Biochemists talk about protein structure on four levels: primary, secondary, tertiary and quaternary. Primary structure, as mentioned earlier, is the linear sequence of amino acids that compose the protein. Primary structure can be represented as a string, where each amino acid in the protein is represented by its one-letter code (Figure 2.3).
Secondary structure is characterized by the presence of intra-molecular hydrogen bonds between backbone elements. Secondary structure includes α-helices, β-sheets, and tight turns. In all three forms of secondary structure the backbone nitrogen donates its bound hydrogen to some other residue’s backbone-carbonyl oxygen. Except for proline, whose backbone nitrogen does not have a hydrogen to donate, any amino acid can be in a helix or a sheet. This means that a random mutation to a helix or a sheet residue will likely preserve the residue’s ability to form that secondary structural element. The key structural features of secondary structure depend on the backbone and not on the side chains. The seeming independence of structure from sequence is part of whyα-helices and β-sheets gets their low rank in the hierarchy of protein structure;
a b c
Figure 2.6: Ubiquitin’s Alpha Helix. a) Cartoon and b) ball and stick representations of the α-helix in ubiquitin. The carbonyl oxygens atoms (red) point in the direction towards the C-terminus (up). The nitrogen atoms (blue) point their bound hydrogen atoms towards the N-terminus (down). In c) the outward splaying of the carbonyl oxygens is apparent when viewed down the center of the helix.
secondary structure does not suggest much about side-chain conformation. The other part of α-helices’ and β-sheets’ low rank is simply their commonality. Helices and sheets are found everywhere; complex structures are built from various arrangements of secondary structures.
In an alpha helix (Figure 2.3), the backbone is wrapped in a tight coil. The carbonyl oxygen on residueiforms a hydrogen bond with the backbone nitrogen on residuei+ 3. The hydrogen bond betweeniandi+3 positions the carbonyl oxygen on residuei+1 so that it can form a hydrogen bond with residuei+4. The helices are almost always right- handed – as Jane Richardson would say, as you climb the spiral staircase of the helix, you use your right hand to hold the rail. Left-handed helices have been observed in protein structures, but they are very short – 4 or 5 residues. For a residue in the middle of the helix – that is, not near the ends of the helix – both the residue’s carbonyl oxygen and the nitrogen groups form hydrogen bonds with the backbone nitrogens and oxygens of other helix residues. For a residue at either end of the helix, one of its backbone hydrogen bonding groups is left to find some non-backbone hydrogen bonding partner – either water, or a side-chain hydrogen-bonding group.
In a beta sheet (Figure 2.7), the backbone is extended in a long strand. Two β- strands can either align in parallel (Figure 2.8) where the N-to-C direction is the same for both strands, or anti-parallel (Figure 2.9) where the N-to-C direction of one strand is opposite the N-to-C direction of the other. Both parallel and anti-parallel arrangements align the strands’ backbone nitrogen and oxygen atoms so that they hydrogen bond. A collection of β-strands together form a β-sheet.
a b
Figure 2.7: Ubiquitin’s Beta Sheet. a) Cartoon and b) ball and stick representations of ubiquitin’s beta sheet. The top strand and the middle strand show a parallel arrange- ment, the middle strand and the bottom strand show an anti-parallel arrangement.
Figure 2.8: Parallel Beta Strands: If two β-strands align so that their N-to-C orienta- tions point in the same direction, they are able to form a regular pattern of hydrogen bonds. The hydrogen atom bound to each backbone nitrogen is not shown.
Figure 2.9: Anti-Parallel Beta Strands. If two β-strands align so that their N-to-C orientations point in opposite directions, they are able to form a regular pattern of hydrogen bonds. The hydrogen atom bound to each backbone nitrogen is not shown.
Sequence analysis of secondary structures in proteins reveals that some amino acids are more likely to form α-helices than others, while others are more likely to form β- sheets (Chou and Fasman, 1978; Garnier et al., 1978; Richardson and Richardson, 1988; O’Neil and DeGrado, 1990; Munoz and Serrano, 1994). The statistics can be interpreted as natural propensities for amino acids to form helices or sheets. Biochemists have used these propensities to predict protein secondary structure and from there the complete folded structure (Cohen et al., 1982).
Tertiary structure depends significantly upon side chains. Tertiary structure is a little frustrating to define; certainly specifying the location for all atoms in the pro- tein defines its tertiary structure, however, biochemists often refer to the topological arrangement of secondary structures as tertiary structure (Richardson et al., 1992), as well as some specific types of interactions between pairs of side chains. Structural elements described as elements of tertiary structure include the protein’s fold classi- fication (Murzin et al., 1995), the hydrogen bonding pattern of β-sheets, side-chain salt bridges, the tight packing of hydrophobic side chains in protein cores and disul- fide bonds (chemical bonds formed between the sulfur atoms in cysteine side chains). Disulfide bonds constitute the exception to the rule that protein chemical structure is captured completely by its primary structure – these chemical bonds are not captured in a one-dimensional sequence.
Quaternary structure describes the geometry of two or more chains together as they interact. Quaternary structure differs from tertiary structure only in the number of chains involved.