Oxymyoglobin

spinqualitylabelsall models Structure of Oxymyoglobin (PDB entry 1mbo) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Oxymyoglobin is the oxygenated form of myoglobin which is a single chain globular protein. The physiological function of myoglobin is to store molecular oxygen in muscle tissue so that there is a reserve of O2 over and above that bound to the hemoglobin in the blood. The major structural difference in deoxymyoglobin and oxymyoglobin is that O2 is bound to the heme in oxymyoglobin whereas it is not in myoglobin. This article will gave an overview of the structural similarities of the two forms as well as a more detailed description of the structural differences. Structural Similarities of the Two Forms Oxymyoglobin is shown with 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 yellow 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 yellow 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. Structural Differences of the Two Forms The major difference is the chelation of molecular oxygen to Fe2+ on the side of the heme opposite His 93.  resulting in the Fe2+ being chelated with six ligands.   Compare the displacement of Fe2+ from the plane of the porphyrin in the two scenes below, oxymyoglobin (1mbo) and myoglobin (1mbd). In which scene is the center of Fe2+ displaced slightly more from the porphyrin plane? The binding of O2 pulls on the Fe2+ counter balancing the tug of His so that the center of Fe2+ is positioned closer to the plane of the porphyrin ring. The Fe2+ is 0.055 nm above the porphyrin plane in myoglobin, whereas it is 0.026 nm above the plane in oxymyoglobin. His 93 remains attached to the Fe2+, and it moves to a more perpendicular position as it moves along with the Fe2+. The movement of the His forces a nearby residue to move, and all this side chain movement results in a conformation change of the complete F helix. An animation of this conformation change can be seen in the context of a hemoglobin monomer, go to the subtopic 'Capturing Oxygen', select the 'context of an entire monomer' green link and toggle animation on if necessary. The consequences of this movement for myoglobin is trivial, but for hemoglobin, since it is a tetramer, it is quite consequential, as described at the link above. His 64 is located on the same side of the heme as molecular oxygen but is not close enough to the Fe2+ for its nitrogen to chelate with Fe2+, but it is close enough to the heme to hydrogen bond with the O2, remember that hydrogens are not displayed in this model. Other Ligands Binding at the Sixth position Carbon monoxide; Binding to heme through the carbon, and His 64 interferes with its binding. The free heme binding constant is 25,000 times greater for CO than for O2, but when binding to myoglobin the difference is only 250 times. This lower affinity for myoglobin prevents the very small amount of metabolically formed carbon monoxide from binding to myoglobin, but the amount that may be present in the atmosphere can be large enough to result in binding to myoglobin and causing death of the individual. Nitric oxide; binds through an oxygen; with His 64 displayed Nitrous oxide; binds through the nitrogen; with His 64 displayed Cyanide ion; binds through the carbon; with His 64 displayed 3D structures of myoglobin Myoglobin

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Karl Oberholser, Michal Harel, Eran Hodis, Alexander Berchansky