Beyond the secondary structure of proteins it becomes very difficult to see on an atomic level what is going on with the polypeptide chain. For this reason we must start to use different visualisation techniques in order to look at different aspects of the higher order structure. Here we will use as an example the light-sensitive channelrhodopsin membrane protein as an example of the highly ordered arrangement of secondary structural units that can be found in many protein structures.
The tertiary structure – the way the polypeptide chain and the way the α-helices, β-sheets, etc assemble to give the overall three dimensional structure of the full protein molecule – is extremely difficult to see when we look at the protein as an assemblage of atoms in the way that is common for small molecules. Below is the channelrhodopsin membrane protein displayed with atomic detail (hydrogens omitted) produced with QuteMol v 0.4.1 (http://qutemol.sourceforge.net)
Clearly, using this approach does not yield very much information about the way in which the protein structure is built up from its amino acid sequence:
RMLFQTSYTLENNGSVICIPNNGQCFCLAWLKSNGTNAEKLAANILQWITFALSALCLMFYGYQTWKSTC GWEEIYVATIEMIKFIIEYFHEFDEPAVIYSSNGNKTVWLRYAEWLLTCPVILIHLSNLTGLANDYNKRT MGLLVSDIGTIVWGTTAALSKGYVRVIFFLMGLCYGIYTFFNAAKVYIEAYHTVPKGRCRQVVTGMAWLF FVSWGMFPILFILGPEGFGVLSVYGSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDIRKTTKLNI GGTEIEVETLVEDE
Both the atomistic view and the sequence implicitly contain all the information about the protein three dimensional structure except that it is hidden in the simplicity of the sequence notation and in the complexity of the large numbers of atoms shown above.
Plotting instead the 'cartoon' structure of the channelrhodopsin protein we can now see much more clearly how the poly peptide chain folds in a very complex way to produce the cluster of atoms that appeared in the first figure above. The image below (produced with Pymol v18.104.22.168 http://www.pymol.org) clearly shows α-helices (red), β-sheets (yellow) and disordered/random loops (green) and the way in which these structural features are arranged to produce the global structure becomes apparent.
This channelrhodopsin protein is found spanning biological cell membranes and acts as a light-activated proton channel. The bundle of α-helices seen above represent the part of the protein that sits within the membrane lipid bilayer and the upper and lower loops/β-sheet segments extend into the space on either side of the membrane. The α-helix bundle provides greater structural rigidity for the trans-membrane section of the protein and creates a 'box' around the functional core of the protein which contains the light-absorbing chromophore that triggers the protein's action (not shown). Without this assembly of secondary structural units into such a specific tertiary structure the protein would loose its ability to function.