Ribonuclease Inhibitor: Alpha/Beta Horseshoe-Shaped Structure [PDB:2BNH]
The ribonuclease inhibitor protein is a horseshoe-shaped structure that is built from a repeating leucine-rich motif that corresponds to a beta-strand/loop/alpha-helix unit [1, 2, 3, 4]. These units are arranged so that the inside part of the horseshoe contains a parallel beta-sheet, while alpha-helices form the outside part. The three-dimensional structure of the porcine ribonuclease inhibitor has been solved by x-ray crystallography [2, 3], and can be loaded by selecting Open from the File menu of the ProteinShader program and then using the file chooser box to select the 2BNH.pdb file.
Cartoon-style displays with halftoning
When the ribonuclease inhibitor is first loaded, it will be displayed as a pen-and-ink style drawing of ribbons and tubes as shown in Figure 1A. In the default orientation, the beta-strands (wide ribbons) are mostly obscured by the alpha-helices (spiral tubes), but the mouse can be dragged across the canvas to rotate the image and get a better sense of the protein's three-dimensional structure. The protein can be returned to its original orientation at any time by going to the Orientation menu menu above the canvas and selecting Original.
To switch from the Figure 1A image to the Figure 1B image, first drag the mouse horizontally or vertically across the canvas to get a side view of the horseshoe shape. Then go to the Decorations subpanel of the Control Panel on the right side of the canvas, and click on the β-Strands radio button to select All beta-strands. Next, use the Halftone Texture menu right below the Halftoning button to select a Vertical Bars pattern to map onto the surface of the beta-strand ribbons, and set the Bend Texture menu to None (the bend texture is applied to the middle of each segment of the ribbon that corresponds to an amino acid, and the intensity of the bend texture is scaled according to how curved the ribbon or tube segment is).
To fade out the loop regions that connect the beta-stands, go to the menu at the top right of the Control Panel and use it to change from the Decorations subpanel to the Cartoon Visibility subpanel. Click on the Loops radio button to select all loops, and then click on the Translucent button. By default, the button should be set to use 75% translucency, but the value can be changed by using the slider control below the button.