Beta Barrel

Information about Beta Barrel

A canonical beta-barrel protein, a sucrose-specific porin from the bacterium Salmonella typhimurium, viewed from the side. Porins are transmembrane proteins with hollow centers through which small molecules can diffuse.

The human retinol-binding protein (RBP), a canonical lipocalin eight-strand barrel binding retinol (vitamin A).

A beta barrel is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last. Beta-strands in beta-barrels are typically arranged in an antiparallel fashion. Barrel structures are commonly found in porins and other proteins that span cell membranes and in proteins that bind hydrophobic ligands in the barrel center, as in lipocalins. Porin-like barrel structures account for as many as 2–3% of the genes in gram-negative bacteria.^[1]

In many cases the strands contain alternating polar 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 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.^[2] These two parameters (n and S) are related to the inclination angle of the beta strands relative to the axis of the barrel.^[3]^[4]

Types of beta barrels

Most beta barrels have one of three topologies:

Up-and-down beta 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.

Greek key

Greek key barrels have some beta strands adjacent in space that are not adjacent in sequence. Beta barrels generally consist of at least one Greek key structural motif linked to a beta hairpin, or two successive Greek keys.

Jelly roll

The jelly roll barrel, also known as the Swiss roll, is a complex nonlocal structure in which four pairs of antiparallel beta sheets, only one of which is adjacent in sequence, are "wrapped" in three dimensions to form a barrel shape.

Porins

Main article: Porin (protein)

Sixteen- or eighteen-stranded beta barrel structures are common 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 sheets partially occludes the central channel; the exact size and conformation of the loop helps in discriminating between molecules passing through the transporter.

Lipocalins

Main article: Lipocalin

Lipocalins are typically eight-stranded beta barrel proteins that are often secreted into the extracellular environment. Their most distinctive feature is their ability to bind and transport small hydrophobic molecules. The most famous example of the family is retinol binding protein (RBP), which binds and transports retinol (vitamin A). In humans, retinol is stored in the liver and transported by RBP to other tissues. Each RBP molecule transports a single retinol molecule in a process mediated by protein-protein interactions with prealbumin and various cell-surface receptors; after the retinol has been delivered, the RBP molecule is degraded in the kidney.

References

1. ^ Wimley WC. (2003). "The versatile beta-barrel membrane protein". Curr Opin Struct Biol 13(4): 404–11. PMID 12948769.
2. ^ Murzin A, Lesk A, Chothia C (1994). "Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis". J Mol Biol 236 (5): 1369–81. PMID 8126726.
3. ^ Murzin A, Lesk A, Chothia C (1994). "Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures". J Mol Biol 236 (5): 1382–400. PMID 8126727.
4. ^ Liu WM. (1998). "Shear numbers of protein beta-barrels: definition refinements and statistics". J Mol Biol 275(4): 5415. PMID 9466929.

External links

Explanation of all-beta topologies: "orthogonal beta-sandwiches" are beta-barrels (as defined in this article); "aligned" beta-sandwiches" correspond to beta-sandwich folds in SCOP classification.
all-beta folds in SCOP database (folds 54 to 100 are water-soluble beta-barrels).
General classification and images of protein structures from Jane Richardson lab
Images and examples of transmembrane beta-barrels
Stockholm Bioinformatics Center review of transmembrane proteins
The Lipocalin Website

• • [ e] Protein tertiary structure
General	Structural domain
All-α folds:	Helix bundle
All-β folds:	Immunoglobulin fold
α/β folds:	TIM barrel
α+β folds:	Ferredoxin fold
Irregular folds:	Conotoxin
←Secondary structure Quaternary structure→

β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins — the first is the alpha helix — consisting of beta strands
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The term antiparallel may refer to:

Antiparallel (biochemistry), the orientation of adjacent molecules
Antiparallel (mathematics), the placement of parallel lines in relation to an angle
Antiparallel (electronics), the polarity of devices run in parallel

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Porins are beta barrel proteins which cross a cellular membrane and act as a pore through which molecules can diffuse. Unlike other membrane transport proteins, porins are large enough to allow passive diffusion - i.e.
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hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water ^[1].
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In chemistry, a ligand is an atom, ion, or molecule (see also: functional group) that generally donates one or more of its electrons through a coordinate covalent bond to, or shares its electrons through a covalent bond with, one or more central atoms or ions (these ligands act as
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Gram-negative bacteria are those that do not retain crystal violet dye in the Gram staining protocol.^[1] Gram-positive bacteria will retain the dark blue dye after an alcohol wash.
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Chemical polarity, also known as bond polarity or simply polarity, is a concept in chemistry which describes how equally bonding electrons are shared between atoms.
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amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H₂NCHRCOOH, where R is an organic substituent.
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hydrophobic effect is the property that nonpolar molecules tend to form intermolecular aggregates in an aqueous medium and analogous intramolecular interactions.^[1]^[2] The name arises from the combination of water in Attic Greek hydro-
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A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.
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Lipids can be broadly defined as any fat-soluble (hydrophobic), naturally-occurring molecules. The term is more-specifically used to refer to fatty-acids and their derivatives (including tri-, di-, and monoglycerides and phospholipids) as well as other fat-soluble sterol-containing
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primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular
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Greek key refers to a kind of supersecondary structure or motif of a protein (amino-acid) sequence. It is named for its resemblance to the Greek key meander pattern in art.
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structural motif is a three-dimensional structural element or fold within the chain, which appears also in a variety of other molecules. In the context of proteins, the term is sometimes used interchangeably with "structural domain," although a domain need not be a motif
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The beta hairpin (or beta-beta unit) structural motif is the simplest protein motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary sequence oriented in an antiparallel arrangement (where the
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This article is about the physical mechanism of diffusion. For alternative meanings, see diffusion (disambiguation).

Diffusion is the net movement of particles from an area of high concentration to an area of low concentration.
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The outer membrane refers to the outside membranes of Gram-negative bacteria, the chloroplast, or the mitochondria. It is used to maintain the shape of the organelle contained within its structure, and it acts as a barrier against certain dangers.
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Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water and carbon dioxide to produce sugars, the raw material for energy and biomass production in all green plants
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The lipocalin family of proteins is a functionally and structurally diverse group. Although these proteins are most commonly found in gram negative bacterial cells, vertebrate cells, and invertebrate cells, plant lipocalins have also recently been researched.
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Retinol (Afaxin), the animal form of vitamin A, is a fat-soluble vitamin important in vision and bone growth. It belongs to the family of chemical compounds known as retinoids.
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liver is an organ present in vertebrates and some other animals. It plays a major role in metabolism and has a number of functions in the body, including glycogen storage, decomposition of red blood cells, plasma protein synthesis, and detoxification.
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Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks.

The interactions between proteins are important for many biological functions.
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Transthyretin (TTR) is a serum and cerebrospinal fluid carrier of the thyroid hormone thyroxine (T4).

TTR was originally called prealbumin^[1] because it ran faster than albumins on electrophoresis gels.
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For other uses, see Receptor.

In biochemistry, a receptor is a protein on the cell membrane or within the cytoplasm or cell nucleus that binds to a specific molecule (a ligand), such as a neurotransmitter, hormone, or other substance, and initiates
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The kidneys are organs that filter wastes (such as urea) from the blood and excrete them, along with water, as urine. The medical field that studies the kidneys and diseases of the kidney is called nephrology^[1].
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