Understanding the Origins of Product Specificity of Protein Methyltransferases from QM/MM MD and Free Energy Simulations

Protein lysine methyltransferases (PKMTs) catalyze the methylation of certain lysine residues on histone tails using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Regulation of chromatin structure and gene expression through histone lysine methylation depends on the degree of methylation. Therefore, it is of importance to understand the features of PKMTs that control how many methyl groups would be added to the target lysine (product specificity). In my dissertation, I have applied quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations to understand the origin of the product specificities of SET8, GLP and their mutants. The relative free energy barriers of the methyl transfers calculated from our simulations are consistent with experimental data on product specificity, suggesting that they may govern the product specificity of PKMTs energetically. Our simulation results on the effects of the Tyr/Phe switch mutations in SET8 and GLP and the Y1124F mutation of GLP suggest that the space around the target lysine may be of importance. Protein arginine methyltransferases (PRMTs) catalyze the methylation of peptidyl arginines using AdoMet as the methyl donor. The product specificity of PRMTs often refers to their ability to form either asymmetric dimethylarginine (ADMA) (type I PRMTs) or symmetric dimethylarginine (SDMA) (type II PRMTs), and different product formation could lead to different biological consequences. The QM/MM MD and free energy simulations have been performed on one member of type I PRMTs, PRMT3. The simulation results suggest that the interactions of the active site residues make the same nitrogen atom of the guanidine to be the target of both 1^st and 2^nd methylations, leading to the formation of the asymmetric product. It is also proposed that Glu326 may function as a general base during the methyl transfer. The results of the MD simulations on the reactant complexes demonstrate that the ability of the reactant complexes to form the reactive configurations for the methyl transfer could be an important factor for the product specificity.