Overall features of protein structure

Shifting from one interdisciplinary nomenclature to another we can view the bidentate molecule as an amino acid, the amide becomes a peptide and the polyamide a polypeptide or a protein. Hence, we have abjured organic chemistry in favour of biochemistry. Proteins are built up from approximately 20-25 different a-amino acids, the individual order of which decide the chemical and physical properties of a particular protein. Due to a combination of certain attributes of e peptide linkage, and the presence of functionalities enabling the formation of hydrogen bonds, protein strands fall into one of three geometrically different categories random coil, a-helix and pleated sheet. 

Quaternary structure is akin to the mesostructure of lipid or surfactant self-assemblies, such as the aggregates characteristic of mesh-structures in bacterial protein coats (described in Chapter 4), or the cholesteric liquid crystals found in 

As a consequence of the individual order of the amino acids and the conformation of the ensuing polypeptide strands (the primary and secondary structures) the three-dimensional structure of each molecule (its tertiary structure) is formed. The bulk of this Chapter is focussed on this aspect of molecular structure. Some comments on quaternary structure and protein crystallisation form a shorter afterword. 

A fundamental feature of proteins is their amphiphihc and chiral characteristics, which induce folding of the peptide chain that results in a mainly hydrophobic core covered by a hydrophihc surface layer. In the evolution of protein structure, which has taken place in an aqueous envirorvment, the forces that drive self-assembly (discuss in Chapter 3) have played a central role. 

In order to imderstand tertiary and quaternary structure, we need to explore briefly the secondary structural possibilities of protein molecules. The a-helix was predicted in 1951 by Linus Pauling. The peptide chain forms a compact core with the residues pointing outwards. The pitch is formed by 3.6 amino acid residues, with a helical period of 5.4 A. The structure is stabilised by a very-effective network of hydrogen bonds. 

---