Three Beta Strands of Beta-2 Microglobulin

One purpose of this Interactive is to illustrate different ways of visualizing protein structure and, in particular, the beta sheet 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. A beta strand is shown as a flat arrow. A beta sheet is several strands side by side, either parallel or antiparallel (as in this example). 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 strand. The arrow indicates N-term to C-term. Rotate the structure and note that the three strands are in a flat plane with each strand connected by an irregular loop.

Toggle back and forth 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 50 (toward the end of the middle strand) 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. Be sure to rotate the structure around in the different views and to note that some sidechains are pointing on one side of the sheet and some are pointing on the other side.

Another purpose of this Interactive is to help you understand hydrogen bonding in the beta sheet. The next button shows the hydrogen bonds in the backbone of the polypeptide chain (with no sidechains shown): Notice that as you go along a strand that the C=O group of one strand is hydrogen bonded to the NH group of the neighboring strand. (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 planar structure that is the beta sheet. This hydrogen bonding pattern, repeated over many consecutive amino acid residues with at least two strands is what defines the beta sheet. 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 planar sheet. 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.