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1,013 results for “Acetylation”
Increased Drp1 acetylation by lipid overload induces cardiomyocyte death and heart dysfunction
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Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil
<p>An in-depth genotypic characterisation of a diverse collection of <em>Digitaria insularis</em> was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (H<sub>E</sub> > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by an average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of the presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome-wide association study (GWAS) approach. GWAS revealed the association of three SNPs with reduced sensitivity to haloxyfop and clethodim. <em>In silico</em> analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in the vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥ 0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.</p>
Simulation Input Data for "Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics"
<p>This is the reduced data behind an upcoming manuscript investigating impact of acetylation on plant secondary cell wall. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: </p> <p> </p> <pre><code>tar -zcvf Acetylatedcellwall.tar.gz --exclude="*BAK" --exclude="*dcd" --exclude="*poster*" --exclude="*old" --exclude="*out" --exclude="*vel" --exclude="*ppm" --exclude="*mp4" --exclude="*txt" --exclude="*tga" --exclude="*vmd" --exclude="*log" --exclude="fixed*png" --exclude="frame*png" --exclude="nonacetylation*png" . </code></pre>
Thriving in the heat – Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermoactive PEP-synthase
<p>Over time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of <em>Pyrococcus furious</em>, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of <em>P. furiosus</em>. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes.</p> <p><strong>Molecular dynamics simulations and analysis – </strong>The all-atom structures of the full c1(X4) 24-mer PPSA models, carrying highly acetylated sites at 14 positions (106, 120,185, 187, 427, 466, 492, 496, 557, 574, 641, 726, 737, 805) or unmodified lysines were coarse grained (CG), mapping their atoms to the SIRAH force field (ff), that uses a classical Hamiltonian common to most all-atom potentials to describe particle–particle interactions, and recently extended to support the PTMs most commonly found on proteins(Garay et al., 2020). Both starting structures contained a disulfide bond between Cys42-Cys189 as well as phosphorylation of Thr440. All starting structures, simulation boxes and parameters files used for the minimization, equilibration and production are provided (Supplementary Data 5). Simulation was conducted in GROMACS 2020.4(Hess et al., 2008), for which code can be found here: <a href="https://doi.org/10.5281/zenodo.5636522">https://doi.org/10.5281/zenodo.5636522</a>. The 24-aly system consisted of 94128 CG atoms for the protein representation, solvated with 179271 WT4 CG water beads (Garay et al., 2020). A neutral charge was achieved adding 6617 NaW (Na<sup>+</sup>) and 5633 ClW (Cl<sup>-</sup>), corresponding to a concentration of approximately 150 mM NaCl concentration. The 24-lys system was also prepared accordingly and consisted of 93456 CG atoms for the protein, 186690 WT4 CG water beads and neutralized with 6503 NaW (Na<sup>+</sup>) and 5855 ClW (Cl<sup>-</sup>). Solvation was done using the default radii of 0.105 nm for atoms not present in the VdW database (vdwradii.dat) and then removing the WT4 molecules within 0.3 nm from the solute. In all cases, eventual clashes were relaxed during the solute-restrained energy minimization. Due to the length of the loops connecting the 3 domains, an alternative configuration of the tetramers where the CD-NBD domains are sitting on top of the neighboring PPSA subunit is also possible (see Supplementary Note 1). This was named “alternative” (a) configuration, as opposed to the “original” (o), thus producing 4 starting models: a24-aly, o24-aly, a24-lys and o24-lys (Supplementary Data 5). All these configurations were subjected to a first round of production consisting of 125 ns in duplicate to define the stable configuration for further extension of the simulation time to 500 ns.</p> <p>The main stages of the simulation can be summarized as follows:1) solvent and side-chain relaxation by 2 stages of 20’000 steps of energy minimization, imposing positional restraints of 1000 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the whole protein (stage 1) and only on backbone beads (GN and GO, stage 2); 2) solvent NVT ensemble equilibration with a first stage where the temperature was slowly increased from 303K to 363K in 7 steps of 4 ns each, and a second stage to equilibrate the protein by gradually releasing the positional restraints from 1000 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the backbone beads (GN and GO) to 100 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the C-terminus to compensate for the missing stabilization effect of the Met799-Fe cluster; 3) production simulation of an additional 80 ns in NPT ensemble at 363 K and 1 bar imposing positional restraints of 100 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the C-terminus. Non-bonded interactions were treated with a 1.2 nm cutoff and PME for long-range electrostatics. An integration time-step of 15 fs was used during MD production runs. The system pressure was controlled by the Parrinello-Rahman barostat (Parrinello and Rahman, 1981) with a coupling time of 4 ps. The positional restraints during the production simulation were necessary to maintain the overall system at the high energy of the particles at 363 K (90 ˚C), the temperature mimicking the near-optimum temperature for PPSA catalytic activity. All simulations were run in duplicate. Although the simulations do not accurately reflect the possible dynamics of the protein in native conditions, the computational challenges of simulating >350000 atoms for the protein only drove us to use a CG representation of the system. To analyze the trajectories, every functional module (tetramer) was extracted from the simulation of the full 24-mer for each replicate, resulting in two sets of 12 independent trajectories (6 for each 24-mer) either with and without acetylated Lysine residues. To produce morphed movies and analyze secondary structure and interfaces, the CG tetramers trajectories were back mapped to atomistic detail using SIRAH tools via VMD. A back mapped atomistic model was produced every 35.7 ns, and subjected to 100 cycles of energy minimization in AMBER, resulting in 14 atomistic models describing each trajectory of a given tetramer over the 500 ns of simulation, further interpolated in ChimeraX using the morph command to produce the atomistic representation of the dynamics (Supplementary Data 5). RMSD calculation and trajectory analysis were done with the MDanalysis suite(Michaud-Agrawal et al., 2011).</p> <p>Each probability density in Figure 5B and 5C is calculated over two independent coarse-grained molecular dynamics simulations of the last 250 ns of production of the PPSA 24-mer in the acetylated and non-acetylated form, using a snapshot frequency of 5 ns. In Figure 5B, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) of the NBD region (residues 1-365) in the tetramer form was calculated with respect to their conformation in the tetramer PPSA resting state. The six trajectories of all six tetramers included in the simulated PPSA complex, resulting in 3 μs ([250ns*6]*2) of accumulated tetramer simulation, were used in the probability density calculation. In Figure 5C, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) was calculated over the CD (residues 379-481) and PBD (residues 510-790) regions with respect to the modelled CD-PBD state of PPSA in the monomer form. All 24 PPSA monomers of which the simulated PPSA complex was composed were included in the probability density calculation, resulting in 12 μs ([250ns*24]*2) of accumulated PPSA monomer simulation.</p> <p> </p>
Eluding anemone nematocysts: are clownfish deprived of N-acetylated sugars on their surface?
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Data from: Influence of acetylation levels on dual-modified corn starch in colon-targeted Budesonide tablet formulation
<p>Although starch is an affordable and safe biodegradable polymer, its rapid breakdown in the upper gastrointestinal tract renders it an unsuitable excipient for colon-targeted oral tablets. The current study examined the influence of varying degrees of acetylation on dual-modified (retrograded and acetylated) corn starch as a polymer in the formulation of colon-targeted tablets, emphasizing drug release and suitability for direct compression, utilizing Budesonide as a model drug. Starch acetylation was performed using acetic anhydride as the acetylating agent and water or acetic acid as the solvent to prepare starch with low, medium, and high degrees of substitution. Analysis techniques confirmed the presence of acetyl groups, revealed changes in crystalline structure, and illustrated morphological alterations post-acetylation. Among the various degrees of substitution (DS) studied, it was evident that starch acetylated to a high degree offered the most promising attributes as an excipient for colon-targeted drug delivery. Specifically, tablet formulation with a high DS of 2.01±0.03 (F4) demonstrated optimal mechanical strength, hardness, and desirable physical properties for achieving controlled drug release in the colon. Dissolution studies indicated F4's effectiveness, releasing 15.24% of the drug in pH 1.2 within 2 hours, followed by 37.58% and 22.53% in pH 7.4 and pH 6.8 phosphate buffers, covering the ileo-colonic region. In conclusion, the study emphasized the significance of the degree of substitution (DS) in acetylation for dual-modified starch in colon-targeted tablet formulations, highlighting its potential as an ideal option for drug delivery applications by achieving controlled drug release in the targeted ileo-colonic region.</p>
Cysteine S-acetylation is a post-translational modification involved in metabolic regulation
<p><span>Cysteine is a reactive amino acid central to the catalytic activities of many enzymes. It is also a common target of post-translational modifications (PTMs), such as palmitoylation. This long-chain acyl PTM can modify cysteine residues and induce changes in protein subcellular localization. We hypothesized that cysteine could also be modified by short-chain acyl groups, such as cysteine <em>S</em>-acetylation. To test this, we developed sample preparation and non-targeted mass spectrometry protocols to analyze the mouse liver proteome for cysteine acetylation. Our findings revealed hundreds of sites of cysteine acetylation across multiple tissue types, revealing a previously uncharacterized cysteine acetylome. Cysteine acetylation shows a marked cytoplasmic subcellular localization signature, with tissue-specific acetylome patterns and specific changes upon metabolic stress. This study uncovers a novel aspect of cysteine biochemistry, highlighting short-chain modifications alongside known long-chain acyl PTMs. These findings enrich our understanding of the landscape of acyl modifications and suggest new research directions in enzyme activity regulation and cellular signaling in metabolism.</span></p>
Identification and Characterization of the Novel Post-Translational Modification Cysteine S-Acetylation
<p><span>Protein modifications modulate nearly every aspect of cell biology in organisms ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20<sup>th</sup> century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass spectrometry-based proteomics in the latter part of the 20<sup>th</sup> century enabled a veritable explosion in the number of known protein modifications, with over 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress discovering new protein modifications and determining their function. </span></p> <p><span>Lysine acetylation is one of the most well-known post translational modifications. Acetylation is not limited to lysine with acetylation of serine and threonine having also been reported in the literature. Lysine acetylation is known to occur both enzymatically and non-enzymatically.<span> </span>Cysteine is a reactive amino acid central to the catalytic activities of many enzymes. Given the highly reactive nature of the cysteine side-chain, non-enzymatic acetylation of cysteine would be expected to be more favorable than non-enzymatic acetylation of lysine.<span> </span>Cysteine is also a common target of post-translational modifications (PTMs), such as palmitoylation. This long-chain acyl PTM can modify cysteine residues and induce changes in protein sub-cellular localization.<span> </span>Transfer of an acetyl moiety from the side-chain of cysteine to the side-chain of lysine has been shown <em>in vitro</em>.<span> </span>Cysteine side-chain acetylation has never been shown <em>in vivo</em>.<span> </span>We hypothesized that cysteine could also be modified by short-chain acyl groups, such as cysteine <em>S</em>-acetylation. To test this, we developed sample preparation and non-targeted mass spectrometry protocols to analyze the mouse liver proteome for cysteine acetylation. Our findings revealed hundreds of sites of cysteine acetylation across multiple tissue types, revealing a previously uncharacterized cysteine acetylome. The cysteine acetylome shows distinct patterns in different sub-cellular compartments and is most abundant in the cytoplasm. Cysteine acetylation is present in all tissue types tested and has tissue-specific acetylome patterns.<span> </span>Metabolic stress led to targeted changes in the cysteine acetylome of BAT.<span> </span>Acetylation of the active site cysteines of GAPDH led to a sharp reduction in activity. This study uncovers a novel aspect of cysteine biochemistry, highlighting short-chain modifications alongside known long-chain acyl PTMs. These findings enrich our understanding of the landscape of acyl modifications and suggest new research directions in enzyme activity regulation and cellular signaling in metabolism.</span></p>
Supplementary tables for: CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders
<p>Supplementary tables for: CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders. </p> <p>Supplementary Table 1: S1_AD_H3K27ac_Marzi2018_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions, GO enrichment analysis results using the two sets of differentially acetylated regions. </p> <p>Supplementary Table 2: S2_PD_H3K27ac_Toker2022_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions.</p> <p>Supplementary Table 3: S3_ASD_H3K27ac_Sun2016_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions for the prefrontal cortex and the cerebellum, GO enrichment analysis results using the two sets of differentially acetylated regions in the prefrontal cortex. </p> <p>Supplementary Table 4: S4_SCZ_BPD_H3K27ac_Girdhar2022_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions, GO enrichment analysis results using the two sets of differentially acetylated regions. </p> <p> </p> <p> </p> <p> </p> <p> </p>
Microscopy-based assessment of H3K27-acetylation at RNA polymerase II clusters during early stages of zebrafish embryo development
<p>This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Marcel Sobucki in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert.</p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>Additional data needed to be stored in an extra repository due to size limitations: <a href="https://doi.org/10.5281/zenodo.8028508">https://doi.org/10.5281/zenodo.8028508</a></p>
Fig. 7 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 7. Formation of 3-benzyl-4-hydroxy-2-thioxothiazolidine-4-carboxylic acid (12) from benzylisothiocyanate (11) in mammals.
Fig. 1 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 1. Formation of isothiocyanates (ITCs) from glucosinolates (GLCs) via Lossen type rearrangement is mediated by myrosinases in plants of the order Brassicales.
Fig. 10 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 10. Proposed pathways for transformation of rapalexin A (1) to N-acetyl-S-(8-methoxy-4H-thiazolo[5,4-b]indol-2-yl)-L-cysteine (5, tR = 7.1 min) and 4-hydroxy-3-(4-methoxy-1H-indol-3-yl)-2-thioxothiazolidine-4-carboxylic acid (9, tR = 3.4 min) mediated by Colletotrichum dematium and C. higginsianum and degradation of 9; two arrows indicate more than one step; square brackets indicate potential intermediate; Ea = electron acceptor.
Fig. 3 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 3. Selected HMBC correlations of N-acetyl-S-(8-methoxy-4H-thiazolo[5,4- b]indol-2-yl)cysteine (5, tR = 7.1 min).
Fig. 2 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 2. Detoxification of the cruciferous phytoalexin brassinin (2) to indolyl-3-methanamine (4) and indole-3-carboxaldehyde (3) by the plant fungal pathogens Alternaria brassicicola (A. b.) and Leptosphaeria maculans (L. m.), respectively.
Fig. 6 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 6. Selected HMBC correlations and rotamers of 4-hydroxy-3-(4-methoxy-1H-indol-3-yl)-2-thioxothiazolidine-4-carboxylic acid (9) (tR = 3.4 min) and proposed decomposition of 9 to 1 and β-mercaptopyruvic acid.
Fig. 9 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 9. Synthesis of 4-hydroxy-3-benzyl-2-thioxothiazolidine-4-carboxylic acid (12), ethyl 3-benzyl-4-hydroxy-2-thioxothiazolidine-4-carboxylate (17), 3-benzyl-2- thioxo-2,3-dihydrothiazole-4-carboxylic acid (16), and 4-hydroxy-3-(4-methoxy-1H-indol-3-yl)-2-thioxothiazolidine-4-carboxylic acid (9).
Fig. 5 in Unveiling fungal detoxification pathways of the cruciferous phytoalexin rapalexin A: Sequential L-cysteine conjugation, acetylation and oxidative cyclization mediated by Colletotrichum spp.
Fig. 5. Progress curves for formation of compounds with tR = 3.4 min (9) and tR = 7.1 min (5) in cultures of Colletotrichum higginsianum containing rapalexin A (1) (and) or rapalexin A (1) and L-Cys (and).
Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
ClinicalTrials.gov study NCT01098383. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Neuroprotection With N-acetyl Cysteine for Patients With Progressive Multiple Sclerosis
ClinicalTrials.gov study NCT05122559. IPD Sharing: NO. Countries: 1. Publications: 1.
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