Surface Representation of a Protein-Drug Complex
As most drugs bind at the surface of the protein, it is a common task to visualize the protein surface in order to locate the binding pocket. This is a fairly trivial task if a structure of the protein-ligand complex is available from the PDB. Imagine for moment that your task is to save the mankind from the avian influenza pandemic by coming up with a new drug that targets the influenza enzyme neuraminidase. The first goal is to locate the substrate or drug binding pocket in the influenza neuraminidase.
- Reopen or reinitialize (File -> Reinitialize) PyMOL.
- From the Plugin menu, select PDB Loader Service, and enter 2HT8.
- Slowly rotate the molecule on the screen by holding down the left mouse button while dragging. Try to see where the bound ligand is. It is rather hard to identify the ligand in this representation.
- Quick inspection of the PDB page for structure 2HT8 reveals that the ligand is called G39. You could also get the ligand name by showing the Sequence from the Display menu. The ligands typically appear after the protein sequence.
- Coloring is a very useful approach for identifying ligands. There are several ways to color the ligand. For example, you can type color yellow, resn G39 to color the bound ligand in a distinct color. Alternatively, you can click on the label G39 in the sequence window. This creates a new selection (sele) in the right-hand task bar. You can rename this to (ligand) using the Action rename selection. You can then assign the color and picking yellow from the Colors. Rotate the molecule and locate the bound ligand in the structure.
- Create an object for your protein by typing into the PyMOL command line (either in the Tcl/Tk GUI, or in the Viewer), the following PyMOL command: create protein, chain A. If a protein has more than one chain, you should include all of them (e.g. create protein, chain A and chain B and chain C). Notice that the protein object was added to the right-hand task bar.
- If you have not done so already, create an object for your ligand by typing create ligand, resn G39. The program will automatically zoom into the ligand. Zoom out by holding the right mouse button while dragging up. If needed, adjust the cut plane with the mouse button that is tied to the Slab function, or select Clip -> Nothing from the Display menu.
- Color your protein object in your favourite color. For example, to color the protein in a peaceful light wheat color, type color wheat, protein. Notice that not much changed because the original object (2HT8) is still shown by atom colors. To hide this object, click H for Hide, then everything for the 2HT8 row in the right-hand task-bar.
- Show the surface for the protein by typing show surface, protein
- Examine the binding pocket. Does the drug fill all of the pocket? Could the pocket possibly accommodate a longer ether side chain?
- Change the representation of ligand to stick representation by typing show sticks, ligand
- Change the representation of ligand to CPK representation by typing show spheres, ligand
- Reduce the scale of the spheres by typing set sphere_scale, 0.33. You now have "ball-and-stick" model of the ligand.
- You have lots of control over many parameters that control the visual representation of the structure in PyMOL. For example, you could pick one of the many coloring schemes for the ligand from the Color: menu in the right-hand task-bar.
- Save a picture of the view on the screen using Save Image under File menu.
- The monochrome surface view is good for examining the steric requirements for binding but hides the underlying chemical nature of the active site. We will see later in the course how map electrostatic potentials on the surface of the proteins with PyMOL.
Examine how the ligand (which is the anti-flu drug oseltamivir, a.k.a. Tamiflu) fits into the pocket. Do you think one can alter the structure of this ligand such that the presently empty parts of the pocket are used to make favorable contacts?