Protein Secondary Structure: α-Helices and β-Sheets
Secondary structure, as the name suggests, constitute the second level of protein structure (the first being the sequence, which is sometimes called the primary structure). Here I will focus on the general aspects, which are important to keep in mind, for example, when analyzing a sequence alignment, when making a homology model and analyzing model quality, when planning some mutations in a protein or when analyzing protein-ligand interactions. A ligand could be any molecule, which binds to a protein with some affinity - a substrate, an inhibitor, another protein molecule, a DNA or RNA segment, etc.
The most common type of secondary structure in proteins is the alpha-helix. Linus Pauling was the first to predict the existence of alpha-helices, which was confirmed with the determination of the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew). An example of an alpha-helix is shown on the figure below. This type of representation of protein structure is called sticks representation. To give you a better impression of how a helix looks like, I removed the amino acid side chains in the figure. There are 3.6 residues/turn in an alpha-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). Each residue is translated 1.5 Å along the helix axis, giving a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). The repeating structural pattern in helices is a result of repeating Phi and Psi values, which is observed as clustering of the torsion angles within a certain region of the Ramachandran plot.
When looking at the helix in the figure below, notice how the carbonyl oxygen atoms C=O (shown in red) point in one direction, towards the amide NH groups, 4 residues away (i, i+4). Together these groups form a hydrogen bond, one of the main forces of secondary structure stabilization in proteins. Hydrogen bonds are shown on the right figure as dashed lines.
For a hydrogen bond to be formed, two electronegative atoms (in the case of an alpha-helix the amide N, and the carbonyl O) have to interact with the same hydrogen. The hydrogen is covalently attached to one of the atoms (called the hydrogen-bond donor), but interacts electrostatically with the other (the hydrogen bond acceptor, O). In proteins essentially all groups capable of forming H-bonds (both main chain and side chain, independently of whether the residues are within a secondary structure or some other type of structure) are usually H-bonded to each-other or to water molecules. Due to their electronic structure, water molecules may accept 2 hydrogen bonds, and donate 2, thus being simultaneously engaged in a total of 4 hydrogen bonds. Water molecules may also be involved in the stabilization of protein structure by making hydrogen bonds with the main chain and side chain groups in proteins and even linking different protein groups together. In addition, water is often found to be involved in ligand binding to proteins, mediating ligand interactions with protein polar or charged groups. It is useful to remember that the energy of a hydrogen bond, depending on the distance between the donor and the acceptor and the angle between them, is in the range of 2-10 kcal/mol. Other types of helices in proteins include the 3-10 helix, which is stabilized by hydrogen bonds of the type (i, i+3) and the π-helix, which is stabilized by hydrogen bonds of the type (i, i+5). The 3_10 helix has a smaller radius, compared to the alpha-helix, while the π-helix is wider. A paper describing the details of the π-helix has been published by Fodje & Al-Karadaghi in 2002.
Hydrogen bonds also stabilize another type of secondary structure in proteins, namely beta-sheets. An example of a beta-sheet with the stabilizing hydrogen bonds shown as dashed lines is presented on the figure below:
The same beta-sheet is shown on the figure below, this time in the context of the 3D structure to which it belongs and in a so-called "ribbon" representation (protein colored according to secondary structure - beta-sheets in yellow and helices in magenta). The arrows show the direction of the beta-sheet, which is from the N- to the C-terminus. When the arrows point in the same direction, we call such a sheet parallel:
And when they point in opposite directions, it is anti-parallel. In the next figure you can see an example of a protein structure with an anti-parallel beta-sheet:
When we just have 2 anti-parallel beta-strands, like in the figure below, we call this secondary structure motif a beta-hairpin. The loop between the two beta-strands is called a beta-turn. Turns and loops play an important role in protein 3D structures, connecting together beta-strands, strands to alpha-helices, or helices to each other. The amino acid sequences in turn regions may be very variable. But in some cases, when a loop has some specific function, for example interaction with another protein, the sequence may be conserved. Loop length in a protein family may be very variable, which justifies, as it is discussed in the sequence alignment and homology modeling parts, the localization of insertions and deletions to loop regions.
You may have heard the expression "Structure is Function". This also includes various structural motifs, which are often closely linked to protein function. For this reason, when working with protein 3D structures, it is important to be able to recognize the different types of secondary structure elements and to identify structural motifs. In the next section we will look at different ways secondary structure elements are arranged, forming common structural motifs.