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Trimethyllysine

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https://www.readbyqxmd.com/read/29111699/investigation-of-trimethyllysine-binding-by-the-hp1-chromodomain-via-unnatural-amino-acid-mutagenesis
#1
Stefanie A Baril, Amber L Koenig, Mackenzie W Krone, Katherine I Albanese, Cyndi Qixin He, Ga Young Lee, Kendall N Houk, Marcey L Waters, Eric M Brustad
Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding...
November 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29111671/quantitative-and-structural-assessment-of-histone-methyllysine-analogue-engagement-by-cognate-binding-proteins-reveals-affinity-decrements-relative-to-those-of-native-counterparts
#2
Zhonglei Chen, Ryan Q Notti, Beatrix Ueberheide, Alexander J Ruthenburg
Methyllysine analogues (MLAs), furnished by aminoethylation of engineered cysteine residues, are widely used surrogates of histone methyllysine and are considered to be effective proxies for studying these epigenetic marks in vitro. Here we report the first structure of a trimethyllysine MLA histone in complex with a protein binding partner, quantify the thermodynamic distinctions between MLAs and their native methyllysine counterparts, and demonstrate that these differences can compromise qualitative interpretations of binding at the nucleosome level...
November 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/29109980/the-abundance-of-metabolites-related-to-protein-methylation-correlates-with-the-metastatic-capacity-of-human-melanoma-xenografts
#3
Xiaolei Shi, Alpaslan Tasdogan, Fang Huang, Zeping Hu, Sean J Morrison, Ralph J DeBerardinis
Metabolic reprogramming is a major factor in transformation, and particular metabolic phenotypes correlate with oncogenotype, tumor progression, and metastasis. By profiling metabolites in 17 patient-derived xenograft melanoma models, we identified durable metabolomic signatures that correlate with biological features of the tumors. BRAF mutant tumors had metabolomic and metabolic flux features of enhanced glycolysis compared to BRAF wild-type tumors. Tumors that metastasized efficiently from their primary sites had elevated levels of metabolites related to protein methylation, including trimethyllysine (TML)...
November 2017: Science Advances
https://www.readbyqxmd.com/read/29037863/outer-membrane-protein-ompb-methylation-may-mediate-bacterial-virulence
#4
REVIEW
David C H Yang, Amila H Abeykoon, Bok-Eum Choi, Wei-Mei Ching, P Boon Chock
Methylation of outer membrane proteins (OMPs) has been implicated in bacterial virulence. Lysine methylation in rickettsial OmpB is correlated with rickettsial virulence, and N- and O-methylations are also observed in virulence-relevant OMPs from several pathogenic bacteria that cause typhus, leptospirosis, tuberculosis, and anaplasmosis. We summarize recent findings on the structure of methylated OmpB, biochemical characterization, and crystal structures of OmpB methyltransferases. Native rickettsial OmpB purified from highly virulent strains contains multiple clusters of trimethyllysine, in contrast with mostly monomethyllysine, and no trimethyllysine is found in an avirulent strain...
October 13, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28876351/optimization-of-a-synthetic-receptor-for-dimethyllysine-using-a-biphenyl-2-6-dicarboxylic-acid-scaffold-insights-into-selective-recognition-of-hydrophilic-guests-in-water
#5
Isaiah N Gober, Marcey L Waters
In the design of small molecule receptors for polar guests, much inspiration has been taken from proteins that have adapted effective ways to selectively bind polar molecules in aqueous environments. Nonetheless, molecular recognition of hydrophilic guests in water by synthetic receptors remains a challenging task. Here we report a new synthetic receptor, A2I, with improved affinity and selectivity for a biologically important polar guest, dimethyllysine (Kme2). A2I was prepared via redesign of a small molecule receptor (A2B) that preferentially binds trimethyllysine (Kme3) using dynamic combinatorial chemistry (DCC)...
September 26, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28873565/the-betaine-profile-of-cereal-flours-unveils-new-and-uncommon-betaines
#6
Luigi Servillo, Nunzia D'Onofrio, Alfonso Giovane, Rosario Casale, Domenico Cautela, Giovanna Ferrari, Domenico Castaldo, Maria Luisa Balestrieri
We report the LC-ESI-MS/MS determination of betaines in commercial flours of cereals and pseudocereals most utilized in human nutrition. Results showed that glycine betaine, trigonelline, proline betaine, N(ε)-trimethyllysine were metabolites common to all examined flours, whereas an uncommon betaine, valine betaine, and glutamine betaine were present only in flours of barley, rye, oat, durum wheat, winter wheat, Triticum dicoccum and Triticum monococcum. Valine betaine and glutamine betaine, the latter never reported before in plants and animals, are not evenly distributed in the Poaceae family, but their presence or absence in flours depends on the subfamily to which the plant belongs...
January 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28815274/a-new-metabolomics-based-strategy-for-identification-of-endogenous-markers-of-urine-adulteration-attempts-exemplified-for-potassium-nitrite
#7
Andrea E Steuer, Kim Arnold, Tom D Schneider, Michael Poetzsch, Thomas Kraemer
Urine adulteration to circumvent positive drug testing represents a problem for toxicological laboratories. While creatinine is a suitable marker for dilution, detection of chemicals is often performed by dipstick tests associated with high rates of false positives. Several methods would be necessary to check for all possible adulterants. Untargeted mass spectrometry (MS) methods used in metabolomics should theoretically allow detecting concentration changes of any endogenous urinary metabolite or presence of new biomarkers produced by chemical adulteration...
October 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28750641/metabolome-alterations-in-severe-critical-illness-and-vitamin-d-status
#8
Jessica Lasky-Su, Amber Dahlin, Augusto A Litonjua, Angela J Rogers, Michael J McGeachie, Rebecca M Baron, Lee Gazourian, Diana Barragan-Bradford, Laura E Fredenburgh, Augustine M K Choi, Kris M Mogensen, Sadeq A Quraishi, Karin Amrein, Kenneth B Christopher
BACKGROUND: Metabolic homeostasis is substantially disrupted in critical illness. Given the pleiotropic effects of vitamin D, we hypothesized that metabolic profiles differ between critically ill patients relative to their vitamin D status. METHODS: We performed a metabolomics study on biorepository samples collected from a single academic medical center on 65 adults with systemic inflammatory response syndrome or sepsis treated in a 20-bed medical ICU between 2008 and 2010...
July 28, 2017: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/28553538/site-selective-reading-of-epigenetic-markers-by-a-dual-mode-synthetic-receptor-array
#9
Yang Liu, Lizeth Perez, Magi Mettry, Adam D Gill, Samantha R Byers, Connor J Easley, Christopher J Bardeen, Wenwan Zhong, Richard J Hooley
Variably functionalized self-folding deep cavitands form an arrayed, fluorescent indicator displacement assay system for the detection of post-translationally modified (PTM) histone peptides. The hosts bind trimethyllysine (KMe3) groups, and use secondary upper rim interactions to provide more sensitive discrimination between targets with identical KMe3 binding handles. The sensor array uses multiple different recognition modes to distinguish between miniscule differences in target, such as identical lysine modifications at different sites of histone peptides...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28393236/metabolomic-analysis-of-the-saliva-of-japanese-patients-with-oral-squamous-cell-carcinoma
#10
Mitsuyoshi Ohshima, Keisuke Sugahara, Kiyohiro Kasahara, Akira Katakura
The aim of the present study was to characterize the metabolic systems in Japanese patients with oral squamous cell carcinoma (OSCC) using capillary electrophoresis-mass spectrometry (CE-MS) metabolome analysis of saliva samples. A previous study showed variations among ethnicities and tumor sites in the saliva metabolome of patients with OSCC using CE-MS. In the present study, saliva was obtained from 22 Japanese patients with OSCC and from 21 healthy controls who visited the Department of Dentistry, Oral and Maxillofacial Surgery, Tokyo Dental Collage Ichikawa General Hospital, Tokyo, Japan, and all samples were subject to comprehensive quantitative metabolome analysis using CE-MS...
May 2017: Oncology Reports
https://www.readbyqxmd.com/read/28116387/fluorinated-trimethyllysine-as-a-19-f-nmr-probe-for-trimethyllysine-hydroxylase-catalysis
#11
Y Vijayendar Reddy, Abbas H K Al Temimi, Jasmin Mecinović
Trimethyllysine hydroxylase (TMLH) catalyses C-3 hydroxylation of N(ε)-trimethyllysine in the first step of carnitine biosynthesis in humans. Studies on TMLH have been hampered by the lack of established chemical methods. We report that an N(ε)-trimethyllysine analogue that contains the fluoromethyl group can be used as a (1)H and (19)F NMR probe for studies on TMLH catalysis.
January 24, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28045275/evidence-that-trimethyllysine-hydroxylase-catalyzes-the-formation-of-2s-3s-3-hydroxy-n-%C3%AE%C2%B5-trimethyllysine
#12
Y Vijayendar Reddy, Abbas H K Al Temimi, Paul B White, Jasmin Mecinović
Trimethyllysine hydroxylase (TMLH) is an Fe(II) and 2-oxoglutarate (2OG) dependent oxygenase involved in the biomedically important carnitine biosynthesis pathway. A combination of synthetic and NMR studies provides direct evidence that human TMLH catalyzes the stereoselective conversion of (2S)-N(ε)-trimethyllysine to (2S,3S)-3-hydroxy-N(ε)-trimethyllysine.
January 3, 2017: Organic Letters
https://www.readbyqxmd.com/read/27992714/structure-guided-design-of-eed-binders-allosterically-inhibiting-the-epigenetic-polycomb-repressive-complex-2-prc2-methyltransferase
#13
Andreas Lingel, Martin Sendzik, Ying Huang, Michael D Shultz, John Cantwell, Michael P Dillon, Xingnian Fu, John Fuller, Tobias Gabriel, Justin Gu, Xiangqing Jiang, Ling Li, Fang Liang, Maureen McKenna, Wei Qi, Weijun Rao, Xijun Sheng, Wei Shu, James Sutton, Benjamin Taft, Long Wang, Jue Zeng, Hailong Zhang, Maya Zhang, Kehao Zhao, Mika Lindvall, Dirksen E Bussiere
PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in antitumor efficacy. Here, we describe the optimization of a chemical series representing a new class of PRC2 inhibitors which acts allosterically via the trimethyllysine pocket of the noncatalytic EED subunit...
January 12, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27965989/human-carnitine-biosynthesis-proceeds-via-2s-3s-3-hydroxy-n-%C3%AE%C2%B5-trimethyllysine
#14
Robert K Leśniak, Suzana Markolovic, Kaspars Tars, Christopher J Schofield
N(ε)-Trimethyllysine hydroxylase (TMLH) catalyses the first step in mammalian biosynthesis of carnitine, which plays a crucial role in fatty acid metabolism. The stereochemistry of the 3-hydroxy-N(ε)-trimethyllysine product of TMLH has not been defined. We report enzymatic and asymmetric synthetic studies, which define the product of TMLH catalysis as (2S,3S)-3-hydroxy-N(ε)-trimethyllysine.
December 22, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27931018/primary-carnitine-deficiency-and-newborn-screening-for-disorders-of-the-carnitine-cycle
#15
Nicola Longo
Carnitine is needed for transfer of long-chain fatty acids across the inner mitochondrial membrane for subsequent β-oxidation. Carnitine can be synthesized by the body and is also obtained in the diet through consumption of meat and dairy products. Defects in carnitine transport such as those caused by defective activity of the OCTN2 transporter encoded by the SLC22A5 gene result in primary carnitine deficiency, and newborn screening programmes can identify patients at risk for this condition before irreversible damage...
2016: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/27730239/substrate-scope-for-trimethyllysine-hydroxylase-catalysis
#16
Abbas H K Al Temimi, Bas J G E Pieters, Y Vijayendar Reddy, Paul B White, Jasmin Mecinović
Trimethyllysine hydroxylase (TMLH) is a non-haem Fe(ii) and 2-oxoglutarate dependent oxygenase that catalyses the C-3 hydroxylation of an unactivated C-H bond in l-trimethyllysine in the first step of carnitine biosynthesis. The examination of trimethyllysine analogues as substrates for human TMLH reveals that the enzyme does hydroxylate substrates other than natural l-trimethyllysine.
October 12, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27500515/self-aggregating-deep-cavitand-acts-as-a-fluorescence-displacement-sensor-for-lysine-methylation
#17
Yang Liu, Lizeth Perez, Magi Mettry, Connor J Easley, Richard J Hooley, Wenwan Zhong
A dual-mode aggregative host:guest indicator displacement sensing system has been created for the detection of trimethylated peptides and determination of histone demethylase activity. The combination of selective recognition of suitably sized trimethylammonium salts and reversible lipophilic aggregation of the host:guest complex provides a unique quenching mechanism that is not only dependent on affinity for sensitivity but the lipophilicity of the indicator. In addition, aggregation can be controlled by the application of chaotropic anions in the mixture, allowing a second level of discrimination between hard lysine groups and softer trimethyllysines...
August 31, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27387477/supramolecular-affinity-labeling-of-histone-peptides-containing-trimethyllysine-and-its-application-to-histone-deacetylase-assays
#18
Isaiah N Gober, Marcey L Waters
Lysine methylation is an important histone post-translational modification (PTM) for manipulating chromatin structure and regulating gene expression, and its dysregulation is associated with various diseases including many cancers. While characterization of Lys methylation has seen improvements over the past decade due to advances in proteomic mass spectrometry and methods involving antibodies, chemical methods for selective detection of proteins containing PTMs are still lacking. Here, we detail the development of a unique labeling method wherein a synthetic receptor probe for trimethyl lysine (Kme3), CX4-ONBD, is used to direct selective fluorescent labeling of Kme3 histone peptides...
August 3, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26868510/the-carnitine-butyrobetaine-trimethylamine-n-oxide-pathway-and-its-association-with-cardiovascular-mortality-in-patients-with-carotid-atherosclerosis
#19
Karolina Skagen, Marius Trøseid, Thor Ueland, Sverre Holm, Azhar Abbas, Ida Gregersen, Martin Kummen, Vigdis Bjerkeli, Frode Reier-Nilsen, David Russell, Asbjørn Svardal, Tom Hemming Karlsen, Pål Aukrust, Rolf K Berge, Johannes E R Hov, Bente Halvorsen, Mona Skjelland
BACKGROUND AND PURPOSE: γ-butyrobetaine (γBB) is a metabolite from dietary Carnitine, involved in the gut microbiota-dependent conversion from Carnitine to the pro-atherogenic metabolite trimethylamine-N-oxide (TMAO). Orally ingested γBB has a pro-atherogenic effect in experimental studies, but γBB has not been studied in relation to atherosclerosis in humans. The aim of this study was to evaluate associations between serum levels of γBB, TMAO and their common precursors Carnitine and trimethyllysine (TML) and carotid atherosclerosis and adverse outcome...
April 2016: Atherosclerosis
https://www.readbyqxmd.com/read/26578293/chemical-basis-for-the-recognition-of-trimethyllysine-by-epigenetic-reader-proteins
#20
Jos J A G Kamps, Jiaxin Huang, Jordi Poater, Chao Xu, Bas J G E Pieters, Aiping Dong, Jinrong Min, Woody Sherman, Thijs Beuming, F Matthias Bickelhaupt, Haitao Li, Jasmin Mecinović
A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation-π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain...
November 18, 2015: Nature Communications
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