Abstract
Methylation of lysine residues in histone proteins is catalyzed by S-adenosylmethionine (SAM)-dependent histone lysine methyltransferases (KMTs), a genuinely important class of epigenetic enzymes of biomedical interest. Here we report synthetic, mass spectrometric, NMR spectroscopic and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics studies on KMT-catalyzed methylation of histone peptides that contain lysine and its sterically demanding analogs. Our synergistic experimental and computational work demonstrates that human KMTs have a capacity to catalyze methylation of slightly bulkier lysine analogs, but lack the activity for analogs that possess larger aromatic side chains. Overall, this study provides an important chemical insight into molecular requirements that contribute to efficient KMT catalysis and expands the substrate scope of KMT-catalyzed methylation reactions.
Highlights
Methylation of lysine residues in histone proteins is catalyzed by S-adenosylmethionine (SAM)dependent histone lysine methyltransferases (KMTs), a genuinely important class of epigenetic enzymes of biomedical interest
Diazomethane was generated in situ and distilled directly into a solution of 4 containing catalytic amounts of palladium(II) acetate, to yield the α,β-cyclopropyl t-butyl ester, which was selectively hydrolyzed with trifluoroacetic acid (TFA) to yield compound 5
All histone peptides were purified by preparative HPLC, and the purity of synthetic histone peptides bearing lysine analogs was confirmed by analytical HPLC and ESI-MS analyses (Supplementary Tables 1–2 and Supplementary Figs. 3–13)
Summary
Methylation of lysine residues in histone proteins is catalyzed by S-adenosylmethionine (SAM)dependent histone lysine methyltransferases (KMTs), a genuinely important class of epigenetic enzymes of biomedical interest. Combined experimental and computational studies on histone peptides that bear lysine analogs of different chain length revealed that lysine exhibits an optimal chain length for KMT-catalyzed methylation[15], and that the enzymatic methylation is limited to N-nucleophiles[16]. We report enzymatic evaluations of sterically demanding lysine analogs as substrates for human KMTs employing MALDI-TOF MS assays, NMR spectroscopic analyses, and quantum mechanical/ molecular mechanical (QM/MM) molecular dynamics and free energy studies. The zig-zag orientation of the flexible C-C bonds might enable a proper orientation of the lysine’s side chain in a narrow hydrophobic pocket of KMTs, leading to efficient KMT catalysis It remains to be established whether this narrow lysine-binding pocket can accommodate larger moieties that resemble lysine. We selected six sterically demanding lysine analogs: (i) cyclopropyllysine (KCP), which bears an additional methylene group adjacent to the Nε amino group; (ii) benzylamine (Kba), an analog with a larger but highly nucleophilic side chain; (iii) meta-aminophenylalanine (F3a), a significantly larger aromatic lysine analog that possesses the terminal Nε amino group with a weaker nucleophilic character; (iv) para-aminophenylalanine (F4a), another aniline derivative with less nucleophilic Nε amino group; (v) pyridylalanine (AP), which possesses a nucleophilic pyridine functionality; and (vi) tyrosine (Y), an electron-rich aromatic system with a potential to undergo O- or C-methylation (Fig. 1c)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
