A beta bulge can be described as a localized disruption of the regular
hydrogen bond
In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a l ...
ing of
beta sheet
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a ge ...
by inserting extra residues into one or both hydrogen bonded β-strands.
Types
β-bulges can be grouped according to their length of the disruption, the number of residues inserted into each strand, whether the disrupted β-strands are parallel or antiparallel and by their
dihedral angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the un ...
s (which controls the placement of their side chains). Two types occur commonly. One, the ''classic beta bulge'', occurs within, or at the edge of, antiparallel
beta-sheet
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a ge ...
; the first residue at the outwards bulge typically has the α
R, rather than the normal β, conformation.
The other type is the G1 ''beta bulge'', of which there are two common sorts, both mainly occurring in association with antiparallel sheet; one residue has the α
L conformation and is usually a glycine. In one sort, the
beta bulge loop
Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, a ...
, one of the hydrogen bonds of the beta-bulge also forms a
beta turn β turns (also β-bends, tight turns, reverse turns, Venkatachalam turns) are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common mot ...
or alpha turn, such that the motif is often at the loop of a
beta hairpin.
In the other sort, the
beta link, the beta bulge occurs in combination with, and overlaps, a type II
beta turn β turns (also β-bends, tight turns, reverse turns, Venkatachalam turns) are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common mot ...
.
Effects on structure
At the level of the backbone structure, classic β-bulges can cause a simple
aneurysm
An aneurysm is an outward bulging, likened to a bubble or balloon, caused by a localized, abnormal, weak spot on a blood vessel wall. Aneurysms may be a result of a hereditary condition or an acquired disease. Aneurysms can also be a nidus ( ...
of the β-sheet, e.g., the bulge in the long β-hairpin of
ribonuclease A
Pancreatic ribonuclease family (, ''RNase'', ''RNase I'', ''RNase A'', ''pancreatic RNase'', ''ribonuclease I'', ''endoribonuclease I'', ''ribonucleic phosphatase'', ''alkaline ribonuclease'', ''ribonuclease'', ''gene S glycoproteins'', ''Ceratit ...
(residues 88–91). A β-bulge can also cause a β-sheet to fold over and cross itself, e.g., when two residues with left-handed and right-handed α-helical
dihedral angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the un ...
s are inserted opposite to each other in a β-hairpin, as occurs at Met9 and Asn16 in
pseudoazurin (PDB accession code 1PAZ).
Effect on Functionality of Proteins
Conserved bulges regularly affect protein functionality. The most basic function of bulges is to accommodate an extra residue added due to mutation etc., while maintaining the bonding pattern and thus the overall protein architecture. Other bulges are involved with protein binding sites. In specific cases like the Immunoglobulin family proteins, conserved bulges help dimerization of the Ig domains. They are also of functional importance in the proteins DHFR (Dihydrofolate Reductase) and SOD (Superoxide Dismutase), where loops containing bulges surround the active site.
References
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{{DEFAULTSORT:Beta Bulge
Protein structural motifs