In protein structures, a beta barrel (β barrel) is a

beta sheet The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a gene ...

(β sheet) composed of

tandem repeats In genetics, tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other, e.g. ATTCG ATTCG ATTCG, in which the sequence ATTCG is repeated three times. Several protein ...

that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (

hydrogen bond In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ...

). Beta-strands in many beta-barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the

barrel A barrel or cask is a hollow cylindrical container with a bulging center, longer than it is wide. They are traditionally made of wooden stave (wood), staves and bound by wooden or metal hoops. The word vat is often used for large containers ...

s used to contain liquids. Most of them are water-soluble outer membrane proteins and frequently bind

hydrophobic In chemistry, hydrophobicity is the chemical property of a molecule (called a hydrophobe) that is seemingly repelled from a mass of water. In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thu ...

ligand In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's el ...

s in the barrel center, as in

lipocalin The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron (via siderophores or flavonoids) as well as heme. Th ...

s. Others span

cell membrane The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...

s and are commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in

Gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

bacteria. It has been shown that more than 600 proteins with various function such as oxidase, dismutase, and amylase contain the beta barrel structure. In many cases, the strands contain alternating polar and non-polar (

hydrophilic A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press. In contrast, hydrophobes are n ...

and

)

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

s, so that the hydrophobic residues are oriented into the interior of the barrel to form a

hydrophobic core The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and to be excluded by water#Properties, water. The word hydrophobic literally means "water-fearing", and it describes the Segregation in m ...

and the polar residues are oriented toward the outside of the barrel on the solvent-exposed surface. Porins and other

membrane protein Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...

s containing beta barrels reverse this pattern, with hydrophobic residues oriented toward the exterior where they contact the surrounding

lipid Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...

s, 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. These two parameters (n and S) are related to the inclination angle of the beta strands relative to the axis of the barrel.

Types

Up-and-down

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 Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length sca ...

Jelly roll

The

jelly roll fold The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance ...

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.

Examples

Porins

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 Diffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical p ...

across a cellular membrane. Such structures appear in the outer membranes of

gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

bacteria,

chloroplast A chloroplast () is a type of membrane-bound organelle, organelle known as a plastid that conducts photosynthesis mostly in plant cell, plant and algae, algal cells. Chloroplasts have a high concentration of chlorophyll pigments which captur ...

s, and

mitochondria A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...

. 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.

Preprotein translocases

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 The translocase of the outer membrane (TOM) is a complex of proteins found in the outer mitochondrial membrane of the mitochondria. It allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion. M ...

, and Sam50 of the

Sorting and assembly machinery The outer mitochondrial membrane is made up of two essential proteins, Tom40 and Sam50. Tom40 Tom40 is a protein import pore required for the import of precursor proteins across the outer mitochondrial membrane, and it makes up part of the tran ...

. 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

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 protein Retinol-binding proteins (RBP) are a family of proteins with diverse functions. They are carrier proteins that bind retinol. Assessment of retinol-binding protein is used to determine visceral protein mass in health-related nutritional studies. R ...

s (RBPs) and

major urinary proteins Major urinary proteins (Mups), also known as α2u-globulins, are a protein subfamily, subfamily of proteins found in abundance in the urine and other secretions of many animals. Mups provide a small range of identifying information about the don ...

(Mups). RBP binds and transports

retinol Retinol, also called vitamin A1, is a fat-soluble vitamin in the vitamin A family that is found in food and used as a dietary supplement. Retinol or other forms of vitamin A are needed for vision, cellular development, maintenance of skin and ...

(vitamin A), while Mups bind a number of small, organic

pheromones A pheromone () is a secreted or excreted chemical factor that triggers a social response in members of the same species. Pheromones are chemicals capable of acting like hormones outside the body of the secreting individual, to affect the behavi ...

, 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).

Shear number

A piece of paper can be formed into a cylinder by bringing opposite sides together. The two edges come together to form a line. Shear can be created by sliding the two edges parallel to that line. Likewise, a beta barrel can be formed by bringing the edges of a beta sheet together to form a cylinder. If those edges are displaced, shear is created. A similar definition is found in geology, where shear refers to a displacement within rock perpendicular to the rock surface. In physics, the amount of displacement is referred to as

shear strain In mechanics, strain is defined as relative deformation, compared to a position configuration. Different equivalent choices may be made for the expression of a strain field depending on whether it is defined with respect to the initial or the ...

, which has units of length. For shear number in barrels, displacement is measured in units of amino acid residues. The determination of shear number requires the assumption that each amino acid in one strand of a

is adjacent to just one amino acid in the neighboring strand (this assumption may not hold if, for example, a beta bulge is present). To illustrate, ''S'' will be calculated for

green fluorescent protein The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish ''Aequorea victo ...

. This protein was chosen because the beta barrel contains both parallel and antiparallel strands. To determine which amino acid residues are adjacent in the beta strands, the location of hydrogen bonds is determined. Shear Number GFP

The inter-strand hydrogen bonds can be summarised in a table. Each column contains the residues in one strand (strand 1 is repeated in the last column). The arrows indicate the hydrogen bonds that were identified in the figures. The relative direction of each strand is indicated by the "+" and "-" at the bottom of the table. Except for strands 1 and 6, all strands are antiparallel. The parallel interaction between strands 1 and 6 accounts for the different appearance of the hydrogen bonding pattern. (Some arrows are missing because not all of the hydrogen bonds expected were identified. Non-standard amino acids are indicated with "?") The side chains that point to the outside of the barrel are in bold. If no shear were present in this barrel, then residue 12 V, say, in strand 1 should end up in the last strand at the same level as it started at. However, because of shear, 12 V is not at the same level: it is 14 residues higher than it started at, so its shear number, ''S'', is 14.

References

External links

Explanation of all-beta topologies
"orthogonal

beta-sandwich Beta-sandwich or β-sandwich domains consisting of 80 to 350 amino acids occur commonly in proteins. They are characterized by two opposing antiparallel beta sheets (β-sheets). The number of strands found in such domains may differ from one prote ...

es" are beta-barrels (as defined in this article); "aligned" beta-sandwiches" correspond to

folds in

SCOP A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...

classification.
all-beta folds in SCOP database
(folds 54 to 100 are water-soluble beta-barrels).
CATH database - folds and homologous superfamilies within the beta-barrel architecture.
* ttp://www.biologie.uni-konstanz.de/folding/Structure%20gallery%201.html Images and examples of transmembrane beta-barrelsbr>Stockholm Bioinformatics Center review of transmembrane proteins
* The OMPdb database for beta-barrel proteins {{Protein tertiary structure Protein structure Protein folds Protein tandem repeats Protein domains