Journal: Nature Communications

Article Title: Functional and structural characterization of a two-MAb cocktail for delayed treatment of enterovirus D68 infections

doi: 10.1038/s41467-021-23199-5

Figure Lengend Snippet: a Cryo-EM density map of EV-D68/8F12 complex viewed along the two-fold axis. The color bar indicates the corresponding radius from the center of the particle (unit in Å). The black triangle indicates one icosahedral asymmetric unit. b Atomic model of EV-D68/8F12 complex viewed along the two-fold axis. 8F12-V H , 8F12-V L , VP1, VP2, VP3, and VP4 are colored in cyan, hot pink, blue, green, red, and yellow, respectively. Models for only the variable regions of 8F12 Fab were built. c Density map with fitted models of four adjacent protomers around the two-fold axis. 8F12 Fab was removed for clarity. The black pentagon, triangle, and ellipse represent the five-fold, three-fold, and two-fold axes, respectively. d Binding Interface between EV-D68 protomer and 8F12 Fab. The canyon, north rim, and south rim are indicated by black arrows. The five-fold axis is also shown. e Zoom-in views of the three dotted boxed region in Panel ( d ), showing interactions between VP2 EF loop, VP1 BC, GH loops, and VP3 C-terminus of EV-D68 and the CDR and framework (FR) regions of 8F12 Fab. The images were rotated by various angles in order to better show the interactions. Possible hydrogen bonds in the interaction interface are indicated by black dashed lines. The residues of viral proteins are identified: the first digit represents viral capsid protein 1, 2, or 3, and the next three digits indicate position from the N-terminal. f Roadmap illustrating the footprints of 8F12 Fab on the EV-D68 virion surface, generated using RIVEM (Radial Interpretation of Viral Electron density Maps; reference ). Polar angles θ and φ represent latitude and longitude, respectively. Viral residues are colored according to the radius. The color bar indicates the corresponding radius (unit in Å). The V L and V H are indicated by white and yellow contour lines, respectively. Footprint of the sialic acid receptor (generated using EV-D68-6’SLN model, PDB: 5BNO) is also shown in orange. The icosahedral asymmetric unit is indicated by a black triangle.

Article Snippet: Previously published cryo-EM structures of EV-D68 strain 18947 were used as initial models.

Techniques: Cryo-EM Sample Prep, Binding Assay, Generated

Journal: Nature Communications

Article Title: Functional and structural characterization of a two-MAb cocktail for delayed treatment of enterovirus D68 infections

doi: 10.1038/s41467-021-23199-5

Figure Lengend Snippet: a – c Cryo-EM density maps of EV-D68/2H12, resolved in three different states (namely S1, S2, and S3), viewed along the two-fold axes. The color bar indicates the corresponding radius (unit in Å). d – f Density map with fitted model of the two-fold related protomers for the S1 ( d ), S2 ( e ), and S3 ( f ) states. Yellow dashed rectangles indicate the major differences among the three states. 2H12 Fab was removed for clarity. g – i Cryo-EM map central section of S1 ( g ), S2 ( h ), and S3 ( i ) states. j Binding Interface between EV-D68 protomer and 2H12 Fab in the S1 state. 2H12-V H , 2H12-V L , VP1, VP2, VP3, and VP4 are colored in cyan, hot pink, blue, green, red, and yellow, respectively. k Zoom-in view of the five dotted boxed regions in panel ( j ), showing interaction between VP2 EF loop, VP1 GH loop, and VP3 C-terminus of EV-D68 and the CDR and FR regions of 2H12 Fab. Black dashed lines indicate possible hydrogen bonds, and springs indicate both hydrogen bonds and salt bridges. l Roadmap shows footprint of 2H12 Fab (state S1) on the EV-D68 virion surface. The V L and V H are indicated by white and yellow contour lines, respectively. Footprint of the sialic acid receptor (generated using the PDB model 5BNO) is colored orange. The color bar indicates the corresponding radius (unit in Å).

Article Snippet: Previously published cryo-EM structures of EV-D68 strain 18947 were used as initial models.

Techniques: Cryo-EM Sample Prep, Binding Assay, Generated

Journal: PLoS ONE

Article Title: Reliable Screening of Dye Phototoxicity by Using a Caenorhabditis elegans Fast Bioassay

doi: 10.1371/journal.pone.0128898

Figure Lengend Snippet: List of dyes used in the present work, with reference to the chemical group, Colour Index number (C.I.), electric charge (Z), source, and previously reported photoactivity (if any, and only for well known cases).

Article Snippet: 24. Phloxine B (PhB) , Hydroxyxanthene , 45410 , 2− , Panreac , + , Rasooly & Weisz 2002, Herkovits et al . 2007.

Techniques: Activity Assay