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236 results for “active site”
Fig. 2 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 2. Structural formulae of reaction products of target WT enzymes and their mutant forms. 1, colneleic acid; 2, 9,10-epoxy-11-hydroxy-12-octadecenoic acid; 3, 9-hydroxynonanoic acid; 4, colnelenic acid; 4a, (3′E)-colnelenic acid; 5, 9,10-epoxy-11-hydroxy-12,15-octadecadienoic acid; 6, 11-hydroxy-12,13-epoxy-9-octadecenoic acid; 7, (ω5Z)-etherolenic acid; 8, (9Z)-12-hydroxy-9-dodecenoic acid; 9, (10E)-12-hydroxy-10-dodecenoic acid; 10, 11-hydroxy-12,13-epoxy-9,15-octadecadienoic acid; 11, (ω5Z)-etheroleic acid; 12, 9-hydroxy-12,13-epoxy-10-octadecenoic acid; 13, 9,10-epoxy-13-hydroxy-11,15-octadecadienoic acid; 14, 9,10-epoxy- 13-hydroxy-11-octadecenoic acid. (3′E)-Colnelenic acid is a product of thermal isomerization of the ordinary (8E,1′E,3′Z,6′Z)-colnelenic acid occurring during the GC analyses.
Fig. 1 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 1. Multiple alignments of I-helix sequences of following CYP74s: As, Allium sativum; AsDES, CAI30435; Ca, Capsicum annuum; CaDES, ABH03632; CaHPL, AAK27266; Cs, Citrus sinensis; CsAOS, NP_001275835; Gm, Glycine max; GmAOS, NP_001236445; Le, Solanum lycopersicum; LeHPL, CAB43022; LeDES, AAG42261; Lu, Linum usitatissimum; LuDES, ADP03054; Na, Nicotiana attenuata; NaAOS, CAC82911; Nt, Nicotiana tabacum; NtDES, AAL40900; NtHPL, AAZ39884; Ra, Ranunculus acris; RaDES, CYP74Q1, AJU57209; Sm, Selaginella moellendorffii; SmDES1, CYP74M1, EFJ19674; SmDES2, CYP74M3, EFJ34345; St, Solanum tuberosum; StDES, CAC28152. Hydroperoxide-binding domain is circled. Sites with substitutions are marked with arrows.
Fig. 5 in The CYP74B and CYP74D divinyl ether synthases possess a side hydroperoxide lyase and epoxyalcohol synthase activities that are enhanced by the site-directed mutagenesis
Fig. 5. GC-MS analyses of products (Me/TMS) of LuDES F291V mutant form incubations with 9(S)-HPOD (A), 9(S)-HPOT (B), 13(S)-HPOD (C), and 13(S)- HPOT (D). 2, 9,10-epoxy-11-hydroxy-12-octadecenoic acid (Me/TMS); 3, 9- hydroxynonanoic acid (Me/TMS); 5, 9,10-epoxy-11-hydroxy-12,15-octadecadienoic acid (Me/TMS); 6, 11-hydroxy-12,13-epoxy-9-octadecenoic acid (Me/ TMS); 8, (9Z)-12-hydroxy-9-dodecenoic acid (Me/TMS); 9, (10E)-12-hydroxy- 10-dodecenoic acid (Me/TMS); 10, 11-hydroxy-12,13-epoxy-9,15-octadecadienoic acid (Me/TMS). The structural formulae of products are presented in Fig. 2. 9-HOD/T and 13-HOD/T are decrypted in Fig. 3.
Fig. 6. S491A in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 6. S491A mutation increases the rigidity of the active pocket when it binds the pinyl cation. RMSD values of the active site residues between WT and S491A in complex with the pinyl cation (a), terpinyl cation (b) and thujyl cation (c) are compared.
Fig. 5 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 5. The effect of the S491A mutation. Chromatograms in a, b and c show the GC-MS analysis of terpene production for S491A, F482A/S491A, and F482I/S491A, respectively. The x-axis is the retention time and the y-axis is the relative abundance of each species. The numbers in each peak correspond to α-pinene (1), sabinene (2) and limonene (3). d shows the overall activity and the percentage of sabinene within total products produced by F482A, F482A/S491A, F482I and F482I/S491A. The asterisk indicates P <0.05.
Fig. 4 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 4. Conformational differences in the pinyl cation in WT and F482Y as demonstrated by molecular dynamics simulation. The structures of WT and F482Y are superimposed. Results after 0, 1 and 2 ns of simulation are shown in a, d and c, respectively. Carbon in WT is colored in yellow and carbon in F482Y is colored in green. Oxygen is colored in red. Nitrogen is colored in blue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 2. Converting pinene synthase to sabinene synthase by mutations on 482 position. Chromatograms in a, b, c, d and e show the GC-MS analysis of terpene products for WT, F482A, F482I, F482V and F482T, respectively. The x-axis is the retention time and the y-axis is the relative abundance of each species. The numbers in each peak correspond to α-pinene (1), sabinene (2) and limonene (3).
Fig. 3 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 3. Hybrid quadrupole-orbitrap GC-MS/MS. a shows the chromatogram of terpene products of F482L. The elution peak corresponding to sabinene is labeled. The mass spectrum of the product eluted at 9.29 min from a is shown in b. The mass spectrum of the standard sabinene is shown in c.
Fig. 1. a in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 1. a, The proposed reaction mechanism for the synthesis of limonene, pinene and sabinene. b, The structural model of pinene synthase docked with the terpinyl (left), pinyl (middle) and thujyl (right) cations. Carbocations are colored in magenta (terpinyl), wheat (pinyl) and cyan (thujyl). Other atoms are colored according to their types (red: oxygen; yellow: carbon; blue: nitrogen; orange: phosphorus; green: magnesium). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 7. The RMSD profiles of the region with high (RMSD H) and low (RMSD L) mobility from the simulation of WT (a), S491A (b) and F482/S491A (c) in complex with the pinyl cation.
Pre- and Post-treatment Lung Microbiota, Metabolome and Immune Signatures at the Site of Disease in Patients With Active Pulmonary Tuberculosis
ClinicalTrials.gov study NCT04700579. IPD Sharing: YES. Countries: 1. Publications: 12.
Effect of Active Warming on Surgical Site Infections
ClinicalTrials.gov study NCT04187378. IPD Sharing: NO. Countries: 1. Publications: 10.
Effects of Specified Work Site Physical Activity Intervention Among Employees With Physical Heavy Work
ClinicalTrials.gov study NCT01007669. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Late Neolithic phytolith and charcoal records of human activities and vegetation change in Shijiahe culture, Tanjialing site, China
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Nest-site fidelity of Arctic Terns (Sterna paradisaea) in a managed environment exposed to benign human activity
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Renewable energies and biodiversity: impact of ground-mounted solar photovoltaic sites on bat activity
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Data from: Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426
Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ~6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.
Results for "Evaluating the impact of peat soils and snow schemes on simulated active layer thickness at pan-Arctic permafrost sites"
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Figure 2 in Comparing the effectiveness of pitfall traps and active sampling methods for ants and spiders in a Chromolaena odorata invaded site
Figure 2. Ant species richness collected using active and passive sampling techniques in Buffelsdraai Conservancy [AHC = aerial hand collection above the knee; AHC CRYPTIC = aerial hand collection below the knee cryptic; AHC OBV = aerial hand collection below the knee noticeable or non-cryptic; BB = vegetation beating].
Figure. Map of the study area with the locations of actively used white-tailed eagle nests in the years 2009–2011. in Nest-site selection, breeding success, and diet of white-tailed eagles (Haliaeetus albicilla) in the Danube Delta, Romania
Figure. Map of the study area with the locations of actively used white-tailed eagle nests in the years 2009–2011.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.