User:Michael Patrick/Sandbox 1: Difference between revisions

This representation shows the protein as blue strands surround the heme ligand, with accompanying water molecules. This water is strongly attracted to the protein and is part of the structure of any crystalline protein.  <scene name='User:Michael_Patrick/Sandbox_1/1mbo-4/1'>Hiding the water</scene> reveals that the overall tertiary shape is much like a hockey puck. The α-helix is a prominent secondary structural component. The α-helices can be shown to form two layers of backbone, and myoglobin can be classified as an antiparallel α-helix type of globular protein. The [[Myoglobin]] page gives more detail on the secondary structure. The prosthetic group of myoglobin is a <scene name='User:Michael_Patrick/Sandbox_1/1mbo-5/1'>heme</scene>, and as shown here it is inserted into a pocket which is nonpolar. His 93 is the fifth ligand chelated to Fe2+ (the other four are the nitrogens in the pyrole rings), and it binds to one side of the heme. Show protein atoms displayed as spacefill that are within 0.5 nm of the heme. These are the atoms which form the surface of the heme pocket and serve as a reminder that except for the ones on the surface of the molecule most of these atoms are carbon atoms and produce a nonpolar environment for the heme. This nonpolar, water-excluding environment is important for the function of myoglobin. Whenever Fe2+ is in an aqueous environment and it contacts O2, Fe2+ is oxidized to Fe3+. Myoglobin with a heme containing Fe3+ (called metmyoglobin) can not fulfill its physiological function and therefore must be degraded