January 2000 Molecule of the Month by David Goodsell
Keywords: oxygen transporter activity, John Kendrew, oxygen binding
The First Protein Structure
Any discussion of protein structure must necessarily begin with myoglobin, because myoglobin is where the science of protein structure really began. After years of arduous work, John Kendrew and his coworkers determined the atomic structure of myoglobin, laying the foundation for an era of biological understanding. That first glimpse at protein structure is available at the PDB, under the accession code 1mbn. Take a closer look at this molecule (below), or look directly at the PDB information for 1mbn. You will be amazed, just like the world was in 1960, at the beautiful intricacy of this protein.
Myoglobin and Whale Muscles
Myoglobin is a small, bright red protein. It is very common in muscle cells, and gives meat much of its red color. Its job is to store oxygen, for use when muscles are hard at work. If you look at John Kendrew's PDB file, you will notice that the myoglobin that he used was taken from sperm whale muscles. As you can imagine, marine whales and dolphins have a great need for myoglobin, so that they can store extra oxygen for use in their deep dives undersea.
A Closer Look
John Kendrew's original myoglobin structure is available with the accession code
The structure contains one protein chain, a heme group (with a water molecule bound
to the iron), and a sulfate ion. Ignore the sulfate ion -- it's merely along for
the ride. There are several things to look for in this structure. The protein
chain is composed of spring-shaped alpha-helices, linked together by short
loops. The chain surrounds the flat heme group. At the center, you can see
the iron atom, surrounded by four blue nitrogen atoms. This structure file
doesn't have oxygen bound to the iron, but it does have a water molecule,
which shows up as a red sphere. (The file does not contain hydrogen atoms,
so we see only the "O" of "H2O"!)
The two pictures here were created with RASMOL. You can create similar pictures by accessing the PDB file 1mbn, and then clicking on "View Structure."
Oxygen Bound to Myoglobin
A later structure of myoglobin, with the accession code
shows the location of oxygen. The iron atom at the center of the heme group holds
the oxygen molecule tightly. Compare the two pictures. The first shows only a
set of thin tubes to represent the protein chain, and the oxygen is easily seen.
But when all of the atoms in the protein are shown in the second picture, the
oxygen disappears, buried inside the protein.
So how does the oxygen get in and out, if it is totally surrounded by protein? In reality, myoglobin (and all other proteins) are constantly in motion, performing small flexing and breathing motions. Temporary openings constantly appear and disappear, allowing oxygen in and out. The structure in the PDB is merely one snapshot of the protein, caught when it is in a tightly-closed form. Looking at the static structure held in the PDB, we must imagine the dynamic structure that actually exists in nature.
The two pictures above were created with RASMOL. You can create similar pictures by accessing the PDB file 1mbo, and then clicking on "View Structure." Try switching between the two types of pictures shown above, to prove to yourself that the oxygen is buried in this structure!
© 2015 David Goodsell & RCSB Protein Data Bank