Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations

A Computational Study of the Promiscuity of the SAM-Dependent Methyltransferase AtHTMT1

A two-pronged computational approach was taken to study the promiscuity of the SAM⁺-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl^-, Br^-, I^-, NCO^-, NCS^-). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico. The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H₂O molecules at the reactive site favors the reaction of NCS^- over Cl^- and Br^- in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H₂O molecules to the N terminus of NCS^- greatly increases its reactivity, while H₂O molecules attached to Cl^- slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.

The nucleophilic amino group of lysine is central for histone lysine methyltransferase catalysis

Histone lysine methyltransferases (KMTs) are biomedically important epigenetic enzymes that catalyze the transfer of methyl group from S-adenosylmethionine to lysine’s nucleophilic ε-amino group in histone tails and core histones. Understanding the chemical basis of KMT catalysis is important for discerning its complex biology in disease, structure-function relationship, and for designing specific inhibitors with therapeutic potential. Here we examine histone peptides, which possess simplest lysine analogs with different nucleophilic character, as substrates for human KMTs. Combined MALDI-TOF MS experiments, NMR analyses and molecular dynamics and free-energy simulations based on quantum mechanics/molecular mechanics (QM/MM) potential provide experimental and theoretical evidence that KMTs do have an ability to catalyze methylation of primary amine-containing N-nucleophiles, but do not methylate related amide/guanidine-containing N-nucleophiles as well as simple O- and C-nucleophiles. The results demonstrate a broader, but still limited, substrate scope for KMT catalysis, and contribute to rational design of selective epigenetic inhibitors.

Examining Product Specificity in Protein Arginine Methyltransferase 7 (PRMT7) Using Quantum and Molecular Mechanical Simulations

Protein arginine methyltransferase 7 (PRMT7) catalyzes the formation of monomethylarginine (MMA) but is incapable of performing a dimethylation. Given that PRMT7 performs vital functions in mammalian cells and has been implicated in a variety of diseases, including breast cancer and age-related obesity, elucidating the origin of its strict monomethylation activity is of considerable interest. Three active site residues, Glu172, Phe71, and Gln329, have been reported as particularly important for product specificity and enzymatic activity. To better understand their roles, mixed quantum and molecular mechanical (QM/MM) calculations coupled to molecular dynamics and free energy perturbation theory were carried out for the WT, F71I, and Q329S trypanosomal PRMT7 (TbPRMT7) enzymes bound with S-adenosyl- L-methionine (AdoMet) and an arginine substrate in an unmethylated or methylated form. The Q329S mutation, which experimentally abolished enzymatic activity, was appropriately computed to give an outsized Δ G^‡ of 30.1 kcal/mol for MMA formation compared to 16.9 kcal/mol for WT. The F71I mutation, which has been experimentally shown to convert the enzyme from a type III PRMT into a mixed type I/II capable of forming dimethylated arginine products, yielded a reasonable Δ G^‡ of 21.9 kcal/mol for the second turnover compared to 28.8 kcal/mol in the WT enzyme. Similar active site orientations for both WT and F71I TbPRMT7 allowed Glu172 and Gln329 to better orient the substrate for S_N2 methylation, enhanced the nucleophilicity of the attacking guanidino group by reducing positive charge, and facilitated the binding of the subsequent methylated products.

A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily

The SPOUT family of enzymes makes up the second largest of seven structurally distinct groups of methyltransferases and is named after two evolutionarily related RNA methyltransferases, SpoU and TrmD. A deep trefoil knotted domain in the tertiary structures of member enzymes defines the SPOUT family. For many years, formation of a homodimeric quaternary structure was thought to be a strict requirement for all SPOUT enzymes, critical for substrate binding and formation of the active site. However, recent structural characterization of two SPOUT members, Trm10 and Sfm1, revealed that they function as monomers without the requirement of this critical dimerization. This unusual monomeric form implies that these enzymes must exhibit a nontraditional substrate binding mode and active site architecture and may represent a new division in the SPOUT family with distinct properties removed from the dimeric enzymes. Here we discuss the mechanistic features of SPOUT enzymes with an emphasis on the monomeric members and implications of this "novel" monomeric structure on cofactor and substrate binding.

QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate?

Protein lysine methyltransferases (PKMTs) catalyze the methylation of lysine residues on histone proteins in the regulation of chromatin structure and gene expression. In contrast to many other PKMTs for which unmodified lysine is the methylation target, the enzymes in the Suv4-20 family are able to generate dimethylated product (H4K20me2) based exclusively on the monomethylated H4K20 substrate (H4K20me1). The origin of such substrate/product specificity is still not clear. Here, molecular dynamics (MD) and free energy (potential of mean force) simulations are undertaken using quantum mechanical/molecular mechanical (QM/MM) potentials to understand the substrate/product specificities of Suv4-20h2, a member of the Suv4-20 family. The free energy barriers for mono-, di-, and trimethylation in Suv4-20h2 obtained from the simulations are found to be well correlated with the specificities observed experimentally with the allowed dimethylation based on the H4K20me1 substrate and prohibited monomethylation and trimethylation based on H4K20 and H4K20me2, respectively. It is demonstrated that the reason for the relatively efficient dimethylation is an effective transition state (TS) stabilization through strengthening the CH···O interactions as well as the presence of a cation-π interaction at the transition state. The simulations also show that the failures of Suv4-20h2 to catalyze monomethylation and trimethylation are due, respectively, to a less effective TS stabilization and inability of the reactant complex containing H4K20me2 to adopt a reactive (near attack) configuration for methyl transfer. The results suggest that care must be exercised in the prediction of the substrate specificity based only on the existence of near attack configurations in substrate complexes.

Computational Study of the Degradation of S-Adenosyl Methionine in Water

The degradation of S-adenosyl methionine (SAM) to homoserine-γ-lactone (HSL) and methyltioadenine (MTA) in water is studied with MD simulations. The AM1 Hamiltonian is used for the quantum part and the flexible AMBER force field for the H₂O molecules. The MD simulations predict the free energy barrier for the degradation reaction to be between 109 and 112 kJ mol^-1 and an overall gain in free energy of -26 kJ mol^-1. The high barrier and the low energy gain of this reaction can be linked to interactions among the carboxylate group of the SAM molecule and solvent H₂O molecules, which are not observed on the product side. Hence, the H₂O molecules effectively slow down the reaction that otherwise would be much faster.

Facile synthesis of SAM-peptide conjugates through alkyl linkers targeting protein N-terminal methyltransferase 1

We report the first chemical synthesis of SAM-peptide conjugates through alkyl linkers to prepare bisubstrate analogs for protein methyltransferases. We demonstrate its application by developing a series of bisubstrate inhibitors for protein N-terminal methyltransferase 1 and the most potent one exhibits a K_i value of 310 ± 55 nM.

Biochemistry and regulation of the protein arginine methyltransferases (PRMTs)

Many key cellular processes can be regulated by the seemingly simple addition of one, or two, methyl groups to arginine residues by the nine known mammalian protein arginine methyltransferases (PRMTs). The impact that arginine methylation has on cellular well-being is highlighted by the ever growing evidence linking PRMT dysregulation to disease states, which has marked the PRMTs as prominent pharmacological targets. This review is meant to orient the reader with respect to the structural features of the PRMTs that account for catalytic activity, as well as provide a framework for understanding how these enzymes are regulated. An overview of what we understand about substrate recognition and binding is provided. Control of product specificity and enzyme processivity are introduced as necessary but flexible features of the PRMTs. Precise control of PRMT activity is a critical component to eukaryotic cell health, especially given that an arginine demethylase has not been identified. We therefore conclude the review with a comprehensive discussion of how protein arginine methylation is regulated.