Beta barrel

A beta barrel is a beta-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 proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins. Others span cell membranes and commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in Gram-negative bacteria. A beta barrel is a beta-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 proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins. Others span cell membranes and commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in Gram-negative bacteria. 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 aquaeous 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. These two parameters (n and S) are related to the inclination angle of the beta strands relative to the axis of the barrel. Up-and-down barrels are the simplest barrel topology and consist of a series of beta strands, each of which is hydrogen-bonded to the strands immediately before and after it in the primary sequence. The jelly roll fold or barrel, also known as the Swiss roll, typically comprises eight beta strands arranged in two four-stranded sheets. Adjacent strands along the sequence alternate between the two sheets, such that they are 'wrapped' in three dimensions to form a barrel shape. Sixteen- or eighteen-stranded up-and-down beta barrel structures occur in porins, which function as transporters for ions and small molecules that cannot diffuse across a cellular membrane. Such structures appear in the outer membranes of gram-negative bacteria, chloroplasts, and mitochondria. The central pore of the protein, sometimes known as the eyelet, is lined with charged residues arranged so that the positive and negative charges appear on opposite sides of the pore. A long loop between two beta strands partially occludes the central channel; the exact size and conformation of the loop helps in discriminating between molecules passing through the transporter. Beta barrels also function within endosymbiont derived organelles such as mitochondria and chloroplasts to transport proteins. Within the mitochondrion two complexes exist with beta barrels serving as the pore forming subunit, Tom40 of the Translocase of the outer membrane, and Sam50 of the Sorting and assembly machinery. The chloroplast also has functionally similar beta barrel containing complexes, the best characterised of which is Toc75 of the TOC complex (Translocon at the outer envelope membrane of chloroplasts). Lipocalins are typically eight-stranded up-and-down beta barrel proteins that are secreted into the extracellular environment. A distinctive feature is their ability to bind and transport small hydrophobic molecules in the barrel calyx. Examples of the family include retinol binding proteins (RBPs) and major urinary proteins (Mups). RBP binds and transports retinol (vitamin A), while Mups bind a number of small, organic pheromones, including 2-sec-butyl-4,5-dihydrothiazole (abbreviated as SBT or DHT), 6-hydroxy-6-methyl-3-heptanone (HMH) and 2,3 dihydro-exo-brevicomin (DHB).