STRUCTURE & FUNCTION

 

The Beta Turn
beta turnTurns 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. You 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 numerous types on the basis of the details of their geometry.

Gamma turns are three residue turns which often incorporate a hydrogen bond between the C=O of residue i and the N-H of residue i+2.

Random Coil
Some regions of the protein chain do not form regular secondary structure or are not characterized by any regular hydrogen bonding pattern. The regions are known as random coils. There are two places where random coils can be found:

They can be 4 to 20 residues long, although most loops are not longer than 12 residues. Most loops are exposed to the solvent and are characterized by polar or charged side-chains. In some cases loops have a functional role, but in many cases they do not (as can be learned from the fact that in many cases loop regions are poorly conserved in evolution).

KiNG
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View1 shows four residues in a Type I beta turn or reverse turn ("Type I") displayed in ball-and-stick form with its main chain bonds white and its atoms colored according to type (C brown, N blue, H white and O red). The bonds to the H atoms of the main chain and the side chain Ca-Cb bonds, which are controlled by the "Hydrogens" and "R-Groups" buttons, are gray and purple. Click the "H-bonds" button several times to see the H-bond joining the carbonyl oxygen of this reverse turn's first residue (Ser 159) to the amide hydrogen of its fourth residue (Ser 162).

Reverse turns include both polar (magenta) as well as nonpolar (gold) sidechains (here controlled by the "Polar sc" and "Nonpolar sc" buttons), even though they almost always occur at protein surfaces. Proline residues commonly occur at position 2 in a beta turn because a Pro residue can adopt the PHI and PSI angles required at this position and probably because its presence bestows rigidity on the structure. Note that residue 2 in this example is Pro 160.

In View1, ANIMATE to convert the Type I beta turn to a type II beta turn. Type II beta turn ("Type II"), differ from Type I beta turn by a 180 degree flip of the peptide unit linking their residues 2 and 3. Can you see the peptide unit "flip" so as to position the carbonyl oxygen on the opposite side of the turn? Rotate the structure for different views of this flip.

In Type II beta turns, as in Type I beta turns, the carbonyl oxygen of residue 1 (Asn 89) is hydrogen bonded to the amide hydrogen of residue 4 (Gln 92). However, in Type II beta turns, the carbonyl oxygen atom of residue 2 would crowd the beta carbon atom (Cb) of residue 3. Consequently, residue 3 of Type II beta turns is usually Gly as it is here (Gly 91). How does the distance between the sidechain hydrogen of Gly 91 and the carbonyl oxygen of residue 2 (Tyr 90) compare with the C-O van der Waals distance necessary for any other sidechain (2.8Å)?

Beta turns or reverse turns cause the polypeptide chain to abruptly change its direction. They often connect successive strands of an antiparallel beta sheet (which is why they are named beta turns). However, they can occur in any nonrepetitive structure. Turn on the "More" buttons to see that the Type I beta turn shown here is part of a loop structure (View2) and the Type II beta turn joins two approximately perpendicular helices (View3). In both beta turns, their N- and C-terminal extensions are bluetint and pinktint and the hydrogen bonds they form are represented by dashed greentint lines.

 

Some text adapted from: "EXERCISE 3. PROTEIN SECONDARY STRUCTURES" by Kim M. Gernert and Kim M. Kitzler.

Copyright ©2004 Stephen J. Everse, All Rights Reserved.

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