Journal: International Journal of Molecular Sciences

Article Title: Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

doi: 10.3390/ijms241813914

Figure Lengend Snippet: AlphaFold predicted structures of ornithine transcarbamylase (OTC) and arginine/ornithine antiporter (AOA) from P. aeruginosa . ( A ) shows a multiple sequence alignment heatmap showing coverage of the query sequences for OTC. The black line indicates the relative coverage. ( B ) pLDDT (prediction of performance on the local distance difference test) plot shows model confidence per position of the amino acid sequence for each of the five models generated (pLDDT > 90, high confidence). ( C ) shows heatmaps of the predicted aligned error for each residue for the five models generated for OTC. Blue sections represent regions with low predicted error, whereas red indicates regions of higher predicted error. ( D – F ) show the equivalent plots for AOA. ( G , H ) show the final models of OTC and AOA, respectively, following Amber relaxation of the optimal model. Images were generated in PyMol molecular modeling software.

Article Snippet: Unfortunately, as a solved crystal structure for P. aeruginosa , OTC (encoded by arcB ), and AOA (encoded by arcD ), we used Deepmind’s AlphaFold protein structure prediction run from the GitHub site [ ].

Techniques: Sequencing, Generated, Residue, Software

Journal: microPublication Biology

Article Title: Characterization of temperature-sensitive alleles of the septation initiation network protein Mob1 in Schizosaccharomyces pombe

doi: 10.17912/micropub.biology.001595

Figure Lengend Snippet: (A) The mutations encoded by each mob1 allele are listed. (B) The indicated strains were grown in liquid YE media at 25°C until they reached mid-log phase and then adjusted to the same cell concentrations measured by optical density (Moreno et al., 1991). Next, 10-fold serial dilutions were made and 2.5 µL of each was spotted on YE agar plates and incubated at the indicated temperatures for 2-3 days prior to imaging. The spot assays were done twice and a representative is shown. (C) The indicated strains were grown in liquid YE media at 25˚C. Samples were collected before and again after growing the cells for an additional 3.5 hours at 36˚C. The cells were then fixed and stained with DAPI and methylene blue. Representative images are shown. The experiment was performed in duplicate. Scale bar, 5 µm. (D) The number of nuclei per cell (top), and the percentage of septated cells (middle) and lysed cells (bottom) were quantified at 36°C from the same experiments as in C. N≥200 cells of each genotype. (E) Ribbon diagram of a structural model of S. pombe Mob1 using AlphaFold3 (Abramson et al., 2024). The positions of the N- and C-termini and the positions of the mutated residues in the mob1 alleles are indicated. (F) Schematic of sid2 gene product (drawn to scale). Numbers indicate amino acid position (top). Ribbon diagram of a structural model of S. pombe Mob1 bound to the Sid2 regulatory region and kinase domain using AF3. Mob1 is in magenta, the Sid2 regulatory region is in green, and the Sid2 kinase domain is in cyan (bottom).

Article Snippet: AlphaFold3 structural prediction Protein structure predictions were generated with the AlphaFold3 server (Abramson et al., 2024) and visualized using the PyMOL molecular graphics system (version 3.0, Schrodinger, LLC).

Techniques: Comparison, Incubation, Imaging, Staining

Journal: PLOS ONE

Article Title: Functional characterization of Cinnamate 4-hydroxylase gene family in soybean ( Glycine max )

doi: 10.1371/journal.pone.0285698

Figure Lengend Snippet: (A) Schematic diagram of gene structure of GmC4Hs . Exon-intron structures of GmC4H s were compiled from Phyotozome 13 database ( https://phytozome-next.jgi.doe.gov/info/Gmax_Wm82_a4_v1 ) drawn by Gene Structure Display Server 2.0. (B) Multiple sequence alignment of deduced amino acid sequences of candidate GmC4Hs with characterized C4H from other plant species. Identical and similar amino acid residues are indicated by black and gray shades, respectively. Five P450 motifs: the PPGP, the oxygen-binding, the ETLR, the PERF and the heme-binding motifs are indicated by different colored rectangles. Asterisk (*) and red font indicate critical amino acid residues for substrate binding. Accession numbers are as indicated: MsC4H, P37114; CaC4H, O81928; AtC4H, P92994; CsC4H, ASU87408; SbC4H, Q94IP1.

Article Snippet: For docking study, an AlphaFold2 based plant cytochrome P450 protein structure prediction database (PCPD) was used along with imbedded heme cofactor in the structure [ https://p450.biodesign.ac.cn [ ]].

Techniques: Sequencing, Binding Assay