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The primary protein structure refers to the sequence of amino acids and the location of disulfide bonds (Figure 10).
The amino acids when linked by peptide bonds are referred to as residues. Short chains of amino acid residues are often called (oligo-)peptides.
Figure 10 Chemical structure (bottom) and the 3D structure (top) of a peptide bond between two adjacent amino acid residues. The N-terminal end of a polypeptide contains a free amino group and the C-terminal end contains a free carboxylate group. Image from wikipedia.
Protein structures are also classified by their secondary structure. Secondary structure refers to regular, local structure of the protein backbone, stabilised by intramolecular and sometimes intermolecular hydrogen bonding of amide groups.
There are two common types of secondary structure (figure 11). The most prevalent is the alpha helix.
The alpha helix (α has a right-handed spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues before it in the sequence.
The other common type of seconday structure is the beta strand. A Beta strand (β strand) is a stretch of polypeptide chain, typically 3 to 10 amino acids long, with its backbone in an almost fully extended conformation. Two or more parallel or antiparallel adjacent polypeptide chains of beta strand stabilised by hydrogen bonds form a beta sheet. For example, the proteins in silk have a beta-sheet structure. Those local structures are stabilised by hydrogen bonds and connected by tight turns and loose, flexible loops.
Figure 11Alpha helix (blue) and antiparallel beta sheet composed of three beta strands (yellow and red).
A common way for researchers to look at the conformations of amino acids in proteins is to use a Ramachandran plot (Figure 12). If successive amino acids are found in particular so-called "favourable" regions of the plot, these tend to form particular secondary structures (sheets, strands and helices). However, it should be noted that loop and turn residues are also found in these areas and it is possible to find individual amino acids in "unfavourable" regions.
Figure 12: Ramachandran plot generated with coordinates from the human DNA clamp PCNA, showing two regions containing the most favorable combinations of ψ and φ and contain the greatest number of data points (blue) and four allowed regions (green).
The Ramachandran plot is a plot of the torsional angles (angles between two planes) - psi (ψ) and phi (φ) - of amino acids contained in a peptide. It is used to show the ranges of angles that are permissible and the main types of structure adopted by a polypeptide chain (for example, α helix, β sheet). By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.
The spatial arrangement of secondary structure elements results in the formation of the tertiary structure or fold of a protein. The tertiary structure is held together by non-covalent interactions(hydrogen bonding, ionic interactions, van der Waals forces, and hydrophobic packing), disulphide bonds and metal ion coordination.
An example of the tertiary structure is a single-domain globular protein. Globular proteins (6) are sphere-like proteins that are more or less soluble in aqueous solutions (the other two protein classes are membrane and fibrous proteins) (Figure 13).
Some proteins form assemblies (units) with other molecules - this is called the quaternary structure (Figure 14).
Two examples are: haemoglobin which is an assembly of four globular proteins and the actin microfilament, composed of many thousands actin molecules.
In the PDB, assemblies of different proteins or different macromolecules are also reffered to as the quaternary structure; for example, ribosome is described as a quaternary structure.
Figure 14 An example of a quaternary structure composed of two copies of a protein (in yellow and green) and a double-stranded DNA molecule. The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex.