Structural Motifs: Connectivity Between Secondary Structure Elements


In the previous section I discussed protein secondary structure. The next level of protein structure can be described as the structural motif level, sometimes also called super-secondary structure, which is dependent on the connectivity between secondary structure elements. We all know that in protein structures helices and strands are connected to each other and combined in many different ways. Although, from known protein three-dimensional structures we have learned that there is a limited number of possible ways in which secondary structure elements are combined in nature. Here I will show examples of some basic motifs. In the future you should be able to distinguish such motifs by yourself, for example by using a graphics display program, like SwissPDB viewer (Deep View).

Probably the simplest protein structural motif is a helical bundle, shown on the schematic view below. Helix bundles are very common in protein structures and are very often found as separate domains within larger, multi-domain protein molecules.

helix-bundle

Another common connectivity type may be found in a parallel beta-sheet. In this case connections between the strands do not need to be of the type "short loops", described earlier. When a connecting region of a structure is not ordered in any secondary structure type, and it is longer than normal loops (which are usually short), it is called a coiled region. Connectivity between strands in a parallel beta-sheet may also be provided by helices, building the so-called helix-strand-helix motif. In the example below both α-helices and coiled regions connect the strands in a parallel beta-sheet:

flavodoxin

In the fold known as the TIM barrel fold (the name is based on the first protein where it was found, triose phosphate isomerase), probably one of the most widespread type of protein folds, the strands of the beta-sheet are also connected by helices:

tim-barel

Other possible types of connections between strands building an anti-parallel sheet, a Greek-key motif and a sheet consisted of a mixture of parallel and anti-parallel strands are shown below:

anti-parallel

anti-parallel2

In the next section I will discuss a more general level of organization, protein folds and domains.

Basics of Protein Structure