Protein Structure Class: 2(c). Super-Secondary Structures

super-secondary structures

Complex, three-dimensional structures, that still involve localized amino acid sequences close to each other.
Super-secondary structure comprises localized motifs of secondary structures, which are combinations of alpha helices, beta sheets, or both alpha helices and beta sheets.
Motifs give proteins unique structural features that enable their unique function. Motifs provide unique shapes that enable proteins to bind DNA, metals, substrates, cofactors or other proteins.

eight of the most common super-secondary structures

Alpha helices

Helix-turn-helix
Helix-loop-helix
Coiled-coil

Beta motifs

Beta-hairpin
Greek key
Beta barrel.

Combination motifs

Beta-alpha-beta
Zinc finger

alpha helices

Most alpha helices bind DNA.

Helix-turn-helix (or HTH for short)

We connect two helices with a short sequence of amino acids. As the name implies, a helix-turn-helix is two helices connected by a short sequence, or turn of amino acids.*

A turn is a short sequence of 4 to 6 amino acids, which are usually positively charged.

The helix-turn-helix motif binds DNA. In fact, this motif was discovered by comparing sequences of genes that encode regulatory proteins for transcription.*

Helix-loop-helix (or bHLH for short)

We connect two helices with a sequence of amino acids.
Similar to the HTH, the helix-loop-helix is two helices connected by a short sequence, or loop of amino acids that is longer than a turn.
Loops are considerably longer sequences of amino acids than turns.
The helix-loop-helix is a DNA-binding motif commonly found in transcription factors, such as the EF-hand, a calcium-binding domain common to calcium-binding proteins.

Coiled-coil domain

Two alpha helices that wind around each other.
The coiled coil domain comprises at least two alpha helices that wrap around each other.
Coiled coil domains also bind DNA and their individual helices have heptad repeats. For instance, the leucine zipper has a leucine residue that repeats every seventh amino acid.

Again, all three of these alpha helices are DNA-binding domains; in fact almost all DNA-binding domains are helix-rich.

beta-strand super-secondary structures

The beta hairpin

This is the simplest. We join two antiparallel beta strands with a short loop. These two strands form a hairpin shape, hence the name: beta hairpin.
Proline and glycine residues are common in the turn because their structure is favored for the sharp angle of the turn.

The Greek key

A more complex beta motif. We draw four beta strands in the following orientation: up, down, up, down. As you may imagine, we can connect these in a variety of ways using loops of different lengths.
In the Greek key motif, the strands are in the following order: 3, 2, 1, 4. This pattern is characteristic of and unique to the Greek key motif.
We draw loops to connect the arrows in the order that we have just outlined.
The N-terminal end precedes beta strand 1 and the C-terminal end comes after beta strand 4.

The Beta Barrel

The most complex of the beta sheet structures. We draw 9 antiparallel beta strands diagonally in a barrel shape. Beta barrels can also contain alpha helices to help dictate their structure, but we have chosen the simplest form of the beta barrel to draw here, the up-and-down beta barrel.*

As you can imagine, the barrel shape can be made with several variations, which have different names, such as the Greek key barrel and the jellyroll.
Beta barrels are commonly found in proteins that transport ions across cell membranes, called porins.

two of the motifs that contain both alpha helices and beta sheets

The beta-alpha-beta motif

We draw a beta strand linked to an alpha helix, which itself is linked to another beta strand which runs parallel to the first. This structure allows for adjacent parallel beta strands.
The beta-alpha-beta motif is often found in parallel sections of beta sheets.
Beta-alpha-beta motifs are almost always right-handed, meaning the loops and helix have a right-handed twist.

The zinc finger

It combines two beta strands and an alpha helix. We draw a pair of antiparallel beta strands, which are connected to an alpha helix that runs perpendicular to the beta strands.
We draw a zinc atom in the space created by these three elements and dash lines to represent the bonds between the zinc and the polypeptide sequences. This is our zinc finger, a zinc-containing motif that looks kind of like zinc is being held between fingers.
The Cys2His2 zinc finger motif is one of the most common of the zinc fingers and gets its name because two cysteine and two histidine residues form the four bonds to the zinc atom.

Protein Structure Class: 2(c). Super-Secondary Structures

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