Human Growth Hormone: Four Alpha-Helix Bundle [PDB:1HGU]
The core of the hGH (human growth hormone) protein is a four-helix bundle structure comprised of two pairs of parallel alpha-helices that are joined in an antiparallel fashion . X-ray crystallography has been used to determine the three-dimensional structure of the hGH protein by itself [2, 3] and complexed with the extracellular domain of its receptor [4, 5]. To load the hGH protein structure, select Open from the File menu of the ProteinShader program and then use the file chooser box to select the 1HGU.pdb file.
Cartoon-style displays with side chains
When the hGH protein is first loaded, it will be displayed as a pen-and-ink style drawing of ribbons and tubes. To switch to an all tubes style display as shown in Figure 1A, go to the Style menu above the canvas and select Tubes from the Cartoon submenu. The tubes representing alpha-helices have a thicker diameter and are drawn a little more darkly than the loop regions connecting them. The amino-terminus of the polypeptide chain is seen at the top left of the figure, while the carboxyl-terminus is near the top center. What appears to be a chain termination near the bottom right of Figure 1A is in fact a gap in the structure. Amino acid residues 37 to 39 are disordered in the 1HGU crystal structure, presumably because they are part of a flexible loop that is moving around in the solvent that makes up part of the crystal. When data on atom positions is missing from a PDB file, the ProteinShader program does not attempt to fill in missing parts of a tube or ribbon, but rather simply puts end caps on the tube or ribbon before and after the gap.
Amino acid side chains that strongly modulate binding of hGH to its receptor have been identified by a strategy known as alanine-scanning mutagenesis . To illustrate these side chains as shown in Figure 1B, use the menu at the top right of the Control Panel to switch from the Decorations subpanel to the Cartoon Side Chains subpanel. Then go to the list of amino acids on the left side of the Control Panel and left-click with the mouse to select residues number 10, 54, 56, 58, 64, 68, 171, 172, 174, 175, 176, 178, 182, and 185 while holding down the keyboard Ctrl key (command key on Macintosh). When the first of these residues was clicked on, the menu under the Selected radio button near the top of the Control Panel should have automatically switched to Residues, so clicking the Space Filling button should now cause the side chains of the selected residues to appear as spheres. By default, the spheres are colored by atom type. To color by amino acid type, switch from the Cartoon Side Chainssubpanel to the Atom Color subpanel and use the Amino Acid button at the very bottom of the subpanel.
To get a better look at the spatial arrangement of the sides chains that affect receptor binding, use the left-side mouse button to drag the mouse across the canvas and rotate the image to a position similar to Figure 1C (the protein can be returned to its original orientation at any time by using the Orientation menu). For a more schematic view of the side chains, go back to the Cartoon Side Chains subpanel, and, after making sure that Residues is still selected in the menu under the Selected radio button, click on the Balls and Sticks button. To color the balls by atom type, go back to the Atom Color subpanel and use the Atom Type button. To obtain an image similar to Figure 1D, use the Style menu above the canvas to select Ribbons from the Cartoon submenu, and then go back to the Decorations subpanel, choose Model from the menu under the Selected radio button, and select Hatching 1 from the Bend Texture menu.
In addition to rotating the image with the mouse, the center mouse button or scroll-wheel can be used to zoom in and out on the image, while the right-side mouse button can be used for moving the image up and down or side to side (see Mouse Motion Control section for details and for Macintosh single-button mouse options). By using these mouse manipulations, it should be fairly easy to obtain a closeup view of the side chains similar to Figure 2.