Find research datasets worth reusing

opencc-by-4.0Oct 2023View details →

Exploring the competitive dynamic enzyme allocation scheme through enzyme cost minimization

The dataset is for the manuscript entitled "Exploring the competitive dynamic enzyme allocation scheme through enzyme cost minimization".

opencc-by-4.0Sep 2023View details →

The measurement of true initial rates is not always absolutely necessary to estimate enzyme kinetic parameters

Dataset of Excel files used for the publication.

opencc-by-4.0Nov 2023View details →

Mapping Enzyme Activity in Living Systems by Real-Time Mid-Infrared Photothermal Imaging of Nitrile Chameleons

Open the record for dataset details and reuse information.

opencc-by-4.0Dec 2023View details →

Computer-Aided Drug Design (CADD): To Screen Potential Antibiotics Against Klebsiella Pneumoniae Beta-Lactamase Enzyme

Open the record for dataset details and reuse information.

Supporting data for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Simulation data, scripts, and other supporting data for transition path sampling studies conducted as part of: The reaction mechanism of the Ideonella sakaiensis PETase enzyme By authors: Tucker Burgin, Benjamin C. Pollard, Brandon C. Knott, Heather B. Mayes, Michael F. Crowley, John E. McGeehan, Gregg T. Beckham, H. Lee Woodcock Published in Communications Chemistry, 2024 This repository does not contain the aimless shooting coordinate files for each step. Those will be published separately here (for acylation) 10.5281/zenodo.10854858 and here (for deacylation) 10.5281/zenodo.10913134.

Acylation shooting moves for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme

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

Deacylation shooting moves for: The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Shooting moves for the deacylation step of the reaction mechanism of the PETase enzyme. See this repository for more information: https://doi.org/10.5281/zenodo.10854763

Simulation Data for Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

This is supporting information for an upcoming research manuscript. The uploaded tarball contains the directory structure needed to reproduce the simulations conducted to support the forthcoming article. The directory structure has three primary subdirectories, Alphafold which contains the initial structure predictions, Build, which has the Tcl scripts in VMD to assemble the system, and Simulation, which has the simulations themselves and the analysis. Since there is a limit to the file sizes that can be stored on Zenodo, we exclude many files to fit under the limit. The command to create the tarball was: <code>tar --exclude=LukeSim --exclude="*trr" --exclude="*dcd" --exclude="*GO*" --exclude="*HPR*" --exclude="*PGP*" --exclude="*GAT*" --exclude="*#" --exclude="*ppm" --exclude="*BAK" --exclude="*oldpgp*" -zcvf glykthermostable.tar.gz Thermostability/</code> While the full trajectories are too large to be provided, reduced trajectories of only the protein component can be found in the  <code>Thermostability/Simulation/Analysis/prottrajs</code> path. Files with the  <code>.js</code> extension can be read via VMD.

opencc-by-4.0Nov 2024View details →

Dataset for manuscript "Robust Enzyme Discovery and Engineering with Deep Learning using CataPro"

Open the record for dataset details and reuse information.

opencc-zeroNov 2021View details →

Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes

A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling selective mRNA targeting by the enzyme remain elusive. Through extensive genetic analyses we uncover cis-regulatory elements in the Dcp2 C-terminal domain that control selective targeting of the decapping enzyme by forming distinct decapping complexes. Two Upf1-binding motifs target the decapping enzyme to NMD substrates, and a single Edc3-binding motif targets both Edc3 and Dhh1 substrates. Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Xrn1 also has a specific Dcp2 binding site, allowing it to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its targeting specificity and enzymatic activation

opencc-by-4.0Feb 2022View details →

Datasets generated and/or analysed for paper entitled: "Oxysterol 7α,25OHC synthesising enzymes, CH25H and CYP7B1, are upregulated in the blood-brain barrier during inflammation"

Images collected and datasets generated and/or analyzed for a paper entitled: "Oxysterol 7α,25OHC synthesising enzymes, CH25H and CYP7B1, are upregulated in the blood-brain barrier during inflammation"

opencc-by-4.0Mar 2022View details →

Mimicry of the Proton Wire Mechanism of Enzymes Inside a Supramolecular Capsule Enables β-Selective O-Glycosylations

Data underlying the figures in the publication “Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations”, published in Nature Chemistry. Table of contents: 1. Figure 1: An editable chemdraw graphic of Figure 1. 2. Figure 2: .zip archive containing an editable chemdraw graphic of Figure 2, and NMR spectra of compounds 7 and 9. 3. Figure 3: .zip archive containing an editable chemdraw graphic of Figure 3, and source data underlying Figures 3a, 3c and 3d. 4. Figure 4: .zip archive containing an editable chemdraw graphic of Figure 4, NMR spectra of Figure 4c and source data underlying Figures 4d and 4e. 5. Figure 5: .zip archive containing an editable chemdraw graphic of Figure 5, and NMR spectra of compounds 26-31, S8 and S9. 6. Table 1: .zip archive containing an editable chemdraw graphic of Table 1, and NMR spectra of all compounds shown in Table 1.

opencc-zeroApr 2022View details →

Fire decreases soil enzyme activities and reorganizes microbially-mediated nutrient cycles: a meta-analysis

The biogeochemical signature of fire shapes the functioning of many ecosystems. Fire changes nutrient cycles not only by volatilizing plant material, but also by altering organic matter decomposition—a process regulated by soil extracellular enzyme activities (EEAs). However, our understanding of fire effects on EEAs and their feedbacks to nutrient cycles is incomplete. We conducted a meta-analysis with 301 field studies and found that fire significantly decreased EEAs by ~20-40%. Fire decreased EEAs by decreasing soil microbial biomass and organic matter substrates. Soil nitrogen-acquiring EEA decreased alongside decreasing available nitrogen, likely from fire-driven volatilization of nitrogen and decreased microbial activity. Fire decreased soil phosphorus-acquiring EEA but increased available phosphorus, likely from pyro-mineralization of organic phosphorus. These findings suggest that fire suppresses soil microbes and consumes their substrates, thereby slowing microbially-mediated nutrient cycles (especially phosphorus) via decreased EEAs. These changes can become increasingly important as fire regimes in many ecosystems continue to shift in response to global change.

opencc-by-4.0Jan 2022View details →

Massively parallel, computationally-guided design of a pro-enzyme

Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects.  While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to re-design any chosen enzyme to be similarly stimulus-responsive.  Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for pro-enzyme design.  As a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity.  Detailed kinetic characterization of most effective designed variants shows that they are inhibited by approximately 80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases.  Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98%, but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing pro-enzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture.  Structural and thermodynamic characterization provides detailed insights into the pro-domain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of pro-proteins with precise spatial regulation.

opencc-by-4.0May 2022View details →

Structural insights into the inhibition site in the phosphorylcholine phosphatase enzyme of Pseudomonas aeruginosa

Inputs for the simulations (MDs and FEP), plus scripts used to obtain results of the manuscript entitled "Structural insights into the inhibition site in the phosphorylcholine phosphatase enzyme of Pseudomonas aeruginosa"

opencc-by-4.0May 2022View details →

Pathogenic Bacteria Remodel Central Metabolic Enzyme to Build a Cyclopropanol Warhead

MS raw data used for generating Figure 2a/Supplementary Figure 1. NMR raw data of natural gonydiol.

opencc-zeroJul 2022View details →

A single intronic SNP in splicing site of steroidogenic enzyme hsd17b1 is associated with phenotypic sex in oyster pompano, Trachinotus anak

Teleosts show varied master sex determining (MSD) genes and sex determination (SD) mechanisms, with frequent turnovers of sex chromosomes. Tracing the origins of MSD genes and turnovers of sex chromosomes in a taxonomic group is of particular interest in evolutionary biology. Oyster pompano (Trachinotus anak), a marine fish, belongs to the family Carangidae, in which 17b-hydroxysteroid dehydrogenase 1 (hsd17b1) has repeatedly evolved to a MSD gene. Using whole genome resequencing, a single SNP at Chromosome 24 was identified to be strictly associated with phenotypic sex, with females being the heterozygous sex. This SNP is located in a splicing site at the first exon/intron boundary of hsd17b1. The Z-linked SNP results in malfunction of all spliced isoforms, whereas the W-linked isoforms were predicted to have open reading frames (ORF) that are conserved among vertebrates, suggesting that hsd17b1 is a female determining gene. The differential alternative splicing patterns of ZZ and ZW genotypes were consistently observed both in undifferentiated stages and differentiated gonads. We observed elevated recombination around the SD locus and no differentiation between Z and W chromosomes. The extreme diversity of mutational mechanisms that hsd17b1 evolves to a MSD gene highlights frequent in situ turnovers between sex chromosomes in the Carangidae.

opencc-zeroSep 2022View details →

Litter and root traits control soil microbial composition and enzyme activities in 28 common subtropical tree species

1. Plant trait-based approaches are frequently used to explore the linkages between aboveground plant communities and belowground ecosystem functions. However, the role of plant leaf litter and living root traits in driving soil microbial biomass, community composition, and enzyme activities has rarely been explored. 2. Here, we measured the soil microbial biomass, community composition and enzyme activities related to carbon (C), nitrogen (N), and phosphorus (P) acquisition under three-year-old monocultures of 28 common subtropical tree species in China. 3. We found that plant leaf litter and absorptive root traits, including leaf litter C content, litter water holding capacity, and root N content, were the three best predictors for soil microbial biomass and enzyme activities. In particular, resource-exploitative tree species with higher root N contents were associated with microbial communities with lower fungi to bacteria ratios and lower C- and P-acquisition enzyme activities. Tree species with higher leaf litter water holding capacity were associated with microbial resource acquisition strategies for C and P acquisition. 4. Synthesis: Our findings highlighted that plant leaf litter and root traits are important for mechanistically understanding the ecological linkage between the plant community and ecosystem functions.

opencc-by-4.0Jan 2022View details →

Effect of dietary Chlorella vulgaris and carbohydrate-active enzymes on the general health, immune status, antioxidant capacity, and liver lipids and metabolites of weaned piglets

It was evaluated the impact of dietary inclusion of Chlorella vulgaris (CH) and carbohydrases on the general health, immune and oxidative status, and hepatic lipids and metabolites of piglets. Forty-four male weaned piglets were allocated into four diets: control (n=11), CH (control diet with 5% CH, n=10), CH+R (control diet with 5% CH plus 0.005% Rovabio®Excel AP, n=10), and CH+M (control diet with 5% CH plus 0.01% of a pre-selected four-CAZyme mixture, n=11) for 15 days. Total cholesterol, LDL-cholesterol and VLDL-cholesterol were increased by CH. In piglets fed CH-based diets, the interplay observed between IgG increase and IgM decrease contributed for piglets’ survival during weaning. n-6 PUFA were lower in piglets fed CH with or without feed enzymes and the inverse occurred for n-3 PUFA, thus benefiting n-6/n-3 ratio in the liver. The discriminant analysis applied to hepatic variables revealed a good separation between control and CH-based diets but failed to discriminate feed enzymes addition. Minor variations were promoted by Rovabio or the pre-selected enzymatic mixture, thus suggesting some improvement on microalga nutrients digestibility. Taken together, our findings indicate a health promoting effect of CH as feed ingredient in piglets’ nutrition during the weaning period, without negatively impacting on animals’ performance.