Isabella Carter
Beta barrels, or beta-barrel proteins, are a type of transmembrane protein that is found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. They are composed of beta-sheets that twist and coil to form a cylindrical barrel shape, with hydrophobic exteriors and hydrophilic interiors. The hydrophobic exterior allows the protein to interact with the lipidic membrane, while the hydrophilic interior can form an aqueous channel or host other structures. Beta barrels serve essential functions in cargo transport, signalling, and membrane biogenesis, and can also act as porins, transporters, enzymes, virulence factors, and receptors. The biogenesis of beta barrels involves a complex process that includes translocases, barrel assembly machinery, and helper chaperone proteins, and their structure and function have been the subject of extensive research and modelling.
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What You'll Learn
The beta-barrel structure
In protein structures, a beta barrel (β barrel) is a beta sheet (β sheet) that twists and coils to form a closed toroidal structure. Beta barrels are named for their resemblance to the barrels used to contain liquids. They are composed of tandem repeats, with the first strand bonded to the last strand (hydrogen bond).
Beta-barrel structures are most commonly found in water-soluble outer membrane proteins and frequently bind hydrophobic ligands in the barrel centre, as in lipocalins. They also 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. Beta barrels can also be found in mitochondria and chloroplasts, where they function to transport proteins.
The beta-barrel scaffold is a versatile structure that allows proteins with this domain to perform a variety of functions. The cylindrical shape of beta barrels forms a pore that traverses the outer membrane, making it well-suited for transport. Many beta-barrel proteins are involved in the transport of nutrients into the cell or the secretion or excretion of substances out of the cell.
The biogenesis of transmembrane beta barrels (outer membrane proteins, or OMPs) is a complex process involving the orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. OMPs of bacterial origin possess even-numbered strands, while mitochondrial beta barrels have both even and odd-numbered strands.
Transmembrane beta-barrel proteins have a folded domain that presents a hydrophobic surface to the membrane environment. The outside of the cylinder is hydrophobic and faces the lipidic membrane, while the inside of the cylinder, or the lumen, is often hydrophilic. This allows the formation of an aqueous channel through the membrane or the hosting of other structures within it.
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Integral membrane proteins
Beta barrels constitute the transmembrane domain of integral membrane proteins in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. They serve essential functions in cargo transport, signalling, and membrane biogenesis. The loops and accessory domains attached to beta barrels allow these proteins to perform a diverse set of functions, including acting as porins, transporters, enzymes, virulence factors, and receptors.
The biogenesis of transmembrane beta barrels involves a complex process that includes translocases, barrel assembly machinery, and helper chaperone proteins. The bacterial and eukaryotic assembly machineries for beta-barrel folding are well-studied, and the process is conserved across bacteria and mitochondria. The outer membrane of Gram-negative bacteria has unique features, including an asymmetric lipid bilayer and lipopolysaccharides, which contribute to the cell's protection and resistance to harmful compounds.
Transmembrane beta barrels have been identified in large datasets using methods such as coevolution data and feature detection algorithms. These datasets have revealed a high rate of false positives in previous algorithms and have contributed to a better understanding of transmembrane beta barrels, including their structure, function, and evolution. The beta-barrel scaffold is versatile, allowing proteins with this domain to perform a wide range of functions, including the transport of nutrients into the cell and the secretion of substances out of the cell.
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Beta-barrel biogenesis
In Gram-negative bacteria, the beta-barrel assembly machinery (BAM) complex is responsible for beta-barrel biogenesis. The BAM complex consists of proteins such as BamA, BamB, BamC, BamD, and BamE. These proteins fold and insert new beta-barrels into the outer membrane.
In mitochondria, the sorting and assembly machinery (SAM) complex mediates beta-barrel biogenesis. The SAM complex consists of three proteins, Sam50, Sam35, and Sam37, which assemble as a 1:1:1 complex to fold and insert beta-barrel proteins into the mitochondrial outer membrane. Sam50 forms a 16-stranded transmembrane beta-barrel with a single polypeptide-transport-associated (POTRA) domain. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50 and Sam37 interacting extensively with Sam35.
The biogenesis of beta-barrels also involves the translocation of precursor proteins to the periplasm, where they are stabilized by molecular chaperones before interaction with the assembly machinery. In Gram-negative bacteria, the TOM complex translocates precursor proteins from the cytosol to the intermembrane space.
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Beta-barrel functions
One of the key functions of beta barrels is their role as transmembrane domains. Transmembrane beta barrels are a major class of transmembrane proteins that form a folded domain. Unlike alpha-helical membrane proteins, beta barrels have a hydrophobic exterior that interacts with the lipidic membrane and a hydrophilic interior that can form an aqueous channel or accommodate other structures. This unique structure allows beta barrels to act as cellular gatekeepers, directly or indirectly influencing all cellular functions.
Beta barrels are commonly found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts, where they perform essential functions. In mitochondria, beta barrels serve as pore-forming subunits, such as Tom40 and Sam50, facilitating protein transport. In chloroplasts, the Toc75 complex is a well-characterised example of a beta barrel-containing complex. Additionally, beta barrels play a crucial role in cargo transport, signalling, and membrane biogenesis.
The versatility of the beta-barrel scaffold enables proteins with this domain to have a wide range of functions. Beta barrels can act as diffusion pores, transporters, enzymes, adhesins, and receptors. They are also involved in the transport of nutrients into the cell and the secretion or excretion of substances out of the cell. The loops and accessory domains attached to beta barrels further enhance their functional diversity.
Beta barrels have been the subject of extensive research, with large datasets and advanced computational methods contributing to our understanding of their structure and function. The ability to identify and predict transmembrane beta barrels and their properties has improved significantly, providing valuable insights into the world of protein structures and their evolutionary relationships.
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Beta-barrel identification
Currently, the identification of β-barrels in genome annotations relies primarily on their homology to known β-barrel structures. Each Gram-negative bacterial genome contains numerous "putative" and "probable" outer membrane proteins identified through this method. However, there is a need to identify β-barrels based on their fundamental physical properties to discover novel classes and verify homology-based annotations.
Several algorithms and programs have been developed to identify β-barrel membrane proteins in genomic databases. These algorithms aim to predict transmembrane segments and model the geometry of the protein, including the radius of the β-barrel and the axis inclination. One notable algorithm, IsItABarrel, uses coevolution data and evolutionary contact maps to achieve a high accuracy of 95.88% in discriminating among protein classes. Another algorithm, PRED-TMBB2, focuses on improved topology prediction and the detection of β-barrel outer membrane proteins.
The identification of β-barrels also involves understanding their composition and physical properties. For example, β-barrels have a transmembrane domain formed by an antiparallel β-sheet that creates a cylinder. The exterior of this cylinder is hydrophobic, interacting with the lipidic membrane, while the interior is often hydrophilic, forming an aqueous channel or accommodating other structures. Additionally, β-barrels can be classified based on two integer parameters: the number of strands in the β-sheet and the "shear number," which measures the stagger of the strands.
In summary, the identification of β-barrels involves a combination of homology comparisons, algorithmic predictions, and the analysis of their physical properties, composition, and structure. These approaches contribute to our understanding of β-barrels and their functions in various biological systems.
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Frequently asked questions
Beta barrels, or β barrels, are protein structures that resemble barrels used to contain liquids. They are composed of tandem repeats that twist and coil to form a closed toroidal structure.
Beta barrels are formed by bringing the edges of a beta sheet together to create a cylinder. This process is similar to forming a cylinder out of a piece of paper by bringing the opposite sides together.
Transmembrane beta barrels are a type of beta barrel protein that spans the outer membrane of cells. They have a folded domain that presents a hydrophobic surface to the membrane environment.
Transmembrane beta barrels serve essential functions in cargo transport, signalling, and membrane biogenesis. They can act as porins, transporters, enzymes, virulence factors, and receptors.
