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openCC0Jan 2021View details →

Soil extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Bear Brook Watershed in Maine, USA.

Our objective was to detect possible differences in N fertilization responses of soil extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). In addition, we measured microbial allocation to complex C degrading oxidative enzymes phenol oxidase and peroxidase. The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils during the growing season in 2016.

openOpenDec 2015View details →

Proteolytic enzyme activity of organic and mineral soil core samples collected near Toolik Lake field station, Alaska, July 2001

The original focus of this study was an analysis of proteolytic enzyme activity of Alaskan arctic tundra soils, however initial results raised questions regarding the method (Watanabe and Hayano, 1995). Thus, the goals of the study changed to 1) an investigation of the method, and 2) a comparison of enzyme activities of two different soil layers from the arctic tundra. Methodological examination included the impact of toluene, used to prevent immobilization of the product, and blank correction of enzyme activity, and a search for a true 6-h linear rate of activity during a 48-hour incubation. We measured native and potential, using casein as an artificial substrate, activities as net amino acid production in mineral and organic soil layer samples. Varying toluene concentration had no clear effect on activity; omitting toluene resulted in zero native activity and reduced potential for the organic samples, but not for the mineral. Comparison of activities with and without blank correction indicated, particularly for potential activity of samples with low native rates, that correction was required for accuracy. Native and potential activity of the organic samples, and native of the mineral were linear for the first 6 h of incubation; linearity was observed during the 6 to 24 h incubation for potential activity of the mineral. Soil layer activity data indicated that native activity was higher in organic soils as compared with mineral. The organic layer potential activity was ten-fold greater than the native, suggesting substrate limitation; potential and native activities did not differ in the mineral layer, indicating substrate sufficiency. Casein addition changed the kinetic pattern for both layers from hyperbolic to sigmoidal for the mineral and linear for the organic, implying different enzyme pools or behavioral changes of existing pools. Native activity based on total soluble protein was higher for the mineral samples relative to the organic, reiterating substrate

openCC (other)May 2019View details →

Soil enzyme activity in the MELNHE study at Hubbard Brook Experimental Forest, Bartlett Experimental Forest, and Jeffers Brook, NH, 2014 and 2017

The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation through a series of nutrient manipulations in northern hardwood forests. This data set includes soil enzyme activities measured in Oe, Oa, and mineral soil horizons in all 13 of the MELNHE study sites (Bartlett EF, Hubbard EF, and Jeffers Brook, NH). Samples were collected in 2014 and 2017, representing 6 years of N and P fertilization. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.

openCC (other)Jul 2019View details →

Genetic and extracellular enzyme survey of planktonic communities of aquatic habitats in Green Lakes Valley, 2017

Preliminary work done in the soils of Green Lakes Valley (GLV) has shown that the microbial communities are generally carbon and phosphorus limited. While most working examining nutrient limitations in GLV has focused on the terrestrial environment, the aquatic environments lack the same study. Longterm monitoring of the lakes in GLV show that there are shifts in carbon availability (quantity and quality) over course of the Colorado alpine growing season. These shifts have been attributed to changes in the source of DOC as snow packs melt out and flow rates decline in the valley altering the ratio of internal (autochthonous) to external (allochthonous) carbon input to the lakes. We examined the links between the biogeography of planktonic communities and the functional response of those communities to shifting nutrient limitations to test the idea that nutrient limitation and composition of planktonic communities are linked both temporally and spatially in GLV. We determined the composition of GLV’s planktonic communities using amplicon sequencing of the small ribosomal subunit sequences (16S, 18S rDNA) and determined nutrient limitations using extracellular enzyme activity (EEA) assays to examine if communities shifted in conjunction with shifts in EEA. We observed that shifting composition in the planktonic communities of GLV mirrored shifts in nutrient limitation (primarily carbon and phosphorus limitation) over the course of the alpine growing season. Alpine and sub-alpine lakes showed opposite trends in the EEA of carbon acquisition enzymes while all lakes showed high activity for phosphorus acquisition enzymes. The planktonic communities were consistently phosphorus limited throughout the study, but carbon limitation was relieved in the alpine lakes as the season progressed while sub-alpine lakes became more carbon limited. The most likely mechanism behind the observed shifts in carbon limitation are the previously studied shifts where DOC is sourced in the va

opencc-by-4.0Jan 2020View details →

Effect of metabolosome encapsulation peptides on enzyme activity, co-aggregation, incorporation and bacterial microcompartment formation

Supplementary Video 1. This approach revealed the structures formed by fvMT and BMC shell proteins are remarkably varied in size, shape and volume. Supplementary Video 2. Recombinant BMCs containing L20-fvMT and - Supplementary Video 3.  Allowing us to quantitate the volume (empty: 54900±11013 nm3 (n=29); L20-fvMT: 336411±177722 nm3 (n=60)) and the largest diameter (empty: 61.77±15.38 nm (n=29); L20-fvMT: 127.51±60.97 nm (n=60)) of these structures

opencc-by-4.0Feb 2020View details →

Underlying data for "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?"

This dataset contains code, data, trajectories, and figures used in the article "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?".   Contents: code/* - Code used to calculate electric fields from simulation trajectories with either polarizable or additive force fields data/* - Electric fields calculated for the CypA WT cis, WT trans, R55A cis, and R55A trans systems, with AMOEBA, Amber, or Charmm force fields. Each subfolder also includes a set of structural coordinates extracted at 2.5 ns intervals from the first simulation trajectory and used to calculate ONETEP DFT electric fields. figures/* - Underlying data and scripts used to create all figures and movies used in the article. trajectories/* - Simulation trajectories of the CypA WT cis, WT trans, R55A cis, and R55A trans systems   Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages and other software used to generate data are available in Dependencies.txt

opencc-by-4.0Dec 2019View details →

Carbon-Phosphorous Lyase Enzyme Activity Profiles in the North Pacific Subtropical Gyre

These datasets contain oceanic enzyme activity measurements of Carbon-Phosphorus (C-P) lyase, a catalytic enzyme pathway, which cleaves C-P bonds, allowing microbial utilization of phosphonates as a phosphorous source. These activity measurements were made in the North Pacific Subtropical Gyre. Samples were collected in the top 1000 m of the water column on KM1717, KM1821, and KM2001 cruises and in the top 225 m of the water column on FK180310-2.

opencc-zeroJul 2020View details →

HADDOCK screening against human Angiotensin Converting Enzyme 2 (ACE2)

The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process. One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use. Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the Angiotensin Converting Enzyme 2 receptor (ACE2) that acts as one of the main gateways for viral entry in the host cell. We have screened ~2000 compounds against the inhibitor-bound closed form of the receptor. This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations: <ul> <li><a href="https://zenodo.org/record/3929438">Mpro: Shape-based assay</a></li> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929449">RdRp</a></li> </ul> More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1

Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1

Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1

opencc-zeroMay 2020View details →

Data from: Biosynthesis of the redox coenzyme F420 in Thermomicrobia involves reduction by standalone nitroreductase superfamily enzymes.

Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for long that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that PEP is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase superfamily (NTR), converts dehydro-F420 into saturated F420. Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in-vitro assays that standalone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum. These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in E. coli in the future.

opencc-zeroFeb 2020View details →

Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence

Neosinocalamus affinis, a type of cluster bamboo, is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the N. affinis transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the N. affinis transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle Cyrtotrachelus buqueti, and develop low-cost chemical feedstock from bamboo.

opencc-zeroDec 2017View details →

Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies

Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this since amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype - the duration of bioluminescent courtship pulses - is shaped by biochemical function. First, by measuring light production from induced bioluminescence in 38 species, we discovered differences between species in their biochemical reactions. Then, for 16 species of which biochemical, phylogenetic, and behavioral data are all available, we used phylogenetic comparative models to show that differences in biochemical reaction are nonlinearly correlated with the duration of courtship pulses. This relationship indicates that changes to both enzyme (c-luciferase) function and usage have shaped the evolution of courtship displays, but that they differentially contribute to these phenotypic changes. This nonlinear dynamic may have consequences for the disparity of signaling phenotypes observed across species, and demonstrates how unappreciated diversity at the biochemical level can lead to inferences about behavioural evolution.

opencc-zeroDec 2017View details →

Data from: Enzyme polymorphism, oxygen and injury: a lipidomic analysis of flight-induced oxidative damage in a SDH-polymorphic insect

When active tissues receive insufficient oxygen to meet metabolic demand, succinate accumulates and has two fundamental effects: it causes ischemia-reperfusion injury while also activating the hypoxia-inducible factor pathway (HIF). The Glanville fritillary butterfly (Melitaea cinxia) possesses a balanced polymorphism in Sdhd, shown previously to affect HIF pathway activation and tracheal morphology and used here to experimentally test the hypothesis that variation in succinate dehydrogenase affects oxidative injury. We stimulated butterflies to fly continuously in a respirometer (3 min duration), which typically caused episodes of exhaustion and recovery, suggesting a potential for cellular injury from hypoxia and reoxygenation in flight muscles. Indeed, flight muscle from butterflies flown on consecutive days had lipidomic profiles similar to rested paraquat-injected butterflies, but distinct from rested untreated butterflies. Many butterflies showed a decline in flight metabolic rate (FMR) on Day 2, and there was a strong inverse relationship between the ratio of Day 2 to Day 1 FMR and the abundance of sodiated adducts of phosphatidylcholines and coenzyme Q (CoQ). This result is consistent with elevation of sodiated lipids caused by disrupted intracellular ion homeostasis in mammalian tissues after hypoxia-reperfusion. Butterflies carrying the Sdhd M allele had higher abundance of lipid markers of cellular damage, but the association was reversed in field-collected butterflies, where focal individuals typically flew for seconds at a time rather than continuously. These results indicate that Glanville fritillary flight muscles can be injured by episodes of high exertion, but injury severity appears to be determined by an interaction between SDH genotype and behavior (prolonged vs. intermittent flight).

opencc-zeroDec 2019View details →

Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry

The lenticular fiber cells are comprised of extremely long-lived proteins while still maintaining an active biochemical state. Dysregulation of these activities has been implicated in age-related cataracts, and other lens diseases. However, the lenticular protein dynamics underlying health and disease is unclear. We sought to measure the global protein turnover rates in the eye using dietary nitrogen-15 (15N)-labeling of mice between 3 and 15 weeks of age. By performing mass spectrometry we measured the 14N- to 15N-peptide ratios of 248 lens proteins, including Crystallin, Aquaporin, Collagen and Laminin of the lens capsule, and enzymes that catalyze glycolysis as well as oxidation and reduction reactions. Unexpectedly, like the crystallin proteins, many of these enzymes are also exceedingly long-lived. The slow replacement of these enzymes in spite of young age of the mice suggests their potential roles in age-related metabolic changes in the lens.

opencc-by-4.0Feb 2017View details →

Research data supporting "Localized and controlled delivery of nitric oxide to the conventional outflow pathway via enzyme biocatalysis: towards therapy for glaucoma"

Research data supporting the paper above published at DOI: 10.1002/adma.201604932

opencc-zeroDec 2023View details →

Data from: Different dynamics and controls of enzyme activities of leaf and root litter during decomposition

Litter enzyme dynamics are strongly shaped by litter, soil, and microbial attributes during decomposition, however, enzyme dynamics of leaf and root litter remains unresolved due to contrasting differences in rates and controls on leaf and root litter decomposition. Herein, we conducted a 784-day field experiment to evaluate the relative importance of litter, alkaline soil, and microbial attributes to enzyme activities and their C:N:P stoichiometry of leaf and root litter during decomposition under subtropical land use change of China. We found that only the C- and N-acquiring enzyme activities of shrub leaves were greater than those of wood and crop, and there was no significant difference in P-acquiring enzyme activity among the three species of leaves. Both the C- and P-acquiring enzyme activities of crop roots were significantly lower than those of afforested lands (i.e., woodland and shrubland). The N-acquiring activities of wood roots were significantly lower than those of shrub and crop. At the temporal dynamics, the C-, N-, and P-acquiring enzyme activities of the leaves decreased with mass loss, which was affected by the shift in litter nutrients (e.g., N and P) and soil moisture during decomposition. In contrast, the three enzyme activities of roots increased with mass loss, largely due to the increase in microbial biomass of bacteria regulated by litter stoichiometry. The enzymatic C:nutrient (N and P) ratios declined with mass loss, but the enzymatic P:N ratios remained relatively constant with mass loss during the leaf litter decomposition. Whereas, both of the enzymatic C:nutrient ratios and enzymatic P:N ratios decreased with mass during the root litter decomposition. Our results showed that the enzymatic C:N:P stoichiometry of decaying leaves and roots was predominantly predicted by microbial biomass and bacterial biomass, respectively. Overall, we outlined the pattern of contrasting contributions of litter, soil, and microbial attributes to enzyme dynamics during decomposition, which provided a framework for better understanding litter C, N, and P dynamics in relation to microbial resource allocation strategy during decomposition.