of guanidino, blocking the space between guanidino and E144. This conformation of Sub_R increased the difficulty in forming hydrogen bonds between OE2 and NH2, and resulted in the position flexibility of NH2, demonstrated as a broad distribution of angle. This study indicates that E144 contributes to correcting the direction of methyl accepting nitrogen to guarantee SN2-favored in-line geometry. and Geometric Reactant R 1st Methyl Transfer 2nd Methyl Transfer 2.98 3.28 157.8 118.8 Transient R 2.18 2.18 172.1 177.8 E B3LYP Kcal/mol 11.76 11.63 MP2 Kcal/mol 19.08 14.94 Mechanism of PRMT1 Catalyzed Arginine Methylation Methyl Transfer Process. The QM region shown in might be faster than the first, which follows the result of enzyme kinetic test: the experimental rate constant Kcat for apo and monomethylated substrate are 0.39 min-1 and 0.79 min-1, respectively. The same conclusion was obtained by QM/MM-MD study of PRMT3. For Rubisco LSMT, an enzyme with lysine dimethylatio