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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]

Types

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A mouse major urinary protein. The barrel forms a binding pocket for the mouse pheromone, 2-sec-butyl-4,5-dihydrothiazole.[7] (PDB: 1MUP​)

Up-and-down

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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.

Jelly roll

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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.

Examples

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Porins

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Main article: Porin (protein)

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.

Preprotein translocases

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Beta barrels also function within endosymbiont derived organelles such as mitochondria and chloroplasts to transport proteins.[8] 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

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Main article: Lipocalin

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).[9][10][11]

Shear number

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Front view
Right view (90° rotation)
Back view (180° rotation)
Left view (270° rotation)
Hydrogen bonding in the beta sheet slabs of GFP. The residues are labeled with residue number and one-letter amino acid code. Only the backbone atoms of the beta barrel are shown from each of angle of the barrel coloured from blue (N-terminus) to red (C-terminus). (PDB: 1RRX​)

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, 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 beta sheet is adjacent to just one amino acid in the neighboring strand (this assumption may not hold if, for example, a beta bulge is present).[12] To illustrate, S will be calculated for green fluorescent protein. 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.

Table for calculating the shear number. The strand order in this barrel (GFP) is: 1 6 5 4 9 8 7 10 11 3 2.

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.

See also

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References

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Beta barrel

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A beta barrel is a prevalent protein fold characterized by an antiparallel arrangement of β-strands that form a closed, cylindrical structure, typically comprising 8 to 24 strands connected by hydrogen bonds to create a seamless toroidal barrel with a hydrophobic exterior and often hydrophilic interior pore. These structures are predominantly found in the outer membranes of , mitochondria, and chloroplasts, where they serve critical roles in membrane permeation and protein insertion. The topology of beta barrels varies but commonly follows an "up-and-down" pattern, where consecutive β-strands alternate direction around the barrel axis, with the first and last strands hydrogen-bonding to close the structure. Most bacterial outer membrane proteins (OMPs) feature an even number of strands, ranging from 8 (e.g., OmpA) to 24, though exceptions like the mitochondrial voltage-dependent anion channel VDAC contain an odd number of 19 strands arranged with parallel β1 and β19 sheets. This architecture provides mechanical stability in lipid bilayers, with the barrel's shear number (a measure of twist) influencing pore size and selectivity; for instance, porins such as OmpF and PhoE typically have 16 strands forming trimers that allow passive diffusion of ions, nutrients, and small hydrophilic molecules up to about 600 Da. Beyond transport, beta barrels exhibit diverse functions, including enzymatic activity (e.g., the autotransporter EstA with 12 strands acting as a periplasmic esterase) and heme uptake (e.g., the HasR transporter complex). In eukaryotes, mitochondrial beta barrels like Tom40 (part of the TOM translocase complex) facilitate preprotein import, while chloroplast counterparts such as TOC75 enable protein translocation across the outer envelope. Assembly of these proteins involves specialized machinery: in bacteria, the BAM complex inserts OMPs into the outer membrane after periplasmic chaperoning by SurA or Skp, whereas mitochondrial and chloroplast systems use SAM and TOC complexes, respectively. Structural determinations, including high-resolution cryo-EM and X-ray crystallography of full-length examples like PorB (a Neisseria porin) and human VDAC, alongside more recent 2020s cryo-EM studies of the BAM complex and de novo designed barrels, have illuminated their dynamic conformations, lipid interactions, and biogenesis mechanisms, underscoring their evolutionary conservation across kingdoms.

Introduction and Basics

Definition and Characteristics

A beta barrel is a protein fold consisting of eight or more antiparallel beta strands that form a cylindrical, barrel-like structure through inter-strand hydrogen bonds, creating a closed toroidal . The beta strands are connected by loops at both ends, with the first and last strands hydrogen-bonded to each other to enclose the structure, distinguishing it from an open . This arrangement positions hydrophobic residues on the exterior surface to interact with membranes or , while the interior can be lined with polar or charged residues depending on function. The core architecture features alternating polar and non-polar residues along each beta strand, with non-polar side chains typically facing outward toward the hydrophobic environment and polar ones inward, facilitating insertion for transmembrane variants or aqueous for others. bonds between backbone atoms of adjacent strands stabilize the barrel wall, often requiring a minimum of eight strands for structural integrity, with known examples ranging from 8 to 36 strands. These barrels exhibit general dimensions of approximately 20–30 in and 25–40 in , corresponding to the transmembrane span in membrane-embedded forms. In contrast to flat, planar beta sheets, which consist of extended, open arrays of hydrogen-bonded strands, beta barrels adopt a closed, three-dimensional cylindrical that encloses a central pore or cavity, enabling roles in or . This topological closure enhances stability in diverse environments, such as lipid bilayers.

Occurrence in

Beta barrels are predominantly found in the outer membranes of , where they constitute the vast majority of integral outer membrane proteins, alongside a smaller number of alpha-helical exceptions. These structures are also present in the outer membranes of mitochondria and chloroplasts in eukaryotes, reflecting their endosymbiotic origins from ancient bacterial ancestors. In these organelles, beta barrels perform essential roles in maintaining membrane integrity and facilitating intermembrane exchange. Beyond membrane contexts, beta barrels occur in eukaryotic soluble proteins, such as those in the lipocalin family, where they provide a stable scaffold for ligand binding and transport in the cytosol. They are also prevalent in viral capsids, particularly in the jelly-roll fold adopted by many icosahedral viruses across diverse host kingdoms, enabling robust capsid assembly. Evolutionarily, beta barrels trace back to an ancestral ββ-hairpin motif in ancient prokaryotic membrane proteins, which duplicated and diverged to form the diverse barrel topologies seen today. Functionally, beta barrels primarily enable of ions and metabolites across , catalyze enzymatic reactions at the membrane interface, and provide structural support to outer membranes in both prokaryotes and eukaryotic organelles. These roles underscore their versatility in cellular physiology, from nutrient uptake in to protein import in mitochondria. As of 2025, over 100 unique beta barrel structures have been deposited in the , encompassing both membrane-embedded and soluble variants, with metagenomic studies continuing to uncover novel sequences and folds from uncultured microbial communities. Recent 2025 structural studies have further elucidated the beta-barrel assembly machinery (BAM) complex in diverse .

Structural Types

Up-and-Down Barrel

The up-and-down beta barrel is the canonical and simplest topology of beta barrel folds, featuring a sequential arrangement of beta strands connected by short loops or turns that alternate in direction along the barrel's longitudinal axis. This arrangement forms a cylindrical structure where strands run consecutively "up" and then "down," often incorporating a basic Greek key motif in which the connections between strands follow a pattern of adjacent pairings without crossing. The topology is prevalent in both soluble and transmembrane proteins, providing a stable scaffold for functions such as binding or . Up-and-down barrels typically comprise 8 to 12 beta strands, with even numbers favored to ensure topological closure and structural . For instance, many soluble examples feature 8 or 10 strands, while transmembrane variants often have 12 or 16 strands to span bilayers effectively. The strands are connected by loops on one face of the barrel, contributing to its overall compactness and allowing the opposite face to interact with solvents or membranes. The bonding in up-and-down barrels primarily involves antiparallel orientations between adjacent strands, where backbone and carbonyl groups form inter-strand s that wrap the sheet into a closed barrel. This antiparallel alignment maximizes stability through optimal geometry and is supplemented by side-chain interactions that further reinforce . In some cases, the results in continuous bonding across all strands, while others exhibit discontinuities that accommodate functional loops or binding sites. A simple schematic of the up-and-down can be visualized as a series of evenly spaced, vertical arrows alternating in direction (e.g., upward for strand 1, downward for strand 2, and so on), with short connecting loops at the top and bottom, enclosing a central axis without twists or shears. This linear connectivity distinguishes it from more complex barrel types and facilitates straightforward folding pathways in biological systems.

Jelly Roll Barrel

The jelly roll barrel represents a distinctive within beta barrel structures, where beta strands assemble into two antiparallel beta sheets that wrap around each other in a coiled, sandwich-like fashion reminiscent of a rolled jelly roll. This arrangement arises from non-sequential connections between strands, typically involving Greek key motifs with long loops that cross between the sheets, creating a more complex and intertwined architecture compared to simpler barrel forms. The sheets are held together primarily through hydrogen bonding and hydrophobic interactions, forming an elongated, wedge-shaped core rather than a strictly cylindrical barrel. These barrels typically feature 8 beta strands in the single , divided into two four-stranded sheets (BIDG and CHEF), though double jelly roll variants consist of 16 strands. This motif is prevalent in viral proteins and extracellular proteins, where the extended loops facilitate interactions with diverse molecular partners. A hallmark is the right-handed twist of the beta sheets, coupled with a characteristic shear number—defined as the total number of interstrand hydrogen bonds displaced along the diagonal of the barrel—which ranges from 8 to 24 and accommodates larger diameters while enhancing overall stability through optimal packing. The modularity of the jelly roll topology, stemming from its repeatable Greek key connections and loop architectures, has made it a favored target in de novo efforts, enabling the creation of stable, non-natural structures with precise control over folding and function. This evolutionary adaptability underscores its prevalence in diverse protein families, where the crossed loop connections contribute to structural robustness without relying on sequential strand pairing.

Key Topological Features

Shear Number

The shear number (S) serves as a topological invariant for β-barrels, defined as the net displacement of strands between the first and last β-sheet, which quantifies the overall twist and stagger in the barrel structure. This measure captures the hydrogen-bonding registry shifts across the antiparallel β-strands, providing a discrete parameter that classifies barrel topologies independent of specific residue details. The shear number is the total number of residue positions by which consecutive beta strands are displaced relative to each other around the barrel. For membrane-embedded β-barrels, values of S typically range from 8 to 24, reflecting adaptations for transmembrane stability. For example, the 8-stranded OmpA barrel has S=10. The shear number holds significance in determining structural and biophysical properties, correlating with the barrel's strand tilt , which increases with S and decreases with n. Lower shear numbers produce less tilted barrels, while higher shear numbers result in greater tilt that enhances packing efficiency in environments. In structural types like up-and-down or jelly roll barrels, S encapsulates the distinct strand connectivity patterns.

Strand Number and Dimensions

Beta barrels exhibit variability in the number of β-strands, typically ranging from a minimum of 8 to a maximum of 22, with even numbers preferred to facilitate proper closure of the antiparallel β-sheet . The minimum of 8 strands represents a stability threshold, below which the β-sandwich motif cannot form a closed barrel without significant distortion, as exemplified by the smallest known structures like OmpA and OmpX. Larger barrels, such as the 22-stranded BtuB transporter, accommodate more complex functions but require greater topological shear to maintain packing efficiency. The physical dimensions of a β-barrel are primarily determined by the strand count (n) and the length of individual strands. These dimensions also depend on the shear number S, which determines the strand tilt and thus modulates the effective and axial . The barrel (r) can be approximated as r≈n×4.7 A˚2πr \approx \frac{n \times 4.7 \, \text{Å}}{2\pi}, reflecting the circumferential contribution of each strand based on typical β-sheet spacing. The (h) of the barrel is roughly h≈m×3.2 A˚h \approx m \times 3.2 \, \text{Å}, where m is the number of residues per transmembrane strand, corresponding to the axial rise per residue in an extended β-conformation adjusted for tilt. For porins, which average 16 strands, these yield radii of 10–15 Å and heights of 27–35 Å, enabling the formation of water-filled pores suitable for solute across membranes. Structural constraints impose limits on these dimensions to ensure viability. A minimum strand tilt angle of approximately 40° relative to the barrel axis is required to prevent steric clashes between side chains in the hydrophobic core. The resulting pore size, governed by the and modulated by loop constrictions, directly influences efficiency; for instance, porin barrels with radii around 10 permit passage of small hydrophilic molecules up to 600 Da while excluding larger ones. These parameters balance mechanical stability with functional specificity across diverse biological contexts.

Biological Roles and Examples

Porins and Membrane Channels

Porins represent a prominent class of β-barrel membrane proteins embedded in the outer membranes of , where they facilitate passive diffusion across the . These proteins typically adopt a cylindrical β-barrel structure composed of 16 to 18 antiparallel β-strands, forming a water-filled pore with an overall of approximately 20 Å that allows the passage of small hydrophilic molecules. The archetypal example is OmpF porin from , which consists of a 16-stranded β-barrel per and assembles into a stable trimer, with each contributing to the central channel. The primary function of porins is to enable selective of ions, nutrients, and metabolites, such as sugars and , while excluding larger or hydrophobic compounds to maintain cellular integrity. In OmpF, the channel exhibits weak cation selectivity due to basic residues in the pore, and it can undergo voltage-dependent gating, closing at membrane potentials exceeding ±100 mV to prevent excessive under stress conditions. Structurally, the selectivity is modulated by extracellular loops that protrude into the pore; for instance, loop L3 in OmpF forms a constriction zone acting as a molecular filter, narrowing the channel to about 7–11 at its midpoint and interacting with charged residues like Asp113 and Glu117 to influence solute passage. Porins are evolutionarily conserved across , where they are essential for outer membrane permeability and are found in nearly all such species, underscoring their role in bacterial survival and adaptation. This conservation extends to eukaryotic organelles, with mitochondrial voltage-dependent anion channels (VDACs) serving as homologs that share structural and functional similarities, such as forming β-barrels for exchange, reflecting the endosymbiotic origin of mitochondria from Gram-negative ancestors. In humans, VDAC1 adopts a 19-stranded β-barrel configuration, adapting the porin fold for regulating mitochondrial outer membrane permeability to ions and nucleotides.

Translocases and Transporters

Beta barrels play a crucial role in preprotein translocases, facilitating the import and insertion of unfolded proteins across cellular membranes in both bacteria and mitochondria. In , the beta-barrel assembly machinery (BAM) complex, centered on the BamA protein, inserts outer membrane beta-barrel proteins into the . BamA features a 16-stranded transmembrane beta barrel that serves as an insertase, enabling chaperone-assisted folding and membrane integration of substrate proteins without requiring external energy sources. The process involves recognition of a conserved beta signal motif in the substrate, which orients the beta strands for proper assembly. In mitochondria, the translocase of the outer membrane (TOM) complex, with its core component Tom40 forming a 19-stranded beta barrel, acts as the primary entry gate for nuclear-encoded preproteins destined for various mitochondrial compartments. This barrel forms a hydrophilic pore that allows passage of unfolded polypeptide chains from the cytosol into the intermembrane space, often in cooperation with receptor subunits like Tom20 and Tom22 for initial substrate binding. The TOM complex supports chaperone-assisted translocation, where cytosolic and intermembrane space chaperones maintain substrates in an import-competent state, and dynamic conformational changes in the barrel facilitate unidirectional protein flow. In chloroplasts, the translocon of the outer chloroplast membrane (TOC) complex features Toc75, a 16-stranded beta barrel that facilitates protein import across the outer envelope, analogous to Tom40. Structural features of these beta barrels include asymmetric loops that contribute to substrate specificity and recognition. In BAM, the periplasmic loops of BamA, particularly those connecting beta strands, interact with accessory lipoproteins like BamD to stabilize substrates and promote folding, while extracellular loops exhibit greater flexibility for gating. Similarly, in TOM, the Tom40 barrel has unevenly distributed loops on the cytosolic and intermembrane sides, enabling selective engagement with presequence-containing proteins and preventing back-sliding. These barrels typically exhibit high shear numbers, such as 22 for BamA, which dictate the tilt of beta strands and the overall barrel geometry for efficient pore formation and lateral gating. Recent cryo-EM structures have illuminated the dynamic gating mechanisms underlying these processes. Post-2020 studies of BAM reveal multiple intermediate states during substrate insertion, including hybrid-barrel conformations where the substrate partially unzips the BamA beta seam between strands β1 and β16, allowing lateral opening for membrane integration. For the TOM complex, high-resolution cryo-EM maps from 2021 show the dimeric arrangement of Tom40 pores with flexible β-hairpins that modulate the channel diameter and enable transient opening for preprotein threading, highlighting energy-independent gating driven by substrate binding. These advances underscore the conserved yet adapted mechanisms of beta barrel translocases across evolutionary lineages.

Lipocalins and Soluble Proteins

Lipocalins represent a prominent family of soluble proteins characterized by beta barrel folds that facilitate the binding and transport of small hydrophobic molecules in extracellular environments. These proteins typically feature an eight-stranded antiparallel beta barrel with an up-and-down , forming a cup-shaped calyx in the interior that serves as a binding pocket for ligands. For instance, human (RBP4) utilizes this calyx to bind and transport , a hydrophobic of , protecting it from degradation in aqueous solutions. The primary functions of lipocalins include the transport and storage of small hydrophobic ligands such as retinoids, steroids, and lipids, as well as enzymatic activities in select members, like prostaglandin D synthase which catalyzes the synthesis of signaling molecules. These proteins are predominantly secreted extracellularly, enabling roles in immune modulation, cell homeostasis, and clearance of endogenous compounds from circulation. Unlike membrane-embedded beta barrels, lipocalins exhibit a hydrophilic exterior that ensures solubility in aqueous media, while their hydrophobic barrel interior accommodates ligands without requiring insertion into lipid bilayers. The lipocalin family displays significant diversity, with 19 functional LCN-like genes identified in the human genome, reflecting adaptations to varied physiological roles. Despite this sequence variability, the beta barrel core remains highly conserved across eukaryotic species, underscoring its evolutionary stability for ligand-binding functions.

Other Examples

Beyond the canonical roles in membrane transport and soluble binding, beta barrels exhibit versatility in enzymatic catalysis, viral architecture, eukaryotic lipid handling, and emerging applications in extremophiles and engineered systems. In enzymatic contexts, UDP-sugar epimerases exemplify beta barrels in sugar metabolism. For instance, dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase (RmlC) from features an 8-stranded antiparallel beta barrel fold that facilitates the stereochemical inversion essential for L-rhamnose , a key component of bacterial cell walls. Viral capsids provide another prominent example of beta barrel utility. In picornaviruses like , the major capsid proteins VP1, VP2, and VP3 each adopt a jelly roll beta barrel —an up-and-down arrangement of eight beta strands forming two four-stranded sheets—that confers mechanical stability and enables icosahedral assembly for protecting the viral genome. Among eukaryotic proteins, binding proteins (FABPs) represent soluble beta barrels distinct from lipocalins despite functional similarities in transport. These intracellular proteins, such as heart FABP, fold into a 10-stranded antiparallel beta barrel that creates a hydrophobic cavity for binding long-chain s, aiding their shuttling within cells for energy metabolism and signaling. Emerging examples highlight beta barrels in non-bacterial domains and design. In , surface proteins like those in incorporate incomplete beta barrel motifs in their head domains, potentially contributing to cell envelope stability in hypersaline environments. In , de novo designed beta barrels serve as modular scaffolds; for example, computationally engineered 8- to 12-stranded barrels activate upon binding, enabling applications in biosensors and nanoscale assemblies.

Biophysical Properties

Stability and Folding

The stability of beta barrel proteins primarily arises from an extensive network of inter-strand hydrogen bonds, typically involving 10-17 bonds per strand, which satisfy the backbone polar groups and prevent unfavorable exposure in the hydrophobic environment. These bonds, combined with tight van der Waals packing between adjacent strands, contribute to a robust cylindrical structure that resists unfolding, with free energies of unfolding (ΔG) ranging from 10 to 32 kcal/mol depending on the barrel size and context. This thermodynamic stability is further reinforced by hydrophobic interactions between the barrel's exterior and the tails, minimizing exposure of nonpolar residues. The folding pathway of beta barrels proceeds through a multi-step process, where partial beta strands form a hydrophobic collapse intermediate, followed by cooperative insertion and closure of the remaining strands to complete the barrel. This process is kinetically controlled, with slow insertion rates overcome by periplasmic chaperones such as Skp, which sequesters unfolded polypeptides in a protective cavity to facilitate membrane targeting and prevent aggregation during to the outer . , the beta-barrel assembly machinery (BAM) complex catalyzes the final insertion and zipping of strands in a concerted manner. Compared to soluble beta barrels, transmembrane variants exhibit enhanced stability due to the lipid bilayer's role in hydrophobic matching, where the barrel's height aligns with the bilayer's thickness to reduce deformation and strengthen inter-strand interactions. Mismatches in bilayer thickness can destabilize the structure by ~0.34 kcal/mol per Å, whereas optimal matching increases overall ΔG of unfolding by promoting residue burial and cooperative unfolding transitions. Experimental studies using (NMR) spectroscopy and (MD) simulations reveal that beta barrel twist angles are minimized to achieve the lowest energy configuration, with right-handed twists optimizing geometry and packing density. MD trajectories confirm that deviations from optimal twist lead to higher free energies, underscoring its role in structural integrity, as observed in high-resolution structures like OmpA.

Design and Engineering

De novo design of beta barrels has advanced significantly through computational methods, enabling the creation of novel structures with defined topologies for applications in and . Early efforts utilized the Rosetta software suite for energy-based modeling and sequence optimization. For instance, researchers designed eight-stranded transmembrane beta barrels that spontaneously insert and fold into synthetic bilayers, demonstrating reversible folding and stability comparable to natural porins, as confirmed by NMR and . These designs addressed key architectural constraints, such as balancing hydrophobicity for membrane insertion and preventing aggregation in aqueous environments through negative design strategies. Subsequent work expanded to soluble small beta barrels with 5 to 6 strands, targeting topologies like the OB-fold and up-and-down barrels, using Rosetta's blueprint-based fragment assembly combined with for backbone generation. This approach yielded monomeric proteins with high folding fidelity, as evidenced by 90% success in NMR characterization and low backbone RMSD values (<2.4 Å) to design models. Larger variants, including 12- to 16-stranded transmembrane nanopores, were achieved via parametric specification of shear numbers (8-18) and strand lengths (5-20 residues), followed by refinement with RFdiffusion, resulting in conductances of 200-500 pS suitable for applications. Applications include synthetic pores for single-molecule sensing and , as well as mimics; for example, an eight-stranded barrel was optimized for retro-aldolase activity, catalyzing carbon-carbon bond cleavage with k_cat/K_M values up to 10^3 M^{-1} s^{-1}, and a fluorescence-activating barrel that binds DFHBI to enable cellular . As of 2025, further advances include parametric guided designs for precise control over barrel architecture (PNAS, 2024) and methods to sculpt size and shape for tailored conductance (, 2024), alongside studies on , solute, and ion transport in designed channels with 5-10 Å pores (/, 2025). Challenges in de novo beta barrel design center on achieving precise , including correct hydrogen-bond registry and barrel closure, which is guided by shear number to minimize backbone strain and ensure sheet twisting. Misfolding risks are mitigated by symmetry-breaking elements, such as irregular loops and beta-bulges, to enforce connectivity without off-target aggregates. Recent advances leverage AI-driven tools for higher success rates; models like trRosetta and RFjoint2 have enabled constrained hallucination of backbones, while structure prediction with variants validates designs and supports scaffold engineering for therapeutic proteins, such as stable barrels for binding in .

References

  1. https://pmc.ncbi.nlm.nih.gov/articles/PMC3164749/
  2. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/beta-barrel
  3. https://pubmed.ncbi.nlm.nih.gov/8001736/
  4. https://www.nature.com/articles/s41586-025-09532-8
  5. https://www.pnas.org/doi/10.1073/pnas.2425459122
  6. https://pmc.ncbi.nlm.nih.gov/articles/PMC7115949/
  7. https://www.sciencedirect.com/science/article/pii/S0969212618303381
  8. https://pmc.ncbi.nlm.nih.gov/articles/PMC4930767/
  9. https://pmc.ncbi.nlm.nih.gov/articles/PMC2373429/
  10. https://onlinelibrary.wiley.com/doi/full/10.1002/prot.26552
  11. https://pmc.ncbi.nlm.nih.gov/articles/PMC3265896/
  12. https://journals.biologists.com/jcs/article/138/18/jcs263624/369271/Surface-protein-machineries-in-Gram-negative
  13. https://pubmed.ncbi.nlm.nih.gov/12948769/
  14. https://www.nature.com/articles/s41467-020-17144-1
  15. https://www.nature.com/articles/s41598-018-32136-4
  16. https://www.pnas.org/doi/10.1073/pnas.232580699
  17. https://academic.oup.com/mbe/article/27/6/1348/1112076
  18. https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.13905
  19. https://www.rcsb.org/stats
  20. https://www.nature.com/articles/s41564-025-02132-2
  21. http://kinemage.biochem.duke.edu/teaching/anatax3d
  22. https://doi.org/10.1016/0022-2836(92)90502-B
  23. https://www.pnas.org/doi/10.1073/pnas.2120620119
  24. https://pmc.ncbi.nlm.nih.gov/articles/PMC1301464/
  25. https://doi.org/10.1038/s41594-018-0141-6
  26. https://www.cell.com/biophysj/fulltext/S0006-3495(01)76246-7
  27. https://www.pnas.org/doi/10.1073/pnas.1716817115
  28. https://www.sciencedirect.com/science/article/pii/S0005273604001646
  29. https://www.science.org/doi/10.1126/science.abc8182
  30. https://pubs.acs.org/doi/10.1021/acs.chemrev.0c01213
  31. https://www.sciencedirect.com/science/article/pii/S002192581973885X
  32. https://www.sciencedirect.com/science/article/pii/S0969212601002404
  33. https://pmc.ncbi.nlm.nih.gov/articles/PMC2516885/
  34. https://pmc.ncbi.nlm.nih.gov/articles/PMC1838418/
  35. https://www.pnas.org/doi/10.1073/pnas.0808115105
  36. https://pmc.ncbi.nlm.nih.gov/articles/PMC4883095/
  37. https://www.sciencedirect.com/science/article/pii/S0092867422001969
  38. https://pmc.ncbi.nlm.nih.gov/articles/PMC8439582/
  39. https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.13342
  40. https://www.faseb.onlinelibrary.wiley.com/doi/full/10.1096/fj.202001443RR
  41. https://www.nature.com/articles/s41421-020-00198-2
  42. https://faseb.onlinelibrary.wiley.com/doi/full/10.1096/fj.13-248450
  43. https://pmc.ncbi.nlm.nih.gov/articles/PMC1217580/
  44. https://pmc.ncbi.nlm.nih.gov/articles/PMC8427218/
  45. https://pmc.ncbi.nlm.nih.gov/articles/PMC6381713/
  46. https://humgenomics.biomedcentral.com/articles/10.1186/1479-7364-5-3-170
  47. https://www.nature.com/articles/s41467-024-53986-9
  48. https://link.springer.com/content/pdf/10.1007/978-1-4615-4929-1.pdf
  49. https://pmc.ncbi.nlm.nih.gov/articles/PMC5018216/
  50. https://www.science.org/doi/10.1126/sciadv.adv9568
  51. https://www.pnas.org/doi/10.1073/pnas.2207974120
  52. https://pubmed.ncbi.nlm.nih.gov/36305767/
  53. https://www.nature.com/articles/s41586-018-0509-0
  54. https://www.science.org/doi/10.1126/science.adn3796
  55. https://www.bakerlab.org/wp-content/uploads/2025/02/li-et-al-2024-water-solute-and-ion-transport-in-de-novo-designed-membrane-protein-channels.pdf
  56. https://onlinelibrary.wiley.com/doi/full/10.1002/pro.5033
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