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Creators/Authors contains: "Cao, Yiwei"

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  1. null (Ed.)
  2. Abstract

    This study was undertaken to identify and characterize the first ligands capable of selectively identifying nicotinic acetylcholine receptors containing α7 and β2 subunits (α7β2‐nAChR subtype). Basal forebrain cholinergic neurons express α7β2‐nAChR. Here, they appear to mediate neuronal dysfunction induced by the elevated levels of oligomeric amyloid‐β associated with early Alzheimer's disease. Additional work indicates that α7β2‐nAChR are expressed across several further critically important cholinergic and GABAergic neuronal circuits within the central nervous system. Further studies, however, are significantly hindered by the inability of currently available ligands to distinguish heteromeric α7β2‐nAChR from the closely related and more widespread homomeric α7‐only‐nAChR subtype. Functional screening using two‐electrode voltage‐clamp electrophysiology identified a family of α7β2‐nAChR‐selective analogs of α‐conotoxin PnIC (α‐CtxPnIC). A combined electrophysiology, functional kinetics, site‐directed mutagenesis, and molecular dynamics approach was used to further characterize the α7β2‐nAChR selectivity and site of action of these α‐CtxPnIC analogs. We determined that α7β2‐nAChR selectivity of α‐CtxPnIC analogs arises from interactions at a site distinct from the orthosteric agonist‐binding site shared between α7β2‐ and α7‐only‐nAChR. As numerous previously identified α‐Ctx ligands are competitive antagonists of orthosteric agonist‐binding sites, this study profoundly expands the scope of use of α‐Ctx ligands (which have already provided important nAChR research and translational breakthroughs). More immediately, analogs of α‐CtxPnIC promise to enable, for the first time, both comprehensive mapping of the distribution of α7β2‐nAChR and detailed investigations of their physiological roles.

     
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  3. null (Ed.)
  4. Abstract

    Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the virus causing COVID‐19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor‐binding domain (RBD) of the spike protein, which binds to the human angiotensin‐converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD‐ACE2 interface through N501Y, Q498R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Among the Q493K and Q493R, we report that Q493R shows stronger binding to ACE2 than Q493K due to increased interactions. Our MST data confirmed that the Omicron mutations in RBD are associated with a five‐fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our results could help explain the Omicron variant's prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.

     
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  5. Abstract Motivation

    Glycan microarrays are capable of illuminating the interactions of glycan-binding proteins (GBPs) against hundreds of defined glycan structures, and have revolutionized the investigations of protein–carbohydrate interactions underlying numerous critical biological activities. However, it is difficult to interpret microarray data and identify structural determinants promoting glycan binding to glycan-binding proteins due to the ambiguity in microarray fluorescence intensity and complexity in branched glycan structures. To facilitate analysis of glycan microarray data alongside protein structure, we have built the Glycan Microarray Database (GlyMDB), a web-based resource including a searchable database of glycan microarray samples and a toolset for data/structure analysis.

    Results

    The current GlyMDB provides data visualization and glycan-binding motif discovery for 5203 glycan microarray samples collected from the Consortium for Functional Glycomics. The unique feature of GlyMDB is to link microarray data to PDB structures. The GlyMDB provides different options for database query, and allows users to upload their microarray data for analysis. After search or upload is complete, users can choose the criterion for binder versus non-binder classification. They can view the signal intensity graph including the binder/non-binder threshold followed by a list of glycan-binding motifs. One can also compare the fluorescence intensity data from two different microarray samples. A protein sequence-based search is performed using BLAST to match microarray data with all available PDB structures containing glycans. The glycan ligand information is displayed, and links are provided for structural visualization and redirection to other modules in GlycanStructure.ORG for further investigation of glycan-binding sites and glycan structures.

    Availability and implementation

    http://www.glycanstructure.org/glymdb.

    Contact

    wonpil@lehigh.edu

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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