Representing protein structures
Spacefill model
The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, etc.
In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.
Ball-and-stick molecular model
This view shows chymotrypsin in the familiar representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.
Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example.
Amino acid trace
Here's a much more simplified view that of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
One question this view does raise, is how the three separate chains are held together in the right way? The answer is the that link the chains together to form the correct overall structure.
What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the Introduction to Protein Structure Proteopedia page.
Levels of Protein Structure
Primary structure
Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.
The first, referred to as the , is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.
Secondary Structure
The is the local structure over short distances. This level of structure is stabilized by along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.
Tertiary Structure
These secondary structures to form the overall form of the entire peptide chain, called the .
Quaternary Structure
Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called .
Secondary Structure in chymotrypsin
Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.
This time, we'll display a indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.
Colour key:
Alpha Helices,
Beta Strands .
We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.
Finally, here's chymotrypsin with a molecule of bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.
