γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

Temimi, Abbas H. K. Al; Bruijne, Renate van der Wekken-de; Proietti, Giordano; Guo, Hong; Qian, Ping; Mecinović, Jasmin

doi:10.1021/acs.bioconjchem.9b00313

Cited by 16 publications

(18 citation statements)

References 38 publications

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“…Despite being monomethyltransferases, SETD7 and SETD8 appear to have somewhat different abilities to accept substrates other than lysine. In line with our work on γ-thialysine 18 , SETD8 seems to have a slightly broader substrate scope than SETD7, possibly due to subtle differences of the active sites (e.g. positioning of Y273 in SETD8 and Y305 in SETD7).…”

Section: Resultssupporting

confidence: 87%

Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis

Temimi

Tran

Teeuwen

et al. 2020

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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 KMtcatalyzed 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 KMTcatalyzed methylation reactions. Posttranslational modifications on histone proteins regulate the structure and function of human chromatin 1-3. Well-established examples include lysine acetylation, which is linked with the transcriptionally active region of human genome, and lysine methylation, which is associated with gene activation and suppression, depending on the histone sequence and methylation state 4,5. Histone lysine methylation is catalyzed by S-adenosylmethionine (SAM)-dependent histone lysine methyltransferases (KMTs), and can lead to a formation of monomethyllysine (Kme), dimethyllysine (Kme2) and trimethyllysine (Kme3) 6,7. It is generally believed that the methylation state depends on the constitution of the KMT active site (Fig. 1a) 8. With the exception of DOT1L, all members of KMT family possess the SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) domain 9-11. Structural analyses of KMTs complexed with histone peptide/methylated peptide and S-adenosylhomocysteine product (SAH) revealed that the lysine side chain occupies a narrow, hydrophobic channel, typically comprised of side chains of several tyrosine and phenylalanine residues (Fig. 1b) 8. The positioning of the lysine's N ε amino group towards the electrophilic methyl group of the SAM cosubstrate results in an efficient methyl transfer via S N 2 reaction 12,13. Recent examinations of lysine analogs as substrates for human histone lysine methyltransferases revealed that KMTs possess a high degree of specificity for lysine residues. Enzymatic assays employing MALDI-TOF MS verified that human KMTs preferentially catalyze methylation of lysine residues with L-stereochemistry over D-stereochemistry 14. 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. Members of KMTs were also found to catalyze methylation of the cysteine-derived γ-thialysine on intact histones and histone peptides 17,18. Substrate capturing studies using the genetically encoding photo-lysine showed th...

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Section: Resultssupporting

confidence: 87%

Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis

Temimi

Tran

Teeuwen

et al. 2020

Sci Rep

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“…The promiscuity of AcCoA led to the development of several chemical probes for KATs as well as a click-based labelling procedure for the detection of KATs substrates, employing synthetic CoA surrogates and engineered KATs [37][38][39] . Although in the recent years the investigation of epigenetic enzymes' susceptibility towards lysine chemical modification gathered great attentions, especially with regards to histone lysine methyltransferases (KMTs), histone lysine demethylases (KDMs) and KDACs, we are currently lacking basic molecular knowledge in the context of histone lysine acetylation [40][41][42][43][44][45][46][47] . Enzyme kinetics showed p300 catalytic efficiency towards a collection of Lys analogs; a synthetic H4K8 peptide was found to be the preferred substrate, followed by D-Lys and γ-thiahomolysine that showed very poor catalytic efficiency 48 .…”

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confidence: 99%

Effect of lysine side chain length on histone lysine acetyltransferase catalysis

Proietti

Wang

Rainone

et al. 2020

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Histone lysine acetyltransferase (KAT)-catalyzed acetylation of lysine residues in histone tails plays a key role in regulating gene expression in eukaryotes. Here, we examined the role of lysine side chain length in the catalytic activity of human KATs by incorporating shorter and longer lysine analogs into synthetic histone H3 and H4 peptides. The enzymatic activity of MOF, PCAF and GCN5 acetyltransferases towards histone peptides bearing lysine analogs was evaluated using MALDI-TOF MS assays. Our results demonstrate that human KAT enzymes have an ability to catalyze an efficient acetylation of longer lysine analogs, whereas shorter lysine analogs are not substrates for KATs. Kinetics analyses showed that lysine is a superior KAT substrate to its analogs with altered chain length, implying that lysine has an optimal chain length for KAT-catalyzed acetylation reaction.

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“…Cysteine can be selectively alkylated to obtain analogues that mimic naturally occurring amino acids. Among these are arginine [18], lysine [19,20] and different posttranslationally modified variants of lysine, including acetylated [21] and methylated analogues [22]. For the purpose of generating methylated lysine, simple bromides can be used for chemoselective reaction with the cysteine thiol to obtain intact histone proteins that possess simplest methylated lysine analogues (MLAs) [23].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins

et al. 2020

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Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermodynamic analyses, molecular dynamics simulations and quantum chemical analyses. Collectively, our experimental and computational findings reveal that trimethylthialysine and trimethyllysine exhibit very similar binding characteristics for the association with human reader proteins, thereby justifying the use of trimethylthialysine for studies aimed at dissecting the origin of biomolecular recognition in epigenetic processes that play important roles in human health and disease.The highest mark, trimethyllysine, is recognized by the aromatic cage-containing readers, including tandem tudor domains (TTD), chromodomains (CD) and the plant homeodomain (PHD) zinc finger proteins ( Figure 1B) [6]. To gain a better understanding of the exact role of lysine methylation in epigenetics, it is important to develop novel chemical tools for studying the molecular mechanisms that govern the molecular recognition of methylated lysines by reader proteins. An installation of chemically modified methylated lysine analogues into histone proteins [7] and histone peptides [8][9][10][11] has been a valuable method to study how changes in structure affect the association with reader proteins. In addition, a variety of methods have been developed to incorporate unnatural amino acids in both histone proteins and peptides, notably by auxotrophic expression systems [12] or employing the amber stop codon (TAG) [13]. Major drawbacks of both methods include severe limitations of amino acid variants that can be incorporated into histones. Furthermore, when using auxotrophic strains, the protein expression yield is decreased dramatically, and the process of developing an amber codon pair is time consuming and laborious [14,15].

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γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

Cited by 16 publications

References 38 publications

Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis

Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis

Effect of lysine side chain length on histone lysine acetyltransferase catalysis

Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins

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