scholarly journals Computational insight into the catalytic implication of head/tail-first orientation of arachidonic acid in human 5-lipoxygenase: consequences for the positional specificity of oxygenation

2016 ◽  
Vol 18 (33) ◽  
pp. 23017-23035 ◽  
Author(s):  
Patricia Saura ◽  
Jean-Didier Maréchal ◽  
Laura Masgrau ◽  
José M. Lluch ◽  
Àngels González-Lafont
Keyword(s):  
Arachidonic Acid ◽  
Binding Modes ◽  
Positional Specificity ◽  
Multi Scale ◽  
Insight Into

Using a multi-scale approach to search for the arachidonic acid binding modes that determine the catalytic specificity of human 5-LOX.

scholarly journals Complex community responses underpin biodiversity change following invasion

2021 ◽  
Author(s):  
Alessandra R. Kortz ◽  
Anne E. Magurran
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Spatial Scales ◽  
Species Abundance ◽  
Ecological Systems ◽  
Multi Scale ◽  
Mechanistic Approach ◽  
Α Diversity ◽  
Biodiversity Change ◽  
Insight Into

AbstractHow do invasive species change native biodiversity? One reason why this long-standing question remains challenging to answer could be because the main focus of the invasion literature has been on shifts in species richness (a measure of α-diversity). As the underlying components of community structure—intraspecific aggregation, interspecific density and the species abundance distribution (SAD)—are potentially impacted in different ways during invasion, trends in species richness provide only limited insight into the mechanisms leading to biodiversity change. In addition, these impacts can be manifested in distinct ways at different spatial scales. Here we take advantage of the new Measurement of Biodiversity (MoB) framework to reanalyse data collected in an invasion front in the Brazilian Cerrado biodiversity hotspot. We show that, by using the MoB multi-scale approach, we are able to link reductions in species richness in invaded sites to restructuring in the SAD. This restructuring takes the form of lower evenness in sites invaded by pines relative to sites without pines. Shifts in aggregation also occur. There is a clear signature of spatial scale in biodiversity change linked to the presence of an invasive species. These results demonstrate how the MoB approach can play an important role in helping invasion ecologists, field biologists and conservation managers move towards a more mechanistic approach to detecting and interpreting changes in ecological systems following invasion.

scholarly journals Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics

Biomolecules ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 61 ◽  
Author(s):  
Fernando Prieto-Martínez ◽  
José Medina-Franco
Keyword(s):  
Kinase Inhibitors ◽  
Binding Mode ◽  
Binding Modes ◽  
Ligand Interaction ◽  
Bet Inhibitors ◽  
Protein Ligand Interaction ◽  
Brd4 Inhibition ◽  
Dynamics Simulations ◽  
Insight Into

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative, and antineoplastic activities. Recently, different studies showed that flavonoids have the potential to inhibit bromodomain and extraterminal (BET) bromodomains. Previous reports suggested that flavonoids bind between the Z and A loops of the bromodomain (ZA channel) due to their orientation and interactions with P86, V87, L92, L94, and N140. Herein, a comprehensive characterization of the binding modes of fisetin and the biflavonoid, amentoflavone, is discussed. To this end, both compounds were docked with BET bromodomain 4 (BRD4) using four docking programs. The results were post-processed with protein–ligand interaction fingerprints. To gain further insight into the binding mode of the two natural products, the docking results were further analyzed with molecular dynamics simulations. The results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was experimentally tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as the basis for scaffold optimization and the further characterization of flavonoids as BET inhibitors.

scholarly journals First-principles insight into CO hindered agglomeration of Rh and Pt single atoms on m-ZrO2

2020 ◽  
Vol 10 (17) ◽  
pp. 5847-5855
Author(s):  
Minttu M. Kauppinen ◽  
Marko M. Melander ◽  
Karoliina Honkala
Keyword(s):  
Thermodynamic Stability ◽  
First Principles ◽  
Single Atom ◽  
Reaction Conditions ◽  
Multi Scale ◽  
Single Atoms ◽  
Thermodynamic Framework ◽  
Insight Into ◽  
Non Equilibrium

Kinetic and thermodynamic stability of single-atom and nanocluster catalysts is addressed under reaction conditions within a DFT-parametrised multi-scale thermodynamic framework combining atomistic, non-equilibrium, and nanothermodynamics.

New insight into the binding modes of TNP-AMP to human liver fructose-1,6-bisphosphatase

2016 ◽  
Vol 165 ◽  
pp. 155-160 ◽  
Author(s):  
Xinya Han ◽  
Yunyuan Huang ◽  
Rui Zhang ◽  
San Xiao ◽  
Shuaihuan Zhu ◽  
...  
Keyword(s):  
Human Liver ◽  
Binding Modes ◽  
Fructose 1,6 Bisphosphatase ◽  
Insight Into

scholarly journals Insight into the Binding and Hydrolytic Preferences of hNudt16 Based on Nucleotide Diphosphate Substrates

2021 ◽  
Vol 22 (20) ◽  
pp. 10929
Author(s):  
Magdalena Chrabąszczewska ◽  
Maria Winiewska-Szajewska ◽  
Natalia Ostrowska ◽  
Elżbieta Bojarska ◽  
Janusz Stępiński ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Ligand Binding ◽  
Regulatory Role ◽  
Stacking Interactions ◽  
Binding Modes ◽  
Biological Functions ◽  
Insight Into ◽  
Potential Regulatory Role

Nudt16 is a member of the NUDIX family of hydrolases that show specificity towards substrates consisting of a nucleoside diphosphate linked to another moiety X. Several substrates for hNudt16 and various possible biological functions have been reported. However, some of these reports contradict each other and studies comparing the substrate specificity of the hNudt16 protein are limited. Therefore, we quantitatively compared the affinity of hNudt16 towards a set of previously published substrates, as well as identified novel potential substrates. Here, we show that hNudt16 has the highest affinity towards IDP and GppG, with Kd below 100 nM. Other tested ligands exhibited a weaker affinity of several orders of magnitude. Among the investigated compounds, only IDP, GppG, m7GppG, AppA, dpCoA, and NADH were hydrolyzed by hNudt16 with a strong substrate preference for inosine or guanosine containing compounds. A new identified substrate for hNudt16, GppG, which binds the enzyme with an affinity comparable to that of IDP, suggests another potential regulatory role of this protein. Molecular docking of hNudt16-ligand binding inside the hNudt16 pocket revealed two binding modes for representative substrates. Nucleobase stabilization by Π stacking interactions with His24 has been associated with strong binding of hNudt16 substrates.

scholarly journals TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models

2021 ◽  
Author(s):  
Rastko Ciric ◽  
William Thompson ◽  
Romy Lorenz ◽  
Mathias Goncalves ◽  
Eilidh MacNicol ◽  
...  
Keyword(s):  
Access Management ◽  
Multi Scale ◽  
Important Challenge ◽  
Brain Models ◽  
The Brain ◽  
Fair Sharing ◽  
Insight Into

Abstract Reference anatomies of the brain and corresponding atlases play a central role in experimental neuroimaging workflows and are the foundation for reporting standardized results. The choice of such references —i.e., templates— and atlases is one relevant source of methodological variability across studies, which has recently been brought to attention as an important challenge to reproducibility in neuroscience. TemplateFlow is a publicly available framework for human and nonhuman brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR —findable, accessible, interoperable, reusable— principles. TemplateFlow supports a multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species, thereby contributing to increasing the reliability of neuroimaging results.

scholarly journals Multi-Scale Simulations Yield Insight into Protein Diffusion and Stability in Crowded Environments

2019 ◽  
Vol 116 (3) ◽  
pp. 38a ◽  
Author(s):  
Stepan Timr ◽  
Simone Melchionna ◽  
Philippe Derreumaux ◽  
Fabio Sterpone
Keyword(s):  
Protein Diffusion ◽  
Multi Scale ◽  
Crowded Environments ◽  
Insight Into
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