The functioning of almost all proteins is based on their specific binding of other molecules. The specificity is based on several features of the protein. Especially important are the complementary shapes of the protein and its ligand. This allows them to join in a "lock and key" relationship. Other factors include polar/nonpolar interactions, electrostatic attraction due to charges, and hydrogen bonding.
Antibodies and T cell receptors recognize antigens ("foreign molecules") by
specifically binding them. Observe the complementary shapes of
the antigen and the antibody.
The antigen is a portion
of an envelope protein of the HIV virus. Not all of the antibody is shown (just one
light chain and two domains of a heavy chain). An intact antibody molecule actually
has two identical binding sites for the antigen.
If you have the chime plug-in, click on hexokinase and follow the directions in the new window for using the mouse button. Hexokinase phosphorylates glucose. ATP and glucose bind in the cleft between the two domains, a conformation change occurs, and a phosphate is transferred from the ATP to glucose. (Directions for obtaining the free Chime software can be found via the home page.)
Another option is to inspect alkaline phosphatase, which is the enzyme we used in lab. Click on alkaline phosphatase and follow the directions on the new page.
G-proteins (GTP binding proteins) are anchored to the inner surface of membranes and are activated following the binding of an extracellular regulatory molecule to a membrane receptor. During this activation, GTP replaces GDP on the G-protein. (GTP and GDP are nucleotides similar to ATP and ADP.)
If you have the Chime plug-in, click here to observe the binding of GTP to the G-protein and to compare the conformations of the G-protein with either GTP or GDP bound.
(The specific protein shown above is a ras G-protein, which we will study later in the quarter.)