Bioinformatics Protein Structure Structure Analysis

Reverse Turns and Loops

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In compact globular proteins, a polypeptide often makes a sharp turn called a reverse turn. For example, these turns often link adjacent strands in an antiparallel β pleated sheet. These are also known as β bends, reverse turns involve four amino acid residues with a hydrogen bond between the C=O group of the first residue and the N–H group of the fourth.

Features

  • Type I and type II β bends differ in respect of the torsion angles for the residues
  • These bends are tighter than the turn in the α helix structure
  • The second residue in the turn is frequently proline, which readily adopts the required conformation for such a turn
  • Another type of turn is the omega loop. This loop has between 6 and 16 residues in a compact structure with a pinched-in shape resembling the Greek upper case character Ω (omega). 
  • The side-chains of omega loops fill the inside of the loop.

A reverse turn is a region of the polypeptide having a hydrogen bond from one main chain carbonyl oxygen to the main chain N-H group 3 residues along the chain such as O(i) to N(i+3). Helical regions are excluded from this definition and turns between beta-strands form a special class of turn known as the beta-hairpin. Reverse turns are very abundant in globular proteins and generally occur at the surface of the molecule. It has been suggested that turn regions act as nucleation centers during protein folding.

In a beta turn, a tight loop is formed  when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain.  This hydrogen bond stabilizes the beta bend structure.

Proline and Glycine are frequently found in beta turns, proline because its cyclic structure is ideally suited for the beta turn, and glycine because, with the smallest side chain of all the amino acids, it is the most sterically flexible. 

Turns generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. The most common is the beta turn, in which the change of direction is executed in the space of four residues. Some commonly observed features of beta turns are a hydrogen bond between the C=O of residue i and the N-H of residue i+3 (i.e, between the first and the fourth residue of the turn) and a tendency to involve glycine and/or proline, but these are not universal. We will sometimes hear the phrase “beta hairpin” which can be used to describe a beta turn joining two anti-parallel beta strands together. Beta turns are subdivided into certain types on the basis of the details of their geometry.

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