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opencc-by-4.0Nov 2023View details →

Raw absorbance data and R codes for analysing enzymatic activities

Raw absorbance data and sample metadata for study by Prokkola et al. (submitted 2023). See README.Statistical analysis of data available in another repository https://doi.org/10.5281/zenodo.8014314.

opencc-by-4.0Oct 2021View details →

HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators

Structure and information of the data file DATA SET; Contains the information to which data set this information belongs. There are four possibilities denoted 1 to 4. Data set1: Enzymatic assay of human HDAC6 with commercial peptide substrate. Data set2: Enzymatic assay of human HDAC6 with custom peptide substrate. Data set3: Hit confirmation of the active molecules of the enzymatic assay of human HDAC6 with custom peptide substrate. Data set4: Determination of IC50 values for inhibition of enzymatic assay of human HDAC6 with custom peptide substrate. INTERNAL NAME; An internal name which enables identification of the compound within data sets from Fraunhofer ITMP ScreeningPort. TYPE; Type of data. Either 'inhibition' for normalized inhibition values or 'IC50' for enzymatic IC50. RELATION; Relation between TYPE and VALUE, always '='. VALUE; Value of the normalized inhibition or the enzymatic IC50. UNITS; Unit of the value. Either '%' for the normalized inhibition or 'uM' for the enzymatic IC50. NAME; Trade name of the chemical compound. SMILES; The canonical Smile of the chemical compound.   Abstract Histone deacetylase 6 (HDAC6) and HDAC10 are unique among the other HDACs as they consist of two domains instead of one. Only in the case of HDAC6 both domains are active resulting in a number of unique deacetylase reactions. Interestingly, HDAC6 can regulate the microtubule network and plays a role in the degradation of misfolded and aggregated proteins. We therefore developed a substrate (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) based on a critical acetylation site of misfolded human Tau, a hallmark of Alzheimer’s Disease. This substrate was used to screen a 5632 compound encompassing repurposing library at 10 µM in a coupled, luminescence based assay. The assay was miniaturised to 10 µL per enzymatic reaction. For comparison, a generic HDAC substrate (BOC-Gly-(Ac)Lys-aminoluciferin) was also used to screen the same library. Both substrates rely on a cascade of enzymatic reactions. First, HDAC6 deacetylates the substrate followed by cleavage of aminluciferin from the peptide by porcine Trypsin and conversion of the aminoluciferin using firefly Luciferase. Compounds with an activity of at least 75% inhibition against the custom human Tau based substrate were confirmed in triplicates at the screening concentration of 10 µM. Confirmed hits, activity of at least 75%, where analysed in 8 point or 15 point dose response curves, depending on their activity. The data presented here encompass both primary data sets including 5632 compounds as well as 249 values from hit confirmation screening against the hTau based substrate and 151 IC50 values from confirmed hits.   Methods of data generation Enzymatic assay of human HDAC6 with commercial peptide substrate. The assay using the commercial peptide substrate (BOC-Gly-(Ac)Lys-aminoluciferin) was obtained from Promega Inc.. In the beginning the assay buffer is thawed and the lyophilized substrate is dissolved according to the technical manual (Promega Inc.) to create the substrate reagent. HDAC6 (obtained from BPS Biosciences) is dissolved in assay buffer at 0.2 nM, which is twice the final assay concentration. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and incubated for 10 min at RT. Afterwards, 5 µL/well substrate solution are added to the wells, centrifuged shortly and incubated for 10 min prior detection of the luminescence signal on a multimode reader. Primary screening was done at one concentration (10 µM) in singlicates.   Enzymatic assay of human HDAC6 with custom peptide substrate. The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. Primary screening was done at one concentration (10 µM) in singlicates.   Hit confirmation of the active molecules of the enzymatic assay of human HDAC6 with custom peptide substrate The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. Hit confirmation was done at one concentration (10 µM) in triplicates.   Determination of IC50 values for inhibition of enzymatic assay of human HDAC6 with custom peptide substrate The assay was designed based on a commercial HDAC6 assay available from Promega Inc. This luminescence assay works by an aminoluciferin coupled HDAC6 peptide substrate. Upon deacetylation of the peptidic substrate by HDAC6 (obtained from BPS Biosciences) Trypsin (obtained from Sigma-Aldrich) can cleave the aminoluciferine from the peptide which can be converted by Luciferase (obtained from AAT Bioquest) to the detected signal. First, a twofold concentrated enzyme solution was generated, consisting of 4 nM HDAC6 and 0.1% BSA in HEPES buffer (25 mM HEPES, 137 mM NaCl, 2.7 mM KCl and 1 mM MgCl2, pH 7.0). Second, a twofold peptide solution was generated containing 100 µM custom made peptide (Boc-Ile-Asp-(Dimethyl)Lys-(Ac)Lys-aminoluciferin) in HEPES buffer. Compounds and controls are added to the plates using acoustic dispensing to reach a final concentration of 10 µM in the assay followed by 5 µl enzyme solution per well. Plates are centrifuged shortly and 5 µL/well peptide solution are added to the wells, centrifuged shortly and incubated for 30 min at RT. Afterwards, 5 µL detection reagent (0.067 mg/mL Luciferase, 133.3 µM ATP, 0.133 mg/mL Trypsin in HEPES buffer) were added to each well. Plates were centrifuged shortly and measured on a multimode reader after 30 min incubation at RT in the dark. IC50 values were determined using 7 point dose response curves (DRCs) between 20 µM and 312 nM. In case inhibition values were not below 50% additional 7 point DRCs were measured, starting at 312 nm with a dilution factor of 2. All DRCs were recorded in triplicates.

opencc-by-4.0Oct 2021View details →

Figure 1 in Enzymatic activity of bone markers on Lithobates catesbeianus (Shaw, 1802) growth during the ossification process

Figure 1. Effect of pH on p NPPase activity of alkaline phosphatase released by PIPLC present in the SPIPLC fraction of tadpole epiphysis and diaphysis and frog epiphysis. T.E.= Tadpole Epiphysis; T.D. = Tadpole Diaphysis; F.E. = Frog Epiphysis.

opencc-by-4.0Dec 2023View details →

Figure 2 in Toxicity and larvicidal activity on Aedes aegypti of citronella essential oil submitted to enzymatic esterification

Figure 2. Mortality percentage of Artemia salina nauplii in relation to increased sample concentration.

opencc-by-4.0Dec 2023View details →

Figure 1 in Toxicity and larvicidal activity on Aedes aegypti of citronella essential oil submitted to enzymatic esterification

Figure 1. Kinetics of citronellyl and geranyl cinnamates production (molar ratio alcohol/acid 3:1, enzyme 15 wt%, temperature 70°C, 150 rpm).

opencc-by-4.0Jun 2024View details →

Raw data to: Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule

Initial configuration (PDB) and TIGER2hPE ensemble of all four simulations (R1-4) reported in this study in DCD trajectory format: <ol> <li>AcuA + AcsA + Acetyl-CoA</li> <li>Acua + AcsA + Acetyl-CoA (AcuA:K549 deprotonated)</li> <li>AcuA + AcsA + CoA + AcP (Acetyl-Phosphate)</li> <li>AcuA + AcsA + Desulfo-CoA</li> </ol>

opencc-by-4.0Feb 2023View details →

Simulation data for: "Unique Amphipathic a-helix Drives Membrane Insertion and Enzymatic Activity of ATG3"

Simulation data from Nishimura et al. (2023), "Unique Amphipathic a-helix Drives Membrane Insertion and Enzymatic Activity of ATG3". The dataset contains the MD simulations executed for the Atg3/LC3/lipid membrane system, both in the WT and 5W-mutated variants. More information can be found in the README file and in Table 1 of the cited paper.

zenodo36/100

Effect of temperature on extracellular enzymatic activities in the global ocean

Supplementary data for: Ayo B, Abad N, Artolozaga I, Azua I, Baña Z, Unanue M, Gasol JM, Duarte CM & Iriberri J. Imbalanced nutrient recycling in a warmer ocean driven by differential response of extracellular enzymatic activities. Accepted for publication in Global Change Biology.

opencc-by-4.0May 2017View details →

opencc-zeroJun 2022View details →

Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes

We assessed the enzymatic activation of four different biochars produced from pyrolyzing swine manure and poultry litter, and by co-pyrolyzing these livestock residues with agricultural spent mulch plastic film wastes (plastichars). Enzymatic activation consisted of incubating biochars in soil inoculated with earthworms (Lumbricus terrestris), which acted as biological vectors to facilitate retention of extracellular enzymes onto biochar surface. The activity of carboxylesterase ‒a pesticide-detoxifying enzyme‒ was measured in non-bioturbed soils (reference), linings of the burrows created by earthworms, casts (feces) and biochar particles recovered from the soil.

zenodo36/100

The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity - dataset

Dataset to paper: Błońska E., Jankowiak R., Lasota J., Krzemińska N., Zbyryt A., Ciach M. 2024. The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity. Environmental Science and Pollution Research 31, 2: 2583-2594. https://doi.org/10.1007/s11356-023-31383-x This study was financially supported by the National Science Centre, Poland (grant no. 2021/41/B/NZ8/03456).

opencc-by-4.0Sep 2024View details →

opencc-zeroJan 2023View details →

Data from: Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation

Nitrogen enrichment can alter soil communities and their functioning directly, via changes in nutrient availability and stoichiometry, or indirectly, by changing plant communities or the abundance of consumers. However, most studies have only focused on one of these potential drivers and we know little about the relative importance of the different mechanisms (changes in nutrient availability, in plant diversity or functional composition, or in consumer abundance) by which nitrogen enrichment affects soil functioning. In addition, soil functions could vary dramatically between seasons, however, they are typically measured only once during the peak growing season. We therefore know little about the drivers of intra-annual stability in soil functioning. In this study, we measured activities of β-glucosidase and acid phosphatase, two extracellular enzymes that indicate soil functioning. We did so in a large grassland experiment which tested the effects, and relative importance, of nitrogen enrichment, plant functional composition and diversity, and foliar pathogen presence (controlled by fungicide) on soil functioning. We measured the activity of the two enzymes across seasons and years to assess the stability and temporal dynamics of soil functioning. Overall β-glucosidase activity was slightly increased by nitrogen enrichment over time but did not respond to the other experimental treatments. Conversely, plant functional diversity, and interactions between plant attributes and fungicide application, were important drivers of mean acid phosphatase activity. The temporal stability of both soil enzymes was differently affected by two facets of plant diversity: species richness increased temporal stability and functional diversity decreased it; however, these effects were dampened when nitrogen and fungicide were added. Synthesis: The fungicide effects on soil enzyme activities suggest that foliar pathogens can also affect belowground processes and the interacting effect of fungicide and plant diversity suggests that these plant enemies can modulate the relationship between plant diversity and ecosystem functioning. The contrasting effects of our treatments on the mean versus stability of soil enzyme activities clearly show the need to consider temporal dynamics in belowground processes, to better understand the responses of soil microbes to environmental changes such as nutrient enrichment.

publicJun 2022View details →

Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes

Open the record for dataset details and reuse information.

publicJan 2023View details →

Data from: Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation

Open the record for dataset details and reuse information.

dryad32/100

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.

opencc-zeroApr 2023View details →

Fig. 5 in Distribution of enzymatic and alkaline oxidative activities of phenolic compounds in plants

Fig. 5. UV chromatograms (280 nm) of non-oxidized (grey) and oxidized (black) samples of selected species, illustrating enzymatic oxidative activities of various types of compounds. Dihydroxysubstituted compounds, such as quercetin glycosides and caffeic acid derivatives, are oxidized more efficiently than their monohydroxysubstituted counterparts, i.e. kaempferol glycosides and coumaric acid derivatives.

Fig. 2 in Distribution of enzymatic and alkaline oxidative activities of phenolic compounds in plants

Fig. 2. Plant families arranged according to APG IV, and their phenolic compound classes and total phenolic levels. The dash () and one, two or three asterisks denote different average quantity levels depending on the compound class as follows: FC and ET: <1, 1–30, 31–60 and>60 mg/g; GA: <1, 1–10, 11–20 and>20 mg/ g; PC and PD: <1, 1–15, 16–30 and>30 mg/g; KA, QU and QA: <1, 1–5, 6–10 and>10 mg/g. For the oxidative activity column, dashes and asterisk represent the following: () No activity. The phenolic content of the samples is low overall (total phenolics concentration 10 mg/g or less) with no major peaks present, or the compounds are not affected by the oxidative conditions, the peak area variation remaining within ±10%. (*) Weak activity. The area of most major peaks have reduced by ca. 10–30%. (**) Moderate activity. The areas of most major peaks have reduced by ca. 30–60%. (***) High activity. The areas of most major peaks have reduced by>60%. Abbreviations: FC: Folin-Ciocalteu assay (i.e. total phenolics), HT: hydrolysable tannins, GA: gallic acid derivatives, ET: ellagitannins, PA: proanthocyanidins, PC: procyanidins, PD: prodelphinidins, FL: flavonols, KA: kaempferols, QU: quercetins, QA: quinic acid derivatives, Enz: enzymatic oxidative activity, pH10: alkaline oxidative activity at pH 10. a Myricetin has been left out because of its low quantity in the sample set. It was detected in 20 families, with a maximum concentration of 7 mg/g.

Fig. 4 in Distribution of enzymatic and alkaline oxidative activities of phenolic compounds in plants

Fig. 4. UV chromatograms (280 nm) of non-oxidized (grey) and oxidized (black) samples of selected species, illustrating alkaline oxidative activities of various types of compounds. Monohydroxysubstituted compounds, such as kaempferol glycosides, are inactive. The same applies for compounds containing a catechol moiety, e.g. catechin, quercetin glycosides and procyanidins. However, if the catechol moiety is at the end of an alkane chain, as is the case with e.g. rosmarinic acid, rubranoside A, and oregonin, the alkaline oxidative activity is greatly increased. Myricetin glycosides, prodelphinidins, gallic acid derivatives and ellagitannins – all containing a pyrogallol moiety – are highly active and oxidize completely.

Fig. 3 in Distribution of enzymatic and alkaline oxidative activities of phenolic compounds in plants

Fig. 3. Phenolic compound structures quantified using MRM methods of Engstr¨om et al. (2015, 2014), and how the measurements are related to each other.