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All Alpha Folds
Index to Section 10
 Alpha/Beta Folds

All-Beta Topologies


 

Introduction

Again, this is a review of some of the 'classic' examples.

You should also browse through the Mainly Beta Class of the CATH Protein Structure Classification Database at University College, London. This lists 7 different architectures.

You should also be aware of alternative classifications, such as the Structural Classification of Proteins database (Alexey G. Murzin, Steven E. Brenner, Tim J.P. Hubbard, and Cyrus Chothia). In all, fifty-two categories of all beta folds are listed. A number of the entries have links to diagrams by Manuel Peitsch.

With MAGE installed, study this Kinemage on Alpha Domain Structures, which accompanies the Branden and Tooze book. 

Protein folds which consist of almost entirely beta sheets exhibit a completely or mostly antiparallel arrangement. Many of these antiparallel domains consist of two sheets packed against each other, with hydrophobic side chains forming the interface (refer to Section 9). Bearing in mind that side chains of a beta-strand point alternately to opposite sides of a sheet, this means that such structures will tend to have a sequence of alternating hydrophobic and polar residues.

Beta Sandwiches and Beta Barrels

The immunoglobulin fold is introduced in the section on mosaic proteins . In this fold, the strands form two sheets packed against each other, forming a "beta sandwich". Also look at the fibronectin type 3 domain in the same section.

Aligned and Orthogonal Beta Sandwiches

The packing arrangements in both aligned and orthogonal beta-sandwiches has been described in Section 9.

Click here for a diagram of this beta sheet arrangement in the lipocalin intestinal fatty acid-binding protein. 1ifb (95Kb) [Bbk|BNL|ExP|Waw|Hal] ... SCRIPT

This is just one member of the Lipocalin family, which bind small molecules between the sheets of the sandwich.

Beta barrels

Some antiparallel beta sheet domains are better described as beta barrels rather than beta sandwiches, for example streptavadin.

1stp (87Kb) [Bbk|BNL|ExP|Waw|Hal] See also the diagrams of porin in the section on membrane proteins in the previous chapter. Note that some structures are intermediate between the extreme barrel and sandwich arrangements.

Up-and-down Antiparallel Beta Sheets

The simplest topology for an antiparallel beta sheet involves loops connecting adjacent strands, as shown:

The Greek Key Topology

The Greek Key topology, named after a pattern that was common on Greek pottery, is shown below. Three up-and-down beta strands connected by hairpins are followed by a longer connection to the fourth strand, which lies adjacent to the first.

Folds including the Greek key topology have been found to have 5-13 strands. An example is given below.

plastocyanin (21Kb GIF). 2plt (71Kb) [Bbk|BNL|ExP|Waw|Hal] Here is the crystal structure. Notice that this has a mixed sheet- there are two parallel pairs of strands. This SCRIPT renders the molecule as in the diagram.

Gamma-crystallin

Gamma-crystallin has two domains each of which is an eight- stranded beta barrel-type structure composed of two Greek keys:

In fact, the structure is more accurately described as consisting of two beta sheets, one consisting of strands 2,1,4,7 (white) and the other of strands 6,5,8,3 (red) as indicated in the diagram.

This can be seen by examining the crystal structure of gamma-crystallin. 2gcr (136Kb) [Bbk|BNL|ExP|Waw|Hal] This SCRIPT displays only the N-terminal domain, and colours the two sheets as in the diagram above (white and red). To distinguish the two Greek keys, type the following: 

select 1-39
colour blue
select 40-80
colour [90,90,70]
Sequence homology has been found between the two Greek key motifs within each domain, and also between the two domains themselves. The latter homology is higher than the former; this implies that the structure evolved from a single Greek key fold by means of a gene duplication to produce a domain of two Greek keys, followed by a second duplication resulting in two similar domains. This is supported by the fact that in some crystallins each Greek key motif is coded by a different exon, with introns between them.

The Jellyroll Topology

Richardson(1981) describes the jellyroll fold as being formed by the addition of an extra "swirl" to a Greek key:

Click here for a diagram illustrating this fold in the coat protein of satellite tobacco necrosis virus (21Kb GIF).

2stv (158Kb) [Bbk|BNL|ExP|Waw|Hal] ... SCRIPT to render as in the diagram

Beta Propellors

2bat (304Kb) [Bbk|BNL|ExP|Waw|Hal] Click here to examine the crystal structure of one subunit (about 470 residues) of neuraminidase. One molecule is composed of four of these subunits. Each is a superbarrel of six four-stranded antiparallel sheets. The whole structure has a basically up-down topology as shown:

This fold is called a beta propellor; there are six 'blades' in neuraminidase.

Here are two other examples - how many blades are there in each propellor?:

Beta Trefoils

This fold has an approximately 3-fold axis of symmetry.

Examine the crystal structure of erythrina trypsin inhibitor 1tie (114Kb) [Bbk|BNL|ExP|Waw|Hal] ... SCRIPT

"Beta Helix"

This dramatically unusual fold was discovered quite recently. The beta strands wind round the structure describing a helical topology, as can be seen in this image of pectate lysase. 2pec (245Kb) [Bbk|BNL|ExP|Waw|Hal] 
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All Alpha Folds
Index to Section 10
 Alpha/Beta Folds

Last updated 7th April '97