ProteinShader Tutorial: 3POR

Porin: Transmembrane Beta-Barrel [PDB:3POR]

The porin protein is a transmembrane beta-barrel structure that serves as a water-filled channel that allows nutrients and waste products to diffuse through the outer membrane of gram-negative bacteria [1, 2]. The complete porin protein is composed of three identical subunits, each of which has a functional channel. The three-dimensional structure of porin from Rhodobacter capsulatus has been solved by x-ray crystallography [2, 3], and can be loaded into the ProteinShader program by selecting Open from the File menu and then using the file chooser box to select the 3POR.pdb file.

Cartoon-style displays with halftoning

When the porin subunit is first loaded, it will be displayed as a pen-and-ink style drawing of ribbons and tubes similar to what is shown in Figure 1. To obtain something closer to the image in Figure 1A, first go to the Decorations subpanel and click on the Extra Lines checkbox. The extra lines that show up at regular intervals along the ribbons and tubes mark the length of a ribbon or tube that corresponds to an individual amino acid. Now click on the β-Strands radio button to select all beta-strands, and select Hatching 1 from the Bend Texture menu. The bend texture is the pattern that is applied to the middle of each ribbon segment that corresponds to an amino acid, and the intensity of the texture is scaled according to how bent the ribbon segment is.

To de-emphasize the loop regions, switch from the Decorations subpanel to the Cartoon Visibility subpanel and click on the Loops radio button before pressing the Translucent button. The degree of translucency can be adjusted with the slider control below the button. The semi-transparent loops stand out best against a white background, so if the background is currently another color, use the Background menu above the canvas to select White. The orientation in Figure 1A, which shows one end of the open channel, is the default view (Original or Front from the Orientation menu above the canvas). To obtain a side view of the beta-barrel as shown in Figure 1B, select Bottom from the Orientation menu, and then drag the mouse across the canvas to make minor adjustments to the orientation.

Figure 1. Ribbons and tubes style display of a subunit of porin. (A) View of one open end of the beta-barrel structure. (B) Side view of the beta-barrel structure. The beta-strands are shown as ribbons, three small alpha-helices are shown as tubes, and the loop regions are thin translucent ribbons. The images were captured as described in the Saving Images section of the tutorials main page.

Adding side chains to one loop

The porin channel is partially blocked by a loop region (plus a small alpha-helix) between beta-strands 5 (G68-D74) and 6 (V118-A125) [1, 4]. This loop, which is labeled as loop 7 in the 3POR structure, fits inside the channel, creating a narrow region region called the eyelet. The eyelet is about 8 angstroms in diameter and 9 angstroms in length, and determines the upper limit on the size of solute molecules that can diffuse through the channel.

To visualize loop 7, assuming a starting point of Figure 1B, first select Original from the Orientation menu above the canvas to get back to the orientation shown in Figure 1A. Then go to the Cartoon Visibility subpanel and select Loop 7 from the menu below the Loops radio button before clicking on the Opaque button. Next go back to the Decorations subpanel, and with Loop 7 still selected, click the Plain button at the very bottom of the subpanel. The default color for loop regions is gray, so switch from the Decorations subpanel to the Cartoon Color subpanel, and with Loop 7 still selected, use the Chooser button to open a color chooser dialog box, and select a shade of red. The image should look similar to Figure 2A, although the exact orientation will need to be adjusted by dragging across the canvas with the mouse.

To get a better sense of how much of the channel is filled by loop 7, its amino acid side chains can be shown in a space filling style display as in Figure 2B. First, use the menu at the top right of the Control Panel to switch to the Cartoon Side Chains subpanel. After checking that Loop 7 is still selected, click on the Space Filling button. By default, the spheres used in a space filling style display are colored by atom type. To color them by amino acid type, switch to the Atom Color subpanel, select Loop 7 in the menu below the Loops radio button, and then click on the Amino Acid button at the very bottom of the subpanel. The image should now be very close to Figure 2B.

Figure 2. A loop region narrows the size of the porin channel. (A) The same image as Figure 1A, except that loop 7 is shown in red, and the protein has been tilted slightly to get a better view of the loop. (B) Same as part A, but the amino acid side chains of loop 7 are shown as a space filling style display. The side chains are colored by amino acid type. The images were captured as described in the Saving Images section of the tutorials main page.

References

1. Brandon C, Tooze J: Membrane Proteins. In Introduction to Protein Structure. 2nd edition. New York: Garland Publishing; 1998: 223-250.

2. Weiss MS, Schulz GE: Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution. J Mol Biol 1993, 231: 817-824.

3. Porin PDB entry 3POR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3POR]

4. Weiss MS, Abele U, Weckesser J, Welte W, Schiltz E, Schulz GE: Molecular architecture and electrostatic properties of a bacterial porin. Science 1991, 254: 1627-1630.