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opencc-by-4.0Mar 2023View details →

A PETase enzyme synthesised in the chloroplast of the microalga Chlamydomonas reinhardtii is active against PET and polystyrene

The list contains: 1) raw data for chromatographies: HiprepSPHP and SEC 2) raw data for UV-vis Spectrum 3) raw data for all MS/MS spectra manuscript + supplementary 4) raw data for AFM  5) report data from HPLC

opencc-by-4.0May 2023View details →

MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"

Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site, then on the whole enzyme. We confirmed that the polar modification in 4’-DTMP induces additional local interactions with the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.

opencc-by-4.0Jun 2023View details →

Supplementary data as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (https://doi.org/10.1016/j.xcrp.2023.101422)

Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (<a href="https://doi.org/10.1016/j.xcrp.2023.101422">https://doi.org/10.1016/j.xcrp.2023.101422</a>)

Fig. 2 in Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose

Fig. 2. Diffuse reflectance mid infra-red spectrum of agrocinopine C. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose

Fig. 4. Bioassay detection of agrocinopine C. The left plate shows detection of agrocinopine C in the pH 1.7, anionic paper electrophoretogram segment marked C, by its induction of antibiotic activity in the normally insensitive K478 (syn. A281) overlay, from a source of agrocin 84 produced by the chloroformsterilised, colony of R. rhizogenes strain K84 grown at the centre of both plates. The radius of the normal toxic concentration range of agrocin 84 extends approximately to the location of the paper squares. The right plate demonstrates that glucose 2-phosphate (square A) induces no detectable sensitivity to agrocin 84, glucose 6-phosphate (square B) no detectable sensitivity and purified agrocinopine C (C) induces a very strong uptake of the antibiotic. It is noteworthy that unlike agrocinopine A, which extends the inhibition zone perimeter (Ellis and Murphy, 1981; Ryder et al., 1984) beyond the squares, agrocinopine C only induces sensitivity inwards towards the original agrocin 84 producer colony.

Fig. 3 in Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose

Fig. 3. Relative electrophoretic mobilities (RmDNBS) of ribose-5-P (triangle; pKa1 =1.32, pKa2 =6.58), agrocinopine C (circle) and agrocinopine D (square) between pH 1.7 and 10.

Fig. 5 in Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose

Fig. 5. (a) 31P NMR signals for agrocinopine C, α/β pyranosyl anomers (-2.80 ppm), α/β furanosyl anomers (-3.24 ppm) and the aldehyde anomer and/or its hydrate (-4.03 ppm). No evidence for a detectable amount of the hydrated aldehyde as a separate 6th signal was observed in these 31P NMR observations. Peaks at -3.09 and -3.12 ppm are not correlated to any agrocinopine C protons by 31P gHMBC. (b) Agrocinopine C31P NMR signals collapse to a singlet after borohydride reduction (-1.55 ppm).

Fig. 6. Structural relationships for agrocinopine C in Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose

Fig. 6. Structural relationships for agrocinopine C and its various anomeric equilibria. The presence of the aldehyde anomer and/or its hydrate and α/β pyranosyl and α/β furanosyl anomers is consistent with the three signals detected in the 31P NMR and five anomeric proton signals observed in the 1H NMR (Table 2, Table S1). (ChemBioDraw, 2014).

opennotspecifiedMar 2022View details →

Fig. 1 in Spirornatas A-C from brown alga Turbinaria ornata: Anti-hypertensive spiroketals attenuate angiotensin-I converting enzyme

Fig. 1. Structural representation of 6,6-spiroketal compounds spirornatas A-C isolated from the thallus structure of the marine macroalga Turbinaria ornata.

opennotspecifiedMar 2022View details →

Fig. 3 in Spirornatas A-C from brown alga Turbinaria ornata: Anti-hypertensive spiroketals attenuate angiotensin-I converting enzyme

Fig. 3. Molecular docking interactions of spirornata A and standard antihypertensive agent captopril with ACE-I. Nearer view of molecular binding interfaces of spirornata A (A) and captopril (B) in the catalytic domain (together with WPD loop) of ACE-I. The dotted lines designated the H-bonding connections with the active site of ACE-I. The studied compounds were drawn in ACD/ChemSketch, and saved as MDL-molfiles (ver-2000), which were changed to PDB layout using Open Babel (GUI ver-2.4.1.) software. The macromolecule was assigned for polar hydrogens with added kollman charge of +7.75. The grid box was built by the method of hit and miss, wherein grid box for ACE-I was taken as x = 57, y = 42, z = 38 (54 Å, 33 Å, 55 Å). The binding site was additionally corroborated by keeping the zinc ion in the optimized protein file. Cygwin-I terminal was applied to run the docking algorithm, and after autodocking experiment, RMSD (Root-Mean-Square Deviation) was evaluated, and Cygwin-II was used for further optimization.

opennotspecifiedMar 2022View details →

Fig. 2 in Spirornatas A-C from brown alga Turbinaria ornata: Anti-hypertensive spiroketals attenuate angiotensin-I converting enzyme

Fig. 2. (A–C) Key1H–1H COSY and HMBC correlations of spirornatas A-C.1H–1H COSY correlations are depicted with bold-face bonds and the HMBCs as doublebarbed arrows. (D–F) NOESY correlations (designated as single-barbed arrows) of spirornatas A-C. (G–I) Computer-generated models of spirornatas A-C (correlations are depicted with double-sided arrows), respectively using MM2 force-field calculations.

Fig. 9 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 9. Effects of hypoxic treatment on earlier responses of gene expression. Relative transcript levels calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared before (black bars) and after 3 or 12 h of incubation under normoxic (gray bars) and hypoxic (white bars) conditions. Significant differences (P <0.05) detected by Tukey's multiple comparison test are indicated by different letters above the bars.

Fig. 5 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 5. Phylogenetic tree of sucrose synthase (SUS). Amino acid sequences deduced from SUS genes of Arabidopsis, rice, and carnation, distinguished by AGI ID, locus identifier, or ORF no. shown in parentheses, were aligned by ClustalW. The tree was constructed by the neighbor-joining method using MEGA7.0 software. * indicates carnation SUS described in this study.

Fig. 8 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 8. Expression profiles of sucrose synthase (SUS) gene family of carnation in petals under sucrose and hypoxic treatments. Relative transcript levels calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared among petals after 24 h of incubation with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 7 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 7. Expression profiles of invertase (INV) gene family of carnation in petals under sucrose and hypoxic treatments. Relative transcript levels calculated by realtime RT-PCR using DcUbq3-7 as a standard were compared among petals after 24 h of incubation with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 6 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 6. Expression profiles of invertase (INV) and sucrose synthase (SUS) gene families of carnation among organs. Relative transcript levels of gene families of cellwall INV (A), vacuolar INV (B), cytoplasmic INV (C), and SUS (D) calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared among leaves (dotted bars) and petals (black bars). The graph for the gene with an eminent value is shown as an inset. Data are expressed as mean ± SE of three separate samples. The result of Student's t-test is shown above the bars; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 2 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 2. Sugar content in carnation petals. Contents of reducing sugars (A), sucrose (B), and starch (C) were compared among petals after 24 h of incubation following pretreatment with silver-thiosulfate (STS), and supplied with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively. *** indicates significant difference at P <0.05 detected by Dunnett's test.

Fig. 1 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 1. Effects of chemical treatment on flower senescence of carnation. Carnation florets pretreated with silver-thiosulfate (STS) or incubated with sucrose (Suc, not pretreated with STS) were compared to non-pretreated control florets incubated with distilled water (DW).

Fig. 3 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 3. Enzymatic activities of invertase (INV) and sucrose synthase (SUS) in carnation petals. Activities of cell-wall INV (A), vacuolar INV (B), cytoplasmic INV (C), and SUS (D) were compared among petals after 24 h of incubation following pretreatment with silver-thiosulfate (STS), and supplied with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS and * indicate not significant and significant at P <0.05, respectively.