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132 results for “acylation”
Intensified, Kilogram-Scaled, and Environment-Friendly: Chemoenzymatic Synthesis of Bio-Based Acylated Hydroxystyrenes
<p>Lignin-derived styrene derivatives are versatile building blocks for the manufacture of bio-based polymers. As shown previously, phenol-protected hydroxystyrenes are accessible under industrially-sound conditions (>100 g/L, >95% yield) by subjecting biogenic phenolic acids to enzymatic decarboxylation and base-catalyzed acylation in non-aqueous media (wet cyclopentyl methyl ether, CPME). Herein, we demonstrate the production of 1 kg of 4-acetoxy-3-methoxystyrene in a 10 L reactor and present practical adjustments to the up- and downstream processing that warrant a straightforward process and high isolated yields. Additionally, an environmental assessment is conducted, starting with a thorough E factor analysis to identify the sources that contribute most to the environmental burden (solvent and downstream processing). Also, the total CO2 production of the process is studied, including contributions from energy use and the treatment of generated wastes. The energy impact is evaluated through thermodynamic analysis, and the environmental footprint contributions by wastes – organic and aqueous fractions – are assessed based on CO2 emissions from solvent incineration and wastewater treatment, respectively. Overall, the holistic assessment of the process, its optimization, scale-up, product isolation, and environmental analysis indicate the feasibility of multi-step chemoenzymatic reactions to deliver high volume, low-value chemicals from biorefineries.</p>
An 8-(Diazomethyl) Quinoline Derivatized Acyl-CoA In Silico Mass Spectral Library Reveals the Landscape of Acyl-CoA in the Aging Mouse Organs (Data Supplement)
<p>Data supplement for publication "An 8-(Diazomethyl) Quinoline Derivatized Acyl-CoA In Silico Mass Spectral Library Reveals the Landscape of Acyl-CoA in the Aging Mouse Organs (Data Supplement)" (2024)</p> <p>Jinhui Yu<sup>1†</sup>, Menghao Guo<sup>1,3†</sup>, Sha Li<sup>5</sup>, Jian Ni<sup>2</sup>, Yu-Qi Feng<sup>4,5</sup>*, Jun Ding<sup>1,2</sup>*</p> <p>1. CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, PR China.</p> <p>2. Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, P. R. China.</p> <p>3. College of Life Sciences, Wuhan University, Wuhan 430072, China.</p> <p>4. School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China.</p> <p>5. Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China.</p> <p> </p> <p>†The authors contribute equally to this work.</p> <p>* Corresponding author Email: <a href="mailto:dingjun@wbgcas.cn">dingjun@wbgcas.cn</a>, <a href="mailto:yqfeng@whu.edu.cn">yqfeng@whu.edu.cn</a></p> <p>----<br>Content:<br>1) Developement: XLS template sheet for development (can be used to adjust or create new library)<br>2) MSP library: spectra in NIST MSP format (use with MS-Dial or NIST MS Search)<br>3) NIST library: NIST23 compatible 8-DMQ-acyl-CoA library (use with NIST MS Search)<br>4) Reference spectra msp: 8-DMQ-acyl-CoA authentic MS/MS spectrum in NIST MSP format (generated by Thermo QE HF-X MS (HCD), for searching NIST MS-Search)</p> <p>Version 1.0<br>April 22 2024</p>
Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin
<p>This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin).</p> <p>These files are:</p> <ul> <li>toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level;</li> <li>chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level;</li> <li>farrys.zip: the featurzied NumPy arrays for model training;</li> <li>peephole.zip: an example file for how the optimized MEPs look like; </li> <li>dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. </li> </ul> <p>The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. </p> <p>All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. </p> <p>Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: <a href="https://doi.org/10.1021/acsphyschemau.2c00005">10.1021/acsphyschemau.2c00005</a></p>
Supplementary Material: Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction
<p>Supplementary material to the publication "Investigating Interaction Dynamics of an Enantioselective Peptide Catalyzed Acylation Reaction".</p> <p>The files contain the raw nuclear magnetic resonance (NMR) spectra and computed structures.</p> <p>A README-file with detailed information is provided.</p>
Raw data for article "Acyl-Ethynylbenziodoxolone (acyl-EBX): Access to Ketene Dithio-arylacetals"
<p>Raw NMR, IR and MS data for the article "Acyl-Ethynylbenziodoxolone (acyl-EBX): Access to Ketene Dithio-arylacetals" published in Organic Letters, DOI: </p> <p><a href="https://doi.org/10.1021/acs.orglett.3c02869">https://doi.org/10.1021/acs.orglett.3c02869</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
RefAHL: A curated quorum sensing reference linking diverse LuxI-type signal synthases with their acyl-homoserine lactone products
Open the record for dataset details and reuse information.
Acylation shooting moves for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme
<p>Shooting moves for the acylation step of the reaction mechanism of the PETase enzyme. See this repository for more information: https://doi.org/10.5281/zenodo.10854763</p>
Programmable Selective Acylation of Saccharides Mediated by Carbene and Boronic Acid
<p>This folder /final_xyz_structures/ contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</p> <p>"Programmable Selective Acylation of Saccharides Mediated by Carbene and Boronic Acid"</p> <p>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ...<br> </p>
NHC-Mediated Photocatalytic Para-Selective C-H Acylation of Aryl Alcohols: Regioselectivity Control via Remote Radical Spiro Cyclization
<p><span>This folder /DFT_optimized_structures/ contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</span></p> <p><span>"NHC-Mediated Photocatalytic Para-Selective C-H Acylation of Aryl Alcohols: Regioselectivity Control via Remote Radical Spiro Cyclization"</span></p>
Carbene Catalysed Chirality-Controlled Site-Selective Acylation of Saccharides
<p><span>This folder contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</span></p> <p><span>"Carbene Catalysed Chirality-Controlled Site-Selective Acylation of Saccharides"</span></p> <p><span>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ...</span></p> <p><span>This folder contains the following subfolders:</span></p> <p><span>/NHC_G/ --> DFT optimized structures for the study of NHC carbene G (entry 9, Table 1)</span></p> <p><span>/NHC_entG/ --> DFT optimized structures for the study of NHC carbene ent-G (entry 17, Table 1)</span></p>
Structure, Function and Dynamics in Acyl Carrier Proteins.
<p><strong>Original Article: </strong>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219435</p> <p><strong>Primary GitHub Repository:</strong> https://github.com/rohitfarmer/acp-dynamics</p> <p><strong>Folders</strong></p> <ul> <li><strong>Figures:</strong> Coordinates (.pdb) for structures used in figure panels. The number in the file name denotes the frame number in the simulation. Each frame was captured at 10 ps therefore frame number 100 would mean 100 X 10 = 1000 ps = 1 ns. <a href="https://pymolwiki.org/index.php/Linux_Install">Pymol</a> session files (.pse), and <a href="https://inkscape.org/">Inkscape</a> files (.svg) that were used to generate the figures are also provided.</li> <li><strong>Scripts:</strong> Perl scripts used in the project.</li> <li><strong>Simulations:</strong> Simulations are in compressed .pdb.zip format with the labelling corresponding to Table 1 in the main paper. To comply with the size allowance of GitHub, GROMACS trajectories that were initially recorded at 10 ps time intervals are reduced to 100 ps time intervals for 200 ns simulations and to 500 ps time intervals for 1 microsecond simulations. Trajectories are converted to PDB format with no water molecules and ions and compressed to individual zip files. Uncompressed simulation files can be visualized in <a href="https://www.ks.uiuc.edu/Research/vmd/">VMD</a>. <ul> <li><strong>amber99sb-ildn.ff:</strong> Amber 99 SB ILDN force field with added parameters from GAFF.</li> </ul> </li> </ul>
Fig. 5 in Acylated saponins and flavonoid glycosides from the fruits of Stewartia koreana
Fig. 5. Effect of compound 15 on PCSK9 and LDLR in the HepG2 human hepatocellular carcinoma cell line. (A) Expression of PCSK9 was assayed by qRTPCR in cells treated with compound 15 (2, 10 and 50 μM), and berberine (Ber10, 10 μM) for 24 h. (B) Expression of PCSK9 and LDLR were assayed by western blot in cells treated with compound 15 (10, 40 and 50 μM), and berberine (Ber20, 20 μM) for 24 h *p <0.05.
Fig. 4 in Acylated saponins and flavonoid glycosides from the fruits of Stewartia koreana
Fig. 4. Effect of compounds from S. koreana on PCSK9 and LDLR in the HepG2 human hepatocellular carcinoma cell line. (A) Expression of PCSK9 mRNA was assayed by qRT-PCR in cells treated with compounds (50 μM), and berberine (Ber20, 20 μM) for 24 h. (B) Expression of LDLR mRNA was assayed by qRTPCR in cells treated with compounds (50 μM), and berberine (Ber20, 20 μM) for 24 h.
Fig. 2 in Acylated saponins and flavonoid glycosides from the fruits of Stewartia koreana
Fig. 2. (A) Key HMBC (from H to C) and 1H–1H COSY correlations for compounds 1–3. (B) ROESY correlations of aglycone of compound 1.
Fig. 1 in Acylated pelargonidin and cyanidin 3-sambubiosides from the flowers of Aeschynanthus species and cultivars
Fig. 1. Chemical structures of the anthocyanins from the corollas and calyces of Aeschynanthus species and cultivars.
Fig. 7 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo
Fig. 7. Flow cytometer analysis of LB accumulation in yeast cells. (A) Cytogram of BODIPY fluorescence vs. side scatter of cells expressing forage sorghum SbDGAT1- 1 variants. (B) Mean intensity of P3/fluorescent population (represents BODIPY uptake) events transformed with different variants of forage sorghum SbDGAT1-1 genes. The error bars represent the SD of three biological replicates. Asterisks indicates significant differences according to student t-test results where * = p <0.05.
Fig. 4 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo
Fig. 4. Transcript expression patterns of SbDGAT1-1 and SbDGAT1-2 in (A) bran (B) embryo (C) endosperm of forage sorghum grains. Bar diagram showed the relative expression pattern of SbDGAT1-1 and SbDGAT1-2 genes normalized against serine/threonine-protein phosphatase (PP2A-1, Accession no.: XM_002453490) as the reference gene by qRT-PCR. 10 DAP, 15 DAP, 20 DAP, 25 DAP and 30 DAP represents 10, 15, 20, 25 and 30 days after pollination of forage sorghum grain development. The bars were standard deviations (SD) of three technical replicates prepared from pooled tissues. (D) The SbDGAT1-1 and SbDGAT1-2 tissue-specific expression (embryo, endosperm, seed 5 DAP and seed 10 DAP) patterns were identified using the EMBL-EBI expression atlas database. FPKM; Fragments Per Kilobase of transcript per Million mapped reads.
Fig. 5 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo
Fig. 5. Overexpression of SbDGAT1 genes and its variants in yeast TAG mutant H1246. (A) Schematic representation of the N-terminal region of SbDGAT1 genes. Red arrow indicates the position of truncation in SbDGAT1-1. (B) TAG mutant H1246 strain transformed with SbDGAT1 full-length and truncated variants restores the TAG biosynthesis capability compared with control as visualized in TLC. The spots of triacylglycerol (TAG), diacylglycerol (DAG) and free fatty acids (FFA) are separated in TLC plate (C) Total TAG content of yeast H1246 cells expressed with full-length (SbDGAT1-1 and SbDGAT1-2) and truncated variants (SbDGAT1-1(39-515) and SbDGAT1-1(89-515)). Wild type yeast cells (BY4741) were used as positive control. (D) FA profile of TAG products isolated from yeast H1246 strain expressed with full-length and truncated variants of SbDGAT1 genes. Saturated FA abbreviations are as follows: 10:0, Capric acid; 12:0, Lauric acid; 14:0, Myristic acid; 15:0, Pentadecylic acid; 16:0, Palmitic acid; 18:0, Stearic acid. Mono-unsaturated FA abbreviations are as follows: 14:1, Myristoleic acid; 16:1, Palmitoleic acid; 18:1, Oleic acid. The error bars represent the SD of three biological replicates. Asterisks indicates significant differences according to student t-test results where * = p <0.05, ** = p <0.01. H1246 transformed with the empty pYES2 vector served as negative control and wild type yeast (BY4741) served as a positive control. FA, fatty acid; DW, dry weight. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo
Fig. 3. DISOPRED plot representing the intrinsically disordered regions in (A) SbDGAT1-1 (B) SbDGAT1-2 protein.
Fig. 6 in Identification and functional characterization of two acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) genes from forage sorghum (Sorghum bicolor) embryo
Fig. 6. LB observation of yeast H1246 transformants with SbDGAT1 variants using confocal microscopy. H1246 mutant strains (transformed with the empty pYES2 vector) and SbDGAT1 variants were observed under confocal microscope. Wild type yeast cells (BY4741) were used as positive control and H1246 as negative control. BODIPY493/503 dyes were used to visualize the yeast LBs.
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