Objective 6, What is a motif?

Motifs are briefly mentioned in Patterns of Secondary Structure in the 3rd Ed. Motifs, also called supersecondary structures, are combinations of secondary structures that occur in a number of types of proteins.  This is all you need to know to answer the objective but the following may help you understand the objective better.

The secondary structures in a motif are almost always found next to one another in the polypeptide chain and are alpha-helices, beta-strands, and nonregular, nonrepetitive secondary structures.  A motif is usually not a domain because it is not stable by itself in solution.  Usually, when the primary structure of a protein folds, you first get secondary structures, then motifs, then domains and finally the tertiary structure.

The following are some examples:

In Figure 7.7 in your text for domain 1 of lactate dehydrogenase, you will find the beta-alpha-beta unit that is used for making parallel beta-sheets in many types of proteins.  The three secondary structures are a beta strand, an alpha helix, and another beta strand.

In Figure 7.8 you can see the hairpin loop motif found in most antiparallel beta sheets. The three secondary structures are a beta strand, the loop, and another beta strand.

In the figure of calmodulin (Fig. 9.10), you will see the helix-turn-helix at the very bottom of the figure (also called helix-loop-helix).  The three

There are many more elaborate motifs such as the greek key, beta meander and beta-barrel that have five or more secondary structures but we don’t have time for them and they are not that helpful to a practicing health care provider.