Interactive Protein Tutorial

Oxyhaemoglobin / What Jmol can do

This is has nothing to do with domains. It is just an exercise to demonstrate how the software can display a 'familiar' molecule.

The frame on the right shows the 3D structure of a single chain of the protein haemoglobin. The bonds in all the aminoacids are shown in a "ball and stick" model. Click on the small 'x' buttons below to see how this can be developed to reveal important features of the protein.

Note: You can switch the rotation of the molecule on and off using the button shown on the right.

Note: You can zoom in and out by holding down the shift button and using your mouse.

BACKBONE

The secondary structure becomes more apparent when amino acid side chains are omitted and just the backbone of the polypeptide chain is depicted. Press the button to see the backbone structure. Notice that some helical regions can now be seen.

RIBBONS

The secondary structure is shown more clearly by a ribbon diagram. The computer calculates where regions of secondary structure occur and draws them as ribbons. Notice the α-helical regions are now more apparent.

STRUCTURE COLOURS

Now press the button to colour the ribbons according to their secondary structure.α-helices are now coloured red, reverse (or β turns) would be coloured blue and β strand (extended) structure coloured yellow. However, haemoglobin does not possess any β structure.

HETERO

So far the structure has shown only the protein globin. Haemoglobin consists of four globin chains like the one that is depicted here. Each of these requires a haem group to enable it to bind O₂. Press the button to see the structure of haem as a ball and stick model. The program classifies atoms and groups that are not part of a protein chain hetero-atoms or hetero-groups. Haem is one such; water is another.

The colour coding selected for the haem display is called CPK. Notice that a single Fe²⁺ ion (yellow) occupies the centre of an octahedral complex. The nitrogen atoms (blue) of the planar molecule porphyrin provide four of the six co-ordinating ligands.

In oxyhaemoglobin an O₂ molecule (red) is bound on one side of the porphyrin ring. The remaining ligand is provided by a histidine group on globin (not shown here).

SPACEFILL

These properties of the haem group are more evident when it is depicted as a spacefilled structure. Note the bound oxygen molecule (2 red spheres bound to the yellow Fe²⁺). The sizes of the atoms correspond to their Van der Waals radii.

MIXED VIEWS

Where is the haem group located in haemoglobin? Press here to view haem in its binding pocket. It is bound partly by hydrophobic interactions. The haem is still displayed as a spacefilled structure, while the chain is a ribbon structure.

MOLECULAR SURFACES

Another way of representing a molecule is to calculate the shape of its surface, according to various parameters. This is shown here for haemoglobin. (Note: be patient. The calculation may take a long time).

TRANSPARENCY

By making the surface transparent it is possible to visualise the haem group.

MENUS

All these displays were created by providing JMol with a series of scripts (lists of commands). Many of these commands can be applied directly. Press the button below the JMol window to reset to the original ball and stick mode, then place the cursor over the display and press the right mouse button. See if you can display Hb as a ribbon structure with all its water molecules coloured purple. (Tip: try 'Select' > 'hetero' etc and note that only the selected regions are then affected by the menu commands).