Sandbox Mati: Difference between revisions
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===About This Structure=== | ===About This Structure=== | ||
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<Structure load='1mbo' size='500' frame='true' align='right' caption='oxymyoglobin ([[1mbo]])' scene='Insert optional scene name here' /> | |||
This is a cartoon representation of the myoglobin molecule. Not shown are the layers of water bound to its surface. This water is strongly attracted to the protein and is part of the structure of any crystalline protein. Hiding the water 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 Ramachandran plot shows most of the residues involved in an α-helix are clustered in the area of the plot where one would expect them to be. (Review Ramachandran Plot.) Many of the residues that are outside of the expected cluster are at the end of a helix, and it is not unusual for such residues to have ψ and φ values that are outside of the range for the α-helix. Also notice that many of the residues that are in the quadrants on the right are Gly. (Residues can be identified by hovering over the sphere with the cursor.) The prosthetic group of myoglobin is a heme, and as shown here it is inserted into a pocket which is nonpolar. Empty heme pocket lined with translucent surface shows that except for some oxygen on the bottom and His 93 at the mid point of one side the pocket is lined with nonpolar carbon atoms. The mostly nonpolar heme inserts into this pocket with the two carboxylate groups of the heme being on the molecular surface. Detailed description of heme structure. The heme shown in the pocket with the pocket's surface colored white so that the heme can be distinguished from the protein surface atoms. 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 | |||
