Helix-loop-helix motif

A dimer of the Max protein from mouse, with two identical helix-loop-helix motifs, bound to a 22 bp fragment of DNA.

Each chain is displayed using a different colour: the 2 DNA strands and 2 motifs in the dimeric protein.

The structure common with other proteins, and hence called the motif, consists of:

  1. a stretch of alpha helix, that fits in the major groove of DNA and directly interacts with bases in it (equivalent to the "recognition helix" in the helix-turn-helix motif);
  2. a short stretch of peptide without a defined secondary structure, longer and more flexible than that in the helix-turn-helix motif, called a loop;
  3. another alpha helix that does not interact with DNA but interacts with the other protein chain, stabilising the dimer.

These three components give the motif its name. In addition, each particular protein has other regions forming the remainder of the protein molecule, not shown here.

Quiz:

Identify each part of the molecule and pick the colour used for it in the model:
(click on a coloured square to assign that colour to the item at its right)
Recognition helix
Loop
Dimerisation helix

When you finish, click on

 

Spacefilling model, or spheres.

Another protein with two helix-loop-helix motifs

USF, a human protein ("upstream stimulatory factor"), bound to DNA.

Note how the position and dimensions of the loop and the second helix differ from the former example.