Molecular model:
The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.
SECONDARY STRUCTURE: This next view simplifies things, and just shows a cartoon representation of the secondary structure of the protein.
You see how the hydrogen bonds (yellow) that maintain the main secondary structure of the protein are arranged in this next view.
Some amino acids have specific effects on secondary structure. This next view shows the locations of the PROLINE residues in myoglobin. You can see that they all fall at the end of a stretch of helix. This is because their large, cyclic side chains do not fit within the straight run of α-helix.
THE GLOBIN FOLD: In this next view, the eight individual alpha-helices are each coloured differently. This gives you an impression of the classic globin fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.
HYDROPHOBICITY: Globular folds like this are characterised by a polar, hydrophilic exterior, which interacts with the aqueous solvent, and a hydrophobic core.
Hydrophobic, Polar
The next view shows a section through the protein that highlights the hydrophobic core better.
This view has been produced in the software by a process known as 'slabbing'. You can still rotate the molecule around - whatever view you see will have the front part of the view of the protein cut off.
The Heme Group
Now let's turn our attention to the main function of myoglobin - oxygen binding.
Oxygen is bound by a heme group, (coloured red) which sits in a hydrophobic pocket in the myoglobin protein.
Central to the heme group is an iron (Fe) atom.
PROXIMAL AND DISTAL HISTIDINES: The iron atom sits either side of the side chains of two histidine residues.
One of these (coloured cyan) is attached to the iron atom, and is known as the proximal histidine. The other (green) is called the distal histidine.
Note how the iron is pulled out slightly to one side of the plane of the heam group as a result of it's co-ordination with the side chain of the proximal histidine.
OXYGEN:
The space between the iron and the distal histidine is where the oxygen (pink) binds.
Note the angled orientation of the oxygen relative to the plane of the heam. The natural binding of oxygen to heam in solution would be the O2 molecule perpendicular to the plane. In myoglobin (and haemoglobin) the presence of the distal His forces to O2 to one side, reducing the affinity of the heam-O2 binding, thus allowing release of oxygen when pO2 is low. The same effect of the distal His also reduces the affinity of heam for carbon monoxide.
