Protein Motifs: (Clicking on any link will bring up (in the JMol window) a protein with the corresponding motif or domain highlighted).

Protein motifs are combinations of a few secondary structure elements with a specific geometric arrangement. Listed below are some common protein motifs.

(A). Helix-turn-helix motif - two alpha helices joined by a loop region. The helix-turn-helix nomenclature is used specifically to describe those that are involved in binding DNA. The DNA binding protein from bacteriophage lambda contains a helix-turn-helix motif. The helix-turn-helix motif is highlighted in red.

(B). EF hand motif - two alpha helices joined by a loop region. The EF hand motif is similar to that of the helix-turn-helix motif in that both of these contain two alpha helices connected by a loop region. However, EF hand motif is specific for calcium binding and is found in proteins, such as ,that bind calcium. The EF hand motif is highlighted in red. The Calcium atoms are shown as green spheres. Calmodulin contains four EF hand motifs.

(C). Beta-hairpin motif - two adjacent antiparallel beta strands joined by a loop. The hairpin motif is found in most antiparallel beta structures. Snake venom is an example of a protein that contains a beta-hairpin motif (colored in red).

(D). Greek key motif - four adjacent antiparallel beta strands. A schematic of the greek key motif is shown below.

A greek key motif can be found in . It may be a little difficult to see the ideal arrangement of strands in this particular example. The first and second strands colored in red are antiparallel to each other. The third strand, colored in green, is antiparallel to the second strand and the fourth strand, colored in blue, is antiparallel to the first strand. It is difficult to see that the first and fourth strands are antiparallel to each other, but if you look closely you see that the start of the first strand and the end of the fourth strand are interacting with each other in an antiparallel fashion.

(E). Beta-alpha-beta motif - two parallel beta strands connected via an alpha helix.