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 defined by 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 image 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

β-sheets may also be parallel and anti-parallel and there are many different connectivity types in this case. Probably the simplest and most common type, which was described earlier, is made by short loops, a hairpin-type of connectivity. When a connecting region in a protein structure cannot be classified as a secondary structure, and it is not a normal loop (which is often relatively short), it is called a coiled region. An example is shown on the figure below.

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 β-sheet are also parallel, but the connectivity between them is made by α-helices:

tim-barel

Strands within β-sheets may of course be combined in many different ways. Two examples are shown below, and include one sheet, which can be described as two hairpins connected to each other and another, within which the so-called Greek-key motif type of connectivity connects the strands:

anti-parallel


The figure below shows the topology of a protein called plastocyanin, which is entirely a β–sheet protein. You may easily identify a Greek-key motif in this structure:

anti-parallel2

There are of course other types of connectivity between secondary structure elements. They are described in many books dedicated to protein architecture.
In the next section I will discuss a more general level of organization, protein
folds and domains.

Basics of Protein Structure