Two Alpha Helices of Oxymyoglobin

One purpose of this Interactive is to illustrate different ways of visualizing protein structure and, in particular, the alpha helix structure. The cartoon or ribbon view is the most common view and is shown first. A ribbon is drawn through the backbone of the polypeptide chain. An alpha helix with a coiled flat arrow. This button: will always return you to this original view. Notice the direction of the chain as indicated by the arrowheads at the end of each helical region and at the end of the loop between the two helices. The arrow indicates N-term to C-term. Rotate the structure and look down the axis of each helix and note that it is a hollow tube.

Toggle between the following two buttons:

The atoms of backbone of the polypeptide chain are shown, first, without the ribbon, then with the ribbon. Notice that hydrogen atoms are not shown. See if you can trace the chain from N-term to C-term using the atoms {N (from a peptide bond) followed by C (the alpha carbon) followed by the C=O group}.

The button: increases the atom size for residue 107 (about halfway up the first helix) to help you trace the chain. The following two buttons show the same structures but with the sidechains present: Toggle back and forth between these two buttons and between Backbone Only and All Atoms buttons. Notice that much more of the space is taken up by the sidechains and that the core helix structure is barely observable (even though it is still there). Be sure to rotate the structure around in the different views and to look down the axis of each helix with sidechains off and then on.

Another purpose of this Interactive is to help you understand hydrogen bonding in the alpha helix. The next button shows the hydrogen bonds in the backbone of the polypeptide chain (with no sidechains shown): Notice that as you go up a helix that the C=O group of the nth residue is hydrogen bonded to the NH group of the n+4th residue. (Again, H atoms are not shown.) The carbonyl is the H-bond acceptor, the NH is the H-bond donor. Zoom in as necessary to identify this. Notice how showing the hydrogen bonds shows the rigid tube that is the alpha helix. This hydrogen bonding pattern, repeated over many consecutive amino acid residues is what defines the alpha helix. Turn on the sidechains with this button: This button: shows the hydrogen bonds in the context of the original ribbon view. The following buttons: allow you to toggle H-bonds in any view.

The next two buttons: turn off and on the spacefilling representation. Select the backbone atom only view again: . Then turn on the spacefilling representation. Notice that the helices are rigid rods. If you look down the axis of each helix, you now see that all the space is occupied. Turn on all the atoms: If the sidechains are not shown as spacefilled then turn spacefilling on with the toggle. In this view it is very difficult to trace the chain or see individual amino acid residues. You can begin to appreciate why we use the ribbon representation.

The next button: color codes the structure based on whether the amino acid residue is hydrophobic or hydrophilic. Notice that one side of this two helix structure is predominantly gray (hydrophobic) and one side is blue (hydrophilic). In the full myoglobin structure the gray region is facing the interior of the protein and the blue region is facing the water accessible exterior.