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2 Super-secondary structure

Secondary structure elements are observed to combine in specific geometric arrangements known as motifs or super-secondary structures. In this section we will look at motifs consisting of no more than three secondary structure elements. Larger motifs such as the Greek key will be examined in the sections on tertiary structure and protein folds.

2.1 Beta-hairpins

Beta-hairpins are one of the simplest super-secondary structures and are widespread in globular proteins.

Schematic view of a beta-hairpin
Schematic view of a beta-hairpin. The dotted lines indicate the hydrogen bonds between the beta-strands

They occur as short loop regions between antiparallel hydrogen bonded beta-strands. In general a reverse turn (or beta-turn, as they are sometimes called) is any region of a protein where there is a hydrogen bond involving the carbonyl of residue i and the NH group of residue i+3. An alternative definition states that the alpha-carbons of residues i and i+3 must be within 7.0 Å. The structures of reverse turns are outlined in section 1.4. In this section we will concentrate on those turns which occur between consecutive beta-strands, known as beta-hairpins. At this point three system to classify beta-hairpins shell be mentioned.

The following figure is a "mashup" of the three definitions:

Schematic comparison of different beta-hairpins and their different classification.
Overview of naming conventions for beta-hairpins. Two antiparallel strands connected with a hairpin at the left are shown. Hydrogen bonds are indicated as green dotted lines. Top Left: The structure is drawn and the individual amino acids are marked with dotted black lines. The amino acids are abstracted as "u" with the n-terminal part drawn in blue and the c-terminal part red. The tips represent the NH- resp. CO-group where hydrogen bonds can be formed. Below each figure is the naming according to Sibanda & Thornton according to their 1985, resp. 1989 paper. The rows represent the Classes defined by Milner-White & Poet in their 1986 paper.
Note the shift of the amino acids between the Classes. Amino acids without any hydrogen bonds are not part of the beta sheet.

The occurrence of these different hairpins is by no means equal. In the following a few, smaller, well defined beta-hairpins are described.

2.1.1 Two-residue beta-hairpins

Two-residue beta-hairpins are dominated by 2:2 type (class 2), forming type I' and type II' hairpins and, less frequent, type I.

Type I' : The first residue in this turn adopts the left-handed alpha-helical conformation and therefore shows preference for glycine, asparagine or aspartate. These residues can adopt conformations with positive phi angles due to the absence of a side chain with glycine and because of hydrogen bonds between the side chain and main chain in the case of asparagine or aspartate. The second residue of a type I' turn is nearly always glycine as the required phi and psi angles are well outside the allowed regions of the Ramachandran plot for amino acids with side chains. Were another type of amino acid to occur here there would be steric hindrance between its side chain and the carbonyl oxygen of the preceding residue.

Type II' : The first residue of these turns has a conformation which can only be adopted by glycine (see below Ramachandran plot). The second residue shows a preference for polar amino acids such as serine and threonine.

2.1.2 Three-residue beta-hairpins

Three-residue beta-hairpins are dominated by 3:5 type with much rarer 3:3 type (both class 3). The first residue adopts the right-handed alpha-helical conformation and the second amino acid lies in the bridging region between alpha-helix and beta-sheet. Glycine, asparagine or aspartate are frequently found at the last residue position as this adopts phi and psi angles close to the left-handed helical conformation.

Example of 3:5 and 3:3 type beta-hairpins
Three-residue beta-hairpins Left: The more common 3:5 type beta-hairpin. Three amino acids do not form any hydrogen bonds (2-4) while residue 1 and 5 have a single connection, but are not in a beta-strand conformation. Right: Three amino acids are not involved in the beta-sheet in either of the criteria. For clarity only backbone heavy atoms and Cbeta are shown.

2.1.3 Four-residue beta-hairpins

These are also quite common with the first two residues adopting the alpha-helical conformation. The third residue has phi and psi angles which lie in the bridging region between alpha-helix and beta-sheet and the final residue adopts the left-handed alpha-helical conformation and is therefore usually glycine, aspartate or asparagine.

Example of a 4:4 type beta-hairpin
Example of a 4:4 type beta-hairpin. Note that residue 4 forms a hydrogen bridge with the residue prior to 1. For clarity only backbone heavy atoms and Cbeta are shown.

2.1.4 Longer loops

For these, a wide range of conformations is observed and the general term 'random coil' is sometimes used. Consecutive antiparallel beta-strands when linked by hairpins form a super-secondary structure known as the beta-meander.

Schematic view of a beta-meander
Schematic view of a beta-meander. The dotted lines indicate the hydrogen bonds between the beta sheets.

2.2 Beta-corners

Beta-strands have a slight right-handed twist such that when they pack side-by-side to form a beta-sheet, the sheet has an overall left-handed curvature. Antiparallel beta-strands forming a beta-hairpin can accommodate a 90 degree change in direction known as a beta-corner. The strand on the inside of the bend often has a glycine at this position while the other strand can have a beta-bulge. The latter involves a single residue in the right-handed alpha-helical conformation which breaks the hydrogen bonding pattern of the beta-sheet. This residue can also be in the left-handed helical or bridging regions of the Ramachandran plot.

Beta-corners are observed to have a right-handed twist when viewed from the concave side.

Example of a structure element containing a beta-corner and a 3:5 type beta-hairpin
Beta-corner and a beta-hairpin containing structure element. The green dotted lines indicate hydrogen bonds. For clarity only backbone heavy atoms and Cbeta are shown.

2.3 Helix hairpins

A helix hairpin or alpha-alpha-hairpin refers to the loop connecting two antiparallel alpha-helical segments. Clearly, the longer the length of the loop the greater the number of possible conformations. However, for short connections there are a limited number of conformations and for the shortest loops of two or three residues, there is only one allowed conformation. Antiparallel alpha-helices will interact generally by hydrophobic interactions between side chains at the interface. Therefore, hydrophobic amino acids have to be appropriately positioned in the amino acid sequence (one per turn of each helix) to generate a hydrophobic core. Efimov has analysed the conformations of alpha-alpha-hairpins and some of his results are summarised below.

The shortest alpha-helical connections involve two residues which are oriented approximately perpendicular to the axes of the helices. Analysis of known structures reveal that the first of these two residues adopts phi and psi angles in the bridging or alpha-helical regions of the Ramachandran plot. The second residue is always glycine and is in a region of the Ramachandran plot with positive phi which is not available to other amino acids.

Example of a helix hairpin
Example of a helix hairpin consisting of two amino acids. Hydrogen bonds are indicated with green dotted lines. For clarity only backbone heavy atoms and Cbeta are shown.

Three residue loops are also observed to have conformational preferences. The first residue occupies the bridging region of the Ramachandran plot, the second adopts the left-handed helical conformation and the last residue is in a beta-strand conformation.

Four-residue loops adopt one of two possible conformations. One is similar to the three residue loop conformation described above except that there is an additional residue in the beta-strand conformation at the fourth position. The other conformation involves the four residues adopting bridging, beta, bridging, and beta conformations, respectively.

2.4 The alpha-alpha corner

Short loop regions connecting helices which are roughly perpendicular to one another are referred to as alpha-alpha-corners. Efimov has shown that the shortest alpha-alpha-corner has its first residue in the left-handed alpha-helical conformation and the next two residues in beta-strand conformations. This conformation can only be adopted when the two helices form a right-handed corner. Indeed, if the helices were linked to form a left-handed corner there would be steric hindrance. This may explain the scarcity of left-handed alpha-alpha-corners in protein X-ray structures.

The C-terminal residue of the first helix, which is in the left-handed alpha-helical conformation, must have a short side chain to avoid steric hindrance and is observed commonly to be glycine. The first residue of the second helix, which is in the beta-conformation, frequently has a small polar side chain such as serine or aspartate which can form hydrogen bonds with the free NH groups at the amino-terminal end of the second helix. The central residue of the alpha-alpha-corner is almost always hydrophobic as it is buried and interacts with other non-polar side chains buried where the ends of the two helices contact each other.

2.5 Helix-turn-helix

The loop regions connecting alpha-helical segments can have important functions. On example is the EF hand. In parvalbumin there is a helix-turn-helix motif which appears three times in the structure. Two of these motifs are involved in binding calcium by virtue of carboxyl side chains and main chain carbonyl groups. This motif has been called the EF hand as one is located between the E and F helices of parvalbumin. It is a ubiquitous calcium binding motif present in several other calcium-sensing proteins such as actin, calmodulin and troponin C.

EF hands are made up from a loop of around 12 residues which has polar and hydrophobic amino acids at conserved positions. These are crucial for ligating the metal ion and forming a stable hydrophobic core. Glycine is invariant at the sixth position in the loop for structural reasons. The calcium ion is octahedrally coordinated by carboxyl side chains, main chain groups and bound solvent.

EF hand in Parvalbumin alpha
EF hand in Parvalbumin alpha. The Calcium ion is shown in green. The protein is represented in Cartoon view and amino acids interacting with the calcium explicitly represented. This figure is from RSCB, PDB entry 1JRV. Representation is with NGL viewer (paper, paper)

A different helix-loop-helix motif is also common to certain DNA binding proteins. This motif was first observed in prokaryotic DNA binding proteins such as the cro repressor from phage lambda. This protein is a homodimer with each subunit being 66 amino acids in length. Each subunit consists of an all-antiparallel three stranded beta-sheet with three helical segments inserted sequentially between the first and second beta-strands. The two subunits of cro associate by virtue of the third beta-strands which interact forming a six-stranded beta-sheet in the centre of the molecule. Mutagenesis and biochemical work had indicated that residues in the second helix of each cro monomer interacted with DNA. Accordingly model building studies indicated that both these helices in the dimeric protein would fit into the major groove of B-DNA. These proteins recognise base sequences which are palindromic, i.e. possess an internal two-fold symmetry axis. The two recognition helices of the cro protein are also related by a two-fold axis passing through the central beta-sheet region of the dimer. Therefore, the recognition helices of the cro dimer fit into the major groove of the DNA and interact with each identical half of the palindrome. Hence, the second helix of the helix-turn-helix motif has an important role in recognising the DNA while the remainder of the structure serves to keep the two helices in the correct relative position for fitting in the major groove of DNA. Many other helix-turn-helix proteins with different folds exhibit essentially the same mode of binding to DNA.

2.6 Beta-alpha-beta motifs

Antiparallel beta-strands can be linked by short lengths of polypeptide forming beta-hairpin structures. In contrast, parallel beta-strands are connected by longer regions of chain which cross the beta-sheet and frequently contain alpha-helical segments. This motif is called the beta-alpha-beta motif and is found in most proteins that have a parallel beta-sheet. The loop regions linking the strands to the helical segments can vary greatly in length. The helix axis is roughly parallel with the beta-strands and all three elements of secondary structure interact forming a hydrophobic core. In certain proteins the loop linking the carboxy terminal end of the first beta-strand to the amino terminal end of the helix is involved in binding of ligands or substrates. The beta-alpha-beta motif almost always has a right-handed fold as demonstrated in the figure.

An example of the beta-alpha-beta protein motif
The beta-alpha-beta motif consists of two parallel beta strands connected with an alpha helix. Left: An abstract representation of the peptide depicting the beta strands in green and the alpha helix in purple. Right: A beta-alpha-beta motif containing protein segment (PDB entry: 2BNH). For clarity only the backbone is shown. Top: View from the alpha helix towards the beta strands. Bottom: A roughly 80 degree tilted view illustrating the the spacial orientation of the secondary structure elements.