Beta bulge

A beta bulge can be described as a localized disruption of the regular hydrogen bonding of beta sheet by inserting extra residues into one or both hydrogen bonded β-strands.[1][2][3][4]

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 angles (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 first residue at the outwards bulge typically has the αR, rather than the normal β, conformation.

The other type is the beta bulge loop (also named type G1 β-bulge), often occurs in association with an antiparallel sheet, but also in other situations. One residue has the αL conformation and is part of a beta turn or alpha turn, such that the motif sometimes forms the loop of a beta hairpin.[5]

Effects on structure

At the level of the backbone structure, classic β-bulges can cause a simple aneurysm of the β-sheet, e.g., the bulge in the long β-hairpin of ribonuclease A (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 angles 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
  1. Richardson, JS; Getzoff, ED; Richardson, DC (1978). "The β-bulge: a common small unit of nonrepetitive protein structure". Proc Natl Acad Sci USA. 75 (6): 2574–8. doi:10.1073/pnas.75.6.2574. PMC 392604. PMID 275827.
  2. Richardson, J. S. (1981). "The anatomy and taxonomy of protein structure". Adv Protein Chem. 34: 167–339. doi:10.1016/S0065-3233(08)60520-3. PMID 7020376.
  3. Chan, AW; Hutchinson, EG; Harris, D; Thornton, JM (1993). "Identification, classification, and analysis of beta-bulges in proteins". Protein Sci. 2 (10): 1574–90. doi:10.1002/pro.5560021004. PMC 2142268. PMID 8251933.
  4. Craveur, P; Joseph, AP; Rebehmed, J; de Brevern, AG (2013). "β-bulges: extensive structural analysis of β-sheet irregularities". Protein Science. 22 (10): 1366–1378. doi:10.1002/pro.2324. PMC 3795495.
  5. Milner-White EJ (1987). "Beta-bulges within loops as recurring features of protein structure". Biochim Biophys Acta. 911 (2): 261–5. doi:10.1016/0167-4838(87)90017-3. PMID 3801498.
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