Author: Anonymous

  Nomura, K., Andreazza, F., Cheng, J., Dong, K., Zhou, P.,…

  Nomura, K., Andreazza, F., Cheng, J., Dong, K., Zhou, P., & He, S. Y. (2023). Bacterial pathogens deliver water- and solute-permeable channels to plant cells. Nature, 621(7979), 586–591.  This is the reference information for an article that appeared recently in the journal Nature about a protein secreted by pathogenic bacteria that cause brown spot in beans, bacterial spec in tomatoes and fire blight in fruit trees. These bacteria infect plant cells, causing them to drain cell material, leading to cell death. Because of the economic impact of this infection, groups have worked for years to elucidate the mechanism by which this protein infects plant cells. The Nature article reports that alpha fold in combination with cryo EM produced a protein structure that led to the solution of this 30-year-old puzzle.  Below is a portion of the text from the article along with one of the figures depicting the structure of the protein.  Based upon the structural information in the text and the figure, suggest a possible way this protein could drain a plant cell such that cell death results. Image Description  AlphaFold2 analysis and cryo-EM imagingTo gain functional insights into the AvrE family of bacterial effectors, we constructed their three-dimensional models predicted by AlphaFold226 using the fast homology search of MMseqs2 (ColabFold) 27. The predicted AlphaFold2 models of DspE from E. amylovora, DspE from P. carotovorum, AvrE from P. syringae pv. tomato (Pst) DC3000 and WtsE from P. stewartii (Fig. 1 and Extended Data Figs. 1 and 2) all reveal an overall similar architecture resembling a mushroom, with a prominent central ẞ-barrel forming the stem, which is surrounded by a globular amino-terminal domain (E. amylovora DspE: K298-H672), a WD40 repeat domain (H673-P912) and two perpendicularly arranged helix bundles (E998-T1222 and A1567-H1647) on the top. The predicted domain arrangement is supported by our cryo- EM imaging of E. amylovora DspE, for which the two-dimensional class averages clearly reveal an overall similar top view to that of the AlphaFold model, with circularly arranged globular domains surrounding a central pore (Fig. 1a,b). Image Description  Fig. 1: Model and cryo-EM images of E. amylovora DspE. (a) Three-dimensional model generated by AlphaFold2 using MMseqs2 (ColabFold). DspE (residues 298–1838) is shown in a rainbow color gradient, with the N terminus in blue and the C terminus in red. (b) Cryo-EM two-dimensional class averages of DspE, revealing a circular arrangement of domains around a pore. Scale bars, 5 nm. (c) Surface representation of DspE. (d) Sliced view of DspE. In (c, d), residues are colored based on hydrophobicity.            

These figures show the protein structure of hemocyanin, the…

These figures show the protein structure of hemocyanin, the copper-containing oxygen transport protein in arthropods, octopuses, and squids. The two figures are of the same protein, one a front view and a back view—a 180o rotation about the vertical axis. The small diamond-shaped dicopper structure is the in the center. This molecule is responsible for the blue color of the oxygenated blood of these animals. Image Description A 3D representation of a protein structure, displaying its complex folding and various regions. The protein features several alpha helices, depicted as spirals, and beta sheets, depicted as arrows, interconnected by loops. The structure is colored with a gradient from blue (N-terminus) to red (C-terminus), illustrating the flow of the polypeptide chain. This visual highlights the intricate architecture crucial for the protein’s specific function. In the three-strand flat ribbon structure, the arrowhead of the middle strand is in the opposite direction from the two other strands. Referring to the figure, briefly describe the secondary structure of the three-strand flat ribbon structure at the top of this protein. (1pt.) The sequence of the vertical helix on the right-hand side of the first figure is IPELEEHLKEI. Briefly explain why this helix has both a polar and a nonpolar side and which way you would expect to find the nonpolar side facing relative to the rest of the protein’s structure. (2 pts.)