Specific Binding By Proteins




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. Below are some figures that show the "lock and key" nature of this specific binding.

Antigen Binding to Antibodies or T cell Receptors

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.



Substrate Binding to an Enzyme (OPTIONAL)

If your computer has Java, 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.

Another option is to inspect alkaline phosphatase, which has the product of the reaction (phosphate) attached to its catalytic site. Click on alkaline phosphatase.