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#receptor

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Public
Giuseppe Michieli

#Receptor #Binding Specificity of a #Bovine #H5N1 #Influenza Virus, BioRxIV: biorxiv.org/content/10.1101/20

We found that A/bovine/OH/B24OSU-432/2024 preferentially binds to #avian type #receptors (alpha2,3-sialosides). Sequence alignments showed that A/bovine has maintained aa in its HA associated with alpha2,3-sialoside (avian) specificity. We conclude that while we find no evidence that A/bovine has acquired human virus RB specificity, ongoing efforts must be placed on monitoring for this trait.

bioRxiv · Receptor Binding Specificity of a Bovine A(H5N1) Influenza VirusOutbreaks in the US of highly pathogenic avian influenza virus (H5N1) in dairy cows have been occurring for months creating new possibilities for direct contact between the virus and humans. Eisfeld et al. examined the pathogenicity and transmissibility of a bovine HPAI H5N1 virus isolated from New Mexico in a series of in vitro and in vivo assays. They found the virus has a dual human- and avian virus-like receptor-binding specificity as measured in a solid phase glycan binding assay. Here, we examined the receptor specificity of a bovine HPAI H5N1 virus (A/bovine/OH/B24OSU-432/2024, H5N1, clade 2.3.4.4b) employing four different assays including glycan array technology, bio-layer interferometry (BLI), a solid phase capture assay and hemagglutination of glycan remodeled erythrocytes. As controls, well characterized avian (A/Vietnam/1203/2004, H5N1, clade 1) and human (A/CA/04/2009, H1N1) IAVs were included that bind alpha2,3- and alpha2,6-sialosides, respectively. We found that A/bovine/OH/B24OSU-432/2024 preferentially binds to avian type receptors (alpha2,3-sialosides). Furthermore, sequence alignments showed that A/bovine has maintained amino acids in its HA associated with alpha2,3-sialoside (avian) receptor specificity. We conclude that while we find no evidence that A/bovine has acquired human virus receptor binding specificity, ongoing efforts must be placed on monitoring for this trait. ### Competing Interest Statement The authors have declared no competing interest.
Public
Martin Vögele

New #preprint about PENSA, our flexible #OpenSource software package for comprehensive and thorough investigation of biomolecular conformational ensembles:

arxiv.org/abs/2212.02714

In three real-world examples, we show how it can be used to understand an #enzyme mechanism, #DNA #forcefield parameters, and #signaling in an #opioid #receptor.

Please share widely with the #MolecularDynamics #simulation #CompChem #MolBio #StructuralBiology #GPCR communities!
Feedback and ideas are always welcome.

arXiv.orgSystematic Analysis of Biomolecular Conformational Ensembles with PENSAMolecular simulations enable the study of biomolecules and their dynamics on an atomistic scale. A common task is to compare several simulation conditions - like mutations or different ligands - to find significant differences and interrelations between them. However, the large amount of data produced for ever larger and more complex systems often renders it difficult to identify the structural features that are relevant for a particular phenomenon. We present a flexible software package named PENSA that enables a comprehensive and thorough investigation into biomolecular conformational ensembles. It provides a wide variety of featurizations and feature transformations that allow for a complete representation of biomolecules like proteins and nucleic acids, including water and ion cavities within the biomolecular structure, thus avoiding bias that would come with manual selection of features. PENSA implements various methods to systematically compare the distributions of these features across ensembles to find the significant differences between them and identify regions of interest. It also includes a novel approach to quantify the state-specific information between two regions of a biomolecule which allows, e.g., the tracing of information flow to identify signaling pathways. PENSA also comes with convenient tools for loading data and visualizing results in ways that make them quick to process and easy to interpret. PENSA is an open-source Python library maintained at https://github.com/drorlab/pensa along with an example workflow and a tutorial. Here we demonstrate its usefulness in real-world examples by showing how it helps to determine molecular mechanisms efficiently.
Public
Joseph P.

The ATP is then converted to adenosine by an enzyme called ectonucleotidase. The adenosine can then bind to either an inhibitory #receptor (A2A or A1) or an excitatory receptor (A2A) on the #postsynaptic neuron. The adenosine is then taken up by a transporter called equilibrative nucleoside transporter (ENT) and is converted to #ADP and ATP. Finally, the A2A adenosine receptors on the #blood vessels cause a vasodilatory effect.

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