Myoglobin: Difference between revisions

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[[Myoglobin]] is a globular protein whose function is to store molecular oxygen. The overall fold of the protein is conserved, especially the <scene name='23/238129/Hydrophobic/1'>hydrophobic</scene> core of the protein (shown in purple), but the sequence is more <scene name='23/238129/Conserved_cartoon/1'>variable</scene> on the surface. {{Template:ColorKey_ConSurf}}

[[Myoglobin]] is a globular protein whose function is to store molecular oxygen. The overall <scene name='23/238129/Surface/1'>shape</scene> of myoglobin is approximately disc-shaped with a diameter that is about twice its thickness. The overall fold of the protein is conserved, especially the <scene name='23/238129/Hydrophobic/1'>hydrophobic</scene> core of the protein (shown in purple), but the sequence is more <scene name='23/238129/Conserved_cartoon/1'>variable</scene> on the surface. {{Template:ColorKey_ConSurf}}

The globin consists mostly of [[Helices in Proteins|alpha helices]] shown in <scene name='23/238129/2ndary_structure/2'>pink</scene>; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The eight structurally conserved alpha helices are labelled <scene name='23/238129/Helix_labels/1'>A through H</scene>. The protein is colored as a N-->C rainbow in this view; the N terminus is blue, while the C terminus is red.

The globin consists mostly of [[Helices in Proteins|alpha helices]] shown in <scene name='23/238129/2ndary_structure/2'>pink</scene>; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The eight structurally conserved alpha helices are labelled <scene name='23/238129/Helix_labels/2'>A through H</scene>. The protein is colored as a N-->C rainbow in this view; the N terminus is blue, while the C terminus is red.

The <scene name='23/238129/Heme/3'>heme ligand</scene>, and specifically the iron atom in the middle of the heme, is what binds oxygen in myoglobin. In this representation, the heme alone is shown in ball and stick form with its c, N and O atoms displayed as grey, blue, and red balls. The iron atom is shown in orange, and is in spacefill to better illustrate its interactions with the heme. The iron is bound by four nitrogen atoms found in the heme ring, as well as an <scene name='23/238129/Fe_ligands/1'>amino acid</scene> from the protein chain. Which amino acid from the myoglobin protein binds to the iron? Notice that in the oxygenated state, the iron is in the plane of the heme ring.

Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (holding the mouse over the atoms reveals their identity.) Can you rationalize this exposure?

The heme ligand is what binds the oxygen is shown in spacefilling form with its N, O, and Fe atoms displayed as blue, red, and orange balls. Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (holding the mouse over the atoms reveals their identity.) Can you rationalize this exposure?

~~The overall <scene name='23/238129/Surface/1'>shape</scene> of myoglobin is approximately disc-shaped with a diameter that is about twice its thickness.~~

''Turn on the "Main Chain" button to display the polypeptide backbone in white with its N and O atoms represented by blue and red balls. How closely does the ribbon follow the main chain?

Click "Animate" until the Mb ribbon is gray. Turn off the "Mb Ribbon" button. What are the orientations of the main chain carbonyl groups and the amide N atoms relative to each other which allows formation of the H-bonds of the alpha helices (not drawn)?

View2 is a closeup of the heme from the same direction as View1. Turn on the "HemeLigand" button to display, in cyan, the sidechain of His 93, the proximal His, liganding the heme's Fe(II) ion (white bond). The Fe(II) is also liganded in a square-planar array by the heme's four pyrrole N atoms and hence has a total of 5 pyramidally arranged ligands. In oxyMb, the reversibly bound O2 molecule ligands the Fe from the opposite side of the heme as does the proximal His so that the Fe(II) becomes octahedrally coordinated. The Fe atom is not oxidized by its O2 ligand; it remains in the Fe(II) oxidation state.

Rotate the image about the vertical axis until you see heme edge-on. Is the Heme planar? Note that the Fe atom is displaced towards the proximal His by 0.55 Å from the best plane though the porphyrin ring atoms. In oxyMb, the Fe is only 0.22 Å out of the heme plane and still on the side of the proximal His (for details see [[Oxymyoglobin]]).''

See also [[Molecular Playground/Myoglobin]]<br />

Myoglobin: Difference between revisions

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 <StructureSection load='1a6m' size='350' side='right' caption='Structure of Sperm whale myoglobin with O2 and sulfate (PDB entry [[1a6m]])' scene=''>
-[[Myoglobin]] is a globular protein whose function is to store molecular oxygen. The overall fold of the protein is conserved, especially the <scene name='23/238129/Hydrophobic/1'>hydrophobic</scene> core of the protein (shown in purple),  but the sequence is more <scene name='23/238129/Conserved_cartoon/1'>variable</scene> on the surface.  {{Template:ColorKey_ConSurf}}
+[[Myoglobin]] is a globular protein whose function is to store molecular oxygen. The overall <scene name='23/238129/Surface/1'>shape</scene> of myoglobin is approximately disc-shaped with a diameter that is about twice its thickness.  The overall fold of the protein is conserved, especially the <scene name='23/238129/Hydrophobic/1'>hydrophobic</scene> core of the protein (shown in purple),  but the sequence is more <scene name='23/238129/Conserved_cartoon/1'>variable</scene> on the surface.  {{Template:ColorKey_ConSurf}}
-The globin consists mostly of [[Helices in Proteins|alpha helices]] shown in <scene name='23/238129/2ndary_structure/2'>pink</scene>; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The eight structurally conserved alpha helices are labelled <scene name='23/238129/Helix_labels/1'>A through H</scene>.  The protein is colored as a N-->C rainbow in this view; the N terminus is blue, while the C terminus is red.
+The globin consists mostly of [[Helices in Proteins|alpha helices]] shown in <scene name='23/238129/2ndary_structure/2'>pink</scene>; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The eight structurally conserved alpha helices are labelled <scene name='23/238129/Helix_labels/2'>A through H</scene>.  The protein is colored as a N-->C rainbow in this view; the N terminus is blue, while the C terminus is red.
+	The <scene name='23/238129/Heme/3'>heme ligand</scene>, and specifically the iron atom in the middle of the heme, is what binds oxygen in myoglobin. In this representation, the heme alone is shown in ball and stick form with its c, N and O atoms displayed as grey, blue, and red balls. The iron atom is shown in orange, and is in spacefill to better illustrate its interactions with the heme.  The iron is bound by four nitrogen atoms found in the heme ring, as well as an <scene name='23/238129/Fe_ligands/1'>amino acid</scene> from the protein chain.  Which amino acid from the myoglobin protein binds to the iron? Notice that in the oxygenated state, the iron is in the plane of the heme ring.
+Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (holding the mouse over the atoms reveals their identity.) Can you rationalize this exposure?
-	The heme ligand is what binds the oxygen is shown in spacefilling form with its N, O, and Fe atoms displayed as blue, red, and orange balls. Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (holding the mouse over the atoms reveals their identity.) Can you rationalize this exposure?
-	The overall <scene name='23/238129/Surface/1'>shape</scene> of myoglobin is approximately disc-shaped with a diameter that is about twice its thickness.
 ''Turn on the "Main Chain" button to display the polypeptide backbone in white with its N and O atoms represented by blue and red balls. How closely does the ribbon follow the main chain?
 	Click "Animate" until the Mb ribbon is gray. Turn off the "Mb Ribbon" button. What are the orientations of the main chain carbonyl groups and the amide N atoms relative to each other which allows formation of  the H-bonds of the alpha helices (not drawn)?
-	View2 is a closeup of the heme from the same direction as View1. Turn on the "HemeLigand" button to display, in cyan, the sidechain of His 93, the proximal His, liganding the heme's Fe(II) ion (white bond). The Fe(II) is also liganded in a square-planar array by the heme's four pyrrole N atoms and hence has a total of 5 pyramidally arranged ligands. In oxyMb, the reversibly bound O2 molecule ligands the Fe from the opposite side of the heme as does the proximal His so that the Fe(II) becomes octahedrally coordinated. The Fe atom is not oxidized by its O2 ligand; it remains in the Fe(II) oxidation state.
-	Rotate the image about the vertical axis until you see heme edge-on. Is the Heme planar? Note that the Fe atom is displaced towards the proximal His by 0.55 Å from the best plane though the porphyrin ring atoms. In oxyMb, the Fe is only 0.22 Å out of the heme plane and still on the side of the proximal His (for details see [[Oxymyoglobin]]).''
 See also [[Molecular Playground/Myoglobin]]<br />