3.0 Loops

Loops, unlike alpha helices or beta sheets, are an irregular secondary structure in proteins (ie. there is no regular geometric repetition of a residue's phi and psi angles along the structure). Loops may be considered a diverse class of secondary structures comprising turns, 'random coils', and strands which connect the main secondary structures (alpha helices and beta strands).

Turns are the third most common secondary structure element in proteins and up to one third of residues may be involved in turns in a globular protein. As their name suggests they are responsible for changing the direction of the polypeptide chain within a globular protein.

Summary of 'loop' characteristics

• formed from 2 to 16 residues (OmpF has loops of up to 46 connecting the beta strands)

• long loops are also sometimes called 'random coils' although they are neither random (because they exhibit some amino acid preferences and some structural preferences ) nor coiled (ie coiled like a helix)

• found on surface of molecule (and contain polar residues)

• irregular structures

• participate in forming binding sites and enzyme active sites eg. antigen binding sites in antibodies are built up from about six loop regions

• amino acids in loops often not conserved

• beta turns are the most abundant 'loop' secondary structures (also called reverse turns because they reverse the direction of the chain). There are three main types of turns Type I, II, and III. There are also the complement of these turns Type I' II' and III'. For our purposes we'll look at Type I and II turns and their complement. The classification of these types of turns varies (see Protein Secondary Structure by Kurt D Berndt). One classification is by the phi and psi angles of the residues which make up the turn. Details of turns are as follows:

1. The two types of turns are Type I and Type II (Figure 3.1). There is also a 'mirror image' or complement of these conformations labeled Type I' and Type II' (Figure 3.2) but these are rare (except in hairpin structures see below) because of steric hindrance between residues involved in the turn.
2. Type I and II turns have phi and psi angles shown in Figure 3.3
3. Type I' and II' turns have phi and psi angles shown in Figure 3.4
4. Type I are the most common turns although Type I' and Type II' occurs more often in beta-hairpin supersecondary structures (see later)
5. There are preferences for particular amino acids at certain positions within the turn as seen in the Ramachandran Plot. for example Residue 2 in Type Type II' turns, and residue 3 in Type II and Type I' are nearly always glycine (see Figure 3.3 and 3.4)
6. Most turns consist of up to four residues (see for example Figure 3.1)