Beta bulge
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A beta bulge is a localized disruption of the regular hydrogen bonding of a beta sheet, usually by inserting a residue with helical dihedral angles into one or both H-bonded β-strands.
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[edit] 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).
[edit] Effects on structure
At the level of the backbone structure, 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).
[edit] Effect on Functionality of Proteins
Bulges play an important role in affecting the functionality of proteins in which they are conserved. The most basic function of Bulges is to accommodate an extra residue, that has been added due to mutation etc, while still maintaining the bonding pattern and thus the overall architecture of the protein. In specific cases like the Immunoglobulin-family proteins, these Bulges are conserved and help in dimerization of the Ig domains. They have found to be of functional importance in the protein DHFR(Di-Hydro Folate Reductase) and SOD(Super Oxide Dismutase) where the loops, containing the bulges, help to enclose the active site.
[edit] References
- Richardson JS, Getzoff ED and Richardson DC. (1978) "The β-bulge: A common small unit of nonrepetitive protein structure", Proc. Natl. Acad. Sci. USA, 75, 2574-2578.
- Richardson JS. (1981) "The anatomy and taxonomy of protein structure", Adv. Protein Chem., 34, 167-339.
- Chan AWE, Hutchinson EG, Harris D and Thornton JM. (1993) "Identification, classification, and analysis of beta-bulges in proteins", Protein Sci., 2, 1574-1590.
| Protein secondary structure | ||
|---|---|---|
| Helices: | α-helix | 310 helix | π-helix | β-helix | Polyproline helix | Collagen helix | |
| Extended: | β-strand | Turn | Beta hairpin | Beta bulge | α-strand | |
| Supersecondary: | Coiled coil | Helix-turn-helix | EF hand | |
| Secondary structure propensities of amino acids | ||
| Helix-favoring: | Methionine | Alanine | Leucine | Glutamic acid | Glutamine | Lysine | |
| Extended-favoring: | Threonine | Isoleucine | Valine | Phenylalanine | Tyrosine | Tryptophan | |
| Disorder-favoring: | Glycine | Serine | Proline | Asparagine | Aspartic acid | |
| No preference: | Cysteine | Histidine | Arginine | |
| ←Primary structure | Tertiary structure→ | |
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