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.
[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] 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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