8.0 All Beta Tertiary Structure

All beta tertiary structural domains can occur in proteins with one domain (eg. concanavalin A, superoxide dismutase), and occurs at least once in proteins with two domains (eg. chymotrypsin), or three domains (eg. OmpF).

• The beta strands making up these domains are all essentially antiparallel and form structures to achieve stable packing arrangements within the protein.

• There are presently (as of version 1.39) about 70 subclasses listed in SCOP for this domain, and some examples of these are outlined below.

8.1 Beta barrels

This is the most abundant beta-domain structure and as the name suggests the domain forms a 'barrel-like' structure. The beta barrels are not geometrically perfect and can be rather distorted.

There are three main types:

1. Up-and-down barrels

2. Greek key barrels

3. Jelly roll (Swiss roll) barrels

Up-and-down beta-sheets or beta-barrels

Figure 8.1 shows the simple topology of an up-and-down barrel (named because the beta strands follow each other in sequence in an up-and-down fashion).

Usually, the loops joining the beta strands do not crossover the 'ends' of the barrel.

Figure 8.2 shows retinol binding protein as an example of this structure. Other examples are streptavadin and porins (eg. OmpF shown in Figure 2.5 ).

Greek key barrels

These are barrels formed from two, or more, Greek Key motifs.

It is a stable structure

Figure 4.5 shows a Greek key barrel in gamma crystallin (which has two Greek key motifs) with one loop connecting the last strand of one motif to the first strand of the second motif.

Jelly roll barrels

These barrels are formed from a 'Greek Key-like' structure called a jelly roll. Supposedly named because the polypeptide chain is wrapped around a barrel core like a jelly roll (swiss roll).

It is a stable structure

This structure is found in coat proteins of spherical viruses, plant lectin concanavalin A, and hemagglutinin protein from influenza virus.

Figure 8.3 shows the topology of the beta strands in a jelly roll barrel and Figure 8.4 shows the domain in CAP protein.

The essential features of a jelly roll barrel are that:

• it is like an inverted 'U' (which is often seen twisted and distorted in proteins)
• it is usually divided into two beta sheets which are packed against each other
• most jelly roll barrels have eight strands although any even number greater than 8 can form a jelly roll barrel
• it folds such that hydrogen bonds exist between strands 1 and 8; 2 and 7; 3 and 6; and 4 and 5

8.2 Beta sandwich

A beta sandwich is essentially a 'flattened' beta barrel with the two sheets packing closely together (like a sandwich!). The first and last strands of the sandwich do not hydrogen bond to each other to complete a 'barrel' structure. Figure 8.5 shows a beta sandwich in beta 2 microglobulin.

8.3 Other beta structures

Other less frequent beta tertiary structures include: beta prism, beta propellers, beta trefoil, and beta helix Figure 8.6 shows a beta helix in pectate lyase.

8.4 Aligned or Orthogonal beta strands

Beta strands in barrels or sandwich structures can be orientated in two general ways:

• where the strands in two sheets are almost aligned, and in the same orientation, to each other and form an 'aligned beta' structure (eg. gamma crystallin seen in Figure 4.5)

• where the strands, in at least two sheets, are roughly perpendicular to each other and form an 'orthogonal beta' structure. Figure 2.5 and Figure 8.1 shows an orthogonal arrangement in a beta barrel and Figure 8.7 shows an orthogonal arrangement in a beta sandwich.