Beta barrel

18-strand β barrel. Bacterial sucrose-specific porin from S. typhimurium. It sits in a membrane and allows sucrose to diffuse through. (PDB: 1A0S​)
8-strand β barrel. Human retinol-binding protein bound to retinol (vitamin A) in blue. (PDB: 1RBP​)

In protein structures, a beta barrel (β barrel) is a beta sheet (β sheet) composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the barrels used to contain liquids. Most of them are water-soluble outer membrane proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins. Others span cell membranes and are commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in Gram-negative bacteria.[1] It has been shown that more than 600 proteins with various function such as oxidase, dismutase, and amylase contain the beta barrel structure.[2]

In many cases, the strands contain alternating polar and non-polar (hydrophilic and hydrophobic) amino acids, so that the hydrophobic residues are oriented into the interior of the barrel to form a hydrophobic core and the polar residues are oriented toward the outside of the barrel on the solvent-exposed surface. Porins and other membrane proteins containing beta barrels reverse this pattern, with hydrophobic residues oriented toward the exterior where they contact the surrounding lipids, and hydrophilic residues oriented toward the aqueous interior pore.

All beta-barrels can be classified in terms of two integer parameters: the number of strands in the beta-sheet, n, and the "shear number", S, a measure of the stagger of the strands in the beta-sheet.[3] These two parameters (n and S) are related to the inclination angle of the beta strands relative to the axis of the barrel.[4][5][6]

  1. ^ Wimley WC (August 2003). "The versatile beta-barrel membrane protein". Current Opinion in Structural Biology. 13 (4): 404–411. doi:10.1016/S0959-440X(03)00099-X. PMID 12948769.
  2. ^ Lu Y, Yeung N, Sieracki N, Marshall NM (August 2009). "Design of functional metalloproteins". Nature. 460 (7257): 855–862. Bibcode:2009Natur.460..855L. doi:10.1038/nature08304. PMC 2770889. PMID 19675646.
  3. ^ Murzin AG, Lesk AM, Chothia C (March 1994). "Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis". Journal of Molecular Biology. 236 (5): 1369–1381. doi:10.1016/0022-2836(94)90064-7. PMID 8126726.
  4. ^ Murzin AG, Lesk AM, Chothia C (March 1994). "Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures". Journal of Molecular Biology. 236 (5): 1382–1400. doi:10.1016/0022-2836(94)90065-5. PMID 8126727.
  5. ^ Liu WM (January 1998). "Shear numbers of protein beta-barrels: definition refinements and statistics". Journal of Molecular Biology. 275 (4): 541–545. doi:10.1006/jmbi.1997.1501. PMID 9466929.
  6. ^ Hayward S, Milner-White EJ (October 2017). "Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments" (PDF). Proteins. 85 (10): 1866–1881. doi:10.1002/prot.25341. PMID 28646497. S2CID 206410314.