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Supersecondary structure

Supersecondary structure refers to a specific, compact arrangement of adjacent secondary structural elements, such as α-helices and β-strands connected by loops or turns, forming recurrent motifs that are intermediate in size between individual secondary structures and full protein domains.^[1] These motifs act as fundamental building blocks in protein architecture, bridging the gap between local secondary folding and global tertiary organization.^[2] Common examples include the β-hairpin, consisting of two antiparallel β-strands linked by a short loop of 2–5 residues, which provides stability through hydrogen bonding and is often found in β-sheet cores;^[2] the helix-turn-helix motif, featuring two α-helices separated by a short β-turn, frequently observed in DNA-binding domains of transcription factors;^[3] and the β-α-β motif, where two parallel β-strands are connected by an intervening α-helix, typically adopting a right-handed crossover to form a hydrophobic interface that stabilizes larger folds like the TIM barrel.^[2] Other notable motifs encompass the Greek key, a topology of four antiparallel β-strands with specific connectivity, and the four-helix bundle, where four α-helices pack together in a coiled arrangement, common in globular proteins for efficient core packing.^[1] Supersecondary structures play a crucial role in protein folding by serving as nucleation sites that initiate and guide the assembly of secondary elements into functional tertiary forms, often exhibiting evolutionary conservation despite sequence divergence.^[3] Their recognition has advanced computational protein design, structure prediction, and understanding of functional sites, as these motifs frequently mediate interactions such as ligand binding or protein-protein associations.^[2]

Introduction

Definition

Supersecondary structures, also known as motifs, are stable, compact arrangements of two or more adjacent secondary structure elements—such as alpha-helices or beta-strands—connected by short loops or turns, forming discrete three-dimensional units smaller than a full protein domain.^[4] These arrangements represent a transitional level in protein organization, bridging the local patterns of secondary structure with the more global folding of tertiary structure.^[4] Key characteristics of supersecondary structures include their typical involvement of 10–25 residues and stabilization through hydrophobic interactions, hydrogen bonds, and van der Waals forces that extend beyond those stabilizing individual secondary elements.^[4] They function as modular building blocks, contributing to the overall architecture of proteins without encompassing the entire chain.^[5] Unlike secondary structures, which are defined by local, repeating patterns such as the intra-chain hydrogen bonds in an alpha-helix, supersecondary structures incorporate the specific inter-element geometry and packing arrangements.^[4] In distinction from tertiary structures, which describe the comprehensive three-dimensional folding of an entire polypeptide chain or domain, supersecondary structures remain local and modular units.^[4] For scale, the helix-turn-helix motif typically spans about 20 residues, contrasting with full domain sizes that commonly range from 50 to 200 residues.^[6]^[7]

Significance

Supersecondary structures play a pivotal role in protein folding by serving as nucleation sites that initiate the formation of tertiary structures. These motifs provide low-energy intermediates that stabilize early folding events, thereby reducing the vast conformational search space implicated in Levinthal's paradox, where random exploration of all possible polypeptide conformations would take an impractically long time. By forming autonomously stable units that bridge secondary elements like alpha-helices and beta-strands, supersecondary structures facilitate a hierarchical folding pathway, allowing proteins to achieve their native conformations efficiently within biological timescales.^[8]^[9] In protein evolution, supersecondary structures function as modular building blocks that are frequently conserved and reused across diverse proteins, enabling domain shuffling and the rapid emergence of new folds through mechanisms like gene duplication and fusion. This modularity promotes evolutionary innovation, as seen in ancient folds such as SH3 and OB domains, where conserved supersecondary elements are inherited and rearranged to support novel functions, including those in enzyme active sites. Such conservation highlights their role in facilitating functional diversification while maintaining structural integrity.^[10]^[9] Functionally, supersecondary structures contribute to key aspects of protein activity, including the formation of ligand binding pockets, allosteric regulation, and specificity in molecular interactions. For instance, these motifs often cluster hydrophobic residues to enhance core packing and stability, while loop-containing elements in supersecondary structures enable flexibility for substrate recognition and signal transduction. In enzymes, they position catalytic residues precisely, underscoring their importance in biochemical specificity.^[11]^[9] Disruptions to supersecondary structures, often caused by mutations, can lead to protein misfolding and aggregation, contributing to diseases such as Alzheimer's and cancer through aberrant amyloid formation or loss of functional conformation. Conversely, their modular nature is exploited in protein engineering for de novo designs, where supersecondary motifs serve as scaffolds to create novel proteins with tailored functions, such as antimicrobial peptides or therapeutic binders. Statistically, supersecondary structures are highly prevalent, with over 2.3 million instances identified across approximately 185,000 Protein Data Bank (PDB) entries as of October 2022, underscoring their ubiquity in bridging sequence to three-dimensional architecture in the majority of known proteins.^[9]^[12]^[9]

Historical Background

Early Observations

The determination of the first three-dimensional protein structures in the late 1950s marked the beginning of empirical observations of recurring patterns beyond individual secondary elements. In 1960, John Kendrew and colleagues reported the X-ray structure of sperm whale myoglobin at 2 Å resolution, revealing a compact bundle of eight alpha-helices that packed together to form the protein's core, providing the initial glimpse of how helical segments could associate in a stable motif.^[13] This helical bundle arrangement suggested that secondary structures did not exist in isolation but combined to create higher-order architectural units. Shortly thereafter, in 1960, Max Perutz and coworkers, including Michael Rossmann, published the structure of horse hemoglobin at 5.5 Å resolution, which displayed similar alpha-helical packing motifs across its subunits, with helices oriented to form pockets for heme groups and highlighting conserved packing geometries in related proteins.^[14] As X-ray crystallography advanced into the 1960s, structures of more diverse proteins began to reveal patterns involving beta-sheets. For instance, the 1967 structure of tosyl-α-chymotrypsin at 2 Å resolution by David Blow and colleagues demonstrated extensive beta-sheet regions composed of paired antiparallel strands connected by short turns, resembling hairpin-like configurations that stabilized the enzyme's active site.^[15] Similarly, the 1966 analysis of carboxypeptidase A at 6 Å resolution by William Lipscomb's group showed a mixed alpha-beta architecture, where alpha-helices flanked beta-strands, illustrating early examples of secondary structure combinations in globular proteins.^[16] These observations built on the foundational predictions of Linus Pauling and Robert Corey in 1951, who proposed alpha-helix and beta-sheet as prevalent secondary structures based on stereochemical constraints, though actual combinations were only visualized through 1960s X-ray data.^[17] Key insights into repeating motifs emerged from comparative analyses of these early structures. In the late 1960s, Michael Rossmann's studies on dehydrogenases, including the 1970 structure of dogfish lactate dehydrogenase, identified recurring beta-alpha-beta units where parallel beta-strands were linked by right-handed alpha-helical crossovers, a pattern noted across several enzymes without yet formalizing it as a distinct motif.^[18] By 1970, patterns in secondary structure associations had been observed in roughly 10 known protein structures, such as myoglobin, hemoglobin, chymotrypsin, and carboxypeptidase, underscoring their prevalence despite the limited dataset.^[19] However, the era's technical constraints—typically resolutions of 2-6 Å—often blurred connecting loops and side-chain details, directing focus primarily to the arrangement of alpha-helices and beta-strands rather than finer tertiary interactions.^[19]

Conceptual Development

The concept of supersecondary structures emerged in the early 1970s as researchers began systematically comparing known protein structures to identify recurring combinations of secondary structural elements. In a foundational 1973 paper, S. T. Rao and Michael G. Rossmann coined the term "supersecondary structures" while analyzing nucleotide-binding domains, highlighting the prevalence of repeating alpha-beta-alpha units as modular building blocks in protein folds.^[20] This work built on initial structural data from X-ray crystallography, shifting focus from isolated secondary elements to their connected motifs as key to understanding protein architecture. Throughout the 1970s and 1980s, theoretical advancements further formalized these ideas, with Alexander V. Efimov proposing "simple supersecondary structures" as fundamental units, such as the beta-hairpin, which serve as minimal scaffolds for assembling larger domains.^[21] Efimov's models emphasized stereochemical constraints and packing principles that favor certain motif topologies. A pivotal contribution came from Jane S. Richardson in 1981, whose review "The Anatomy and Taxonomy of Protein Structure" popularized the classification of approximately 20 common supersecondary motifs through innovative ribbon diagrams, enabling visual taxonomy of protein conformations across the growing Protein Data Bank (PDB).^[22] By the late 1980s, analyses of the PDB—then containing several hundred structures—had recognized around 50 distinct motifs, underscoring their role in structural diversity.^[22] In the 1990s, supersecondary structures were integrated into broader fold classification systems, linking motifs to evolutionary relationships through domain databases like SCOP and CATH. The SCOP database, introduced in 1995, hierarchically organized protein domains by motif connectivity and topology, revealing how supersecondary units recur across evolutionary distant proteins and support functional conservation. Similarly, CATH emphasized motif-based clustering to trace structural evolution. These milestones facilitated studies connecting supersecondary structures to protein folding pathways and divergence. Recent developments, particularly from 2018 to 2023, have validated the enduring relevance of supersecondary motifs using AI-driven structure prediction. AlphaFold2, achieving unprecedented accuracy in the CASP14 competition and beyond, has confirmed these motifs in millions of predicted structures, demonstrating their stability and prevalence without altering the core conceptual framework established in the 1980s. This has reinforced supersecondary structures as reliable predictors of local folding and evolutionary modules in de novo designs.

Helix-Based Supersecondary Structures

Helix Hairpin

The helix hairpin, also known as the α-α-hairpin, consists of two short antiparallel α-helices, each typically comprising 10-12 residues, connected by a tight loop of 2-5 residues. The hydrophobic faces of the helices pack closely together to form a stable core, with the loop providing the necessary reversal in chain direction. This motif is characterized by its compact, U-shaped arrangement, where the interhelical connection allows the helices to align in an antiparallel fashion without significant distortion of the helical geometry.^[2] Geometrically, the two helices in a helix hairpin cross at an angle of approximately 20-30° between their axes, enabling efficient packing of side chains. Stabilization arises from interhelical hydrogen bonds, primarily involving main-chain atoms at the helix-loop interface, as well as van der Waals and hydrophobic interactions between side chains on the inward-facing surfaces. Loops in this motif are often rich in glycine residues to confer flexibility and accommodate the sharp turn, with specific conformations such as the α_m γ_n patterns (where m and n denote residues in α-helical conformation) being prevalent for short connections.^[23] The total length of a helix hairpin spans about 20-25 residues, though variability exists depending on the protein context, with longer loops allowing more conformational freedom but potentially reducing stability. This motif occurs frequently in four-helix bundle proteins, where pairs of helix hairpins assemble to form the overall bundle topology. Notable examples include the structure of cytochrome c' (PDB: 1CGO), where such hairpins contribute to the core packing, and the A-B helical pair in myoglobin, which exemplifies the motif in oxygen-storage proteins.^[24]^[25] In functional terms, the helix hairpin plays a key role in the globin fold, contributing to the hydrophobic pocket that accommodates the heme prosthetic group for oxygen or electron binding and transfer. By positioning helices to shield the heme from solvent while allowing access for ligands, this motif supports the efficient catalysis and stability observed in globin family proteins.^[24]

Helix Corner

The helix corner, also known as the α-α-corner, is a supersecondary structure motif consisting of two consecutive α-helices connected by a short irregular loop of 3-5 residues, typically forming a right-angled arrangement at approximately 90° between the helical axes.^[26] This motif was first described as a novel structural unit where the helices pack crosswise, with the connecting loop often featuring hydrophobic residues and sometimes a proline kink to facilitate the sharp turn.^[26] The overall length of the motif spans about 15-20 residues, encompassing the two α-helices (each roughly 7-10 residues long) and the pivot-like loop that enables the orthogonal orientation.^[27] In terms of geometry, one helix aligns roughly parallel to the polypeptide chain direction, while the other extends perpendicularly, stabilized by ridge-groove interactions where ridges of side chains from one helix fit into grooves on the adjacent helix. This packing often follows a knobs-into-holes pattern, with hydrophobic side chains from one helix (knobs) inserting into spaces formed by four side chains on the other (holes), promoting a compact hydrophobic core. The motif exhibits a preferred left-handed superhelical twist, contributing to the dense interhelical contacts via van der Waals forces and occasional hydrogen bonds. Helix corners commonly occur in the cores of multi-helix bundles, aiding compact folding and stability in all-α or mixed α/β proteins.^[27] Representative examples include the motif in horse methemoglobin (residues 80-108, PDB: 1NS9), where it supports the globin fold's orthogonal helix packing.^[28] In these structures, the motif facilitates directional changes in the chain, enabling efficient assembly of larger helical bundles without compromising overall protein compactness.

Helix-Loop-Helix

The helix-loop-helix (HLH) motif features two alpha-helices connected by a flexible loop typically comprising 4-12 residues, with the helices exhibiting amphipathic character that facilitates interactions such as dimerization or ligand binding.^[29]^[30] In this arrangement, the loop provides conformational flexibility, enabling the helices to adopt varied orientations relative to each other.^[31] Geometrically, the helices diverge from the loop at approximately 90 degrees, promoting independent movement and creating a binding pocket suited for ligand coordination; a prominent example is the EF-hand variant, where a 12-residue loop chelates Ca²⁺ ions in a pentagonal-bipyramidal configuration.^[30] This divergence contrasts with more rigid helical packing observed in other motifs, allowing dynamic responses to environmental cues.^[31] The HLH motif occurs frequently in calcium-binding proteins, such as calmodulin, whose structure (PDB: 3CLN) reveals paired EF-hands for ion coordination, and in transcription factors where it supports regulatory functions.^[32]^[29] Overall, the motif encompasses about 25-35 residues, with loop sequences showing conservation—particularly Asp and Glu residues—to ensure functional specificity in metal binding.^[30] In terms of function, the HLH motif primarily coordinates divalent cations like Ca²⁺ using oxygen atoms from loop side chains and backbone carbonyls, triggering conformational changes that propagate signaling in proteins like calmodulin.^[31] Additionally, in basic HLH transcription factors, the motif drives dimerization through hydrophobic interfaces on the amphipathic helices, enabling sequence-specific DNA binding at sites such as E-box elements.^[29]

Helix-Turn-Helix

The helix-turn-helix (HTH) motif consists of two alpha-helices connected by a short beta-turn of 3-4 residues, typically a type I or type II beta-turn, which serves as a classic DNA-binding structural element in transcription factors. The first helix, often referred to as the stabilizing or scaffold helix, positions the second helix, known as the recognition helix, to interact directly with DNA. This arrangement allows the recognition helix to insert into the major groove of the DNA double helix, enabling sequence-specific contacts. The geometry of the HTH motif orients the recognition helix perpendicular to the scaffold helix, with the beta-turn providing the necessary flexibility and tight curvature to align the recognition helix optimally within the DNA major groove. Conserved glycine or serine residues in the turn region, such as glycine at the third position of the turn, confer conformational flexibility due to their lack of side-chain steric hindrance, facilitating precise positioning. In the lambda repressor from bacteriophage lambda (PDB: 1LMB), the motif spans residues 32-56, exemplifying this geometry where the recognition helix (residues 44-52) forms hydrogen bonds with base pairs in the operator DNA. Similarly, in eukaryotic homeodomains, the motif adopts a comparable spatial arrangement for regulatory functions. The HTH motif typically encompasses about 20-22 residues, with variability in sequence but conservation of hydrophobic cores and key polar residues for stability and binding. In prokaryotic repressors like the lambda repressor, the motif features residues such as glutamine and asparagine in the recognition helix for specific hydrogen bonding to DNA bases. Eukaryotic homeodomains, such as the Antennapedia homeodomain, exhibit sequence conservation in the recognition helix, including a tryptophan-lysine (WK) pair that contacts the DNA backbone and minor groove, enhancing specificity. This length and variability allow the motif to adapt across diverse transcription factors while maintaining functional integrity. The primary function of the HTH motif is to mediate sequence-specific DNA binding through hydrogen bonds and van der Waals interactions from side chains in the recognition helix, which probe the edges of base pairs exposed in the major groove. In the lambda repressor-operator complex, residues like Gln44 and Asn48 in the recognition helix form direct hydrogen bonds with adenine and guanine bases, respectively, ensuring operator specificity. This binding mode underlies gene regulation in both prokaryotes and eukaryotes, distinguishing the HTH from more flexible motifs like helix-loop-helix by its rigid turn for precise contacts.

Beta-Sheet Based Supersecondary Structures

Beta Hairpin

The beta hairpin is a fundamental supersecondary structure consisting of two short antiparallel beta strands, typically each comprising 3 to 10 residues, connected by a short loop of 2 to 16 residues that is often fewer than 7 residues in length.^[33] This motif forms through hydrogen bonding between the backbone amide and carbonyl groups of the opposing strands, creating a stable, compact unit that serves as a building block for larger beta-sheet architectures.^[33] The loop region frequently adopts type I' or II' beta-turn conformations, which reverse the polypeptide chain direction while maintaining phi-psi angles compatible with the extended strand geometry.^[34] Geometrically, the beta hairpin adopts a characteristic U-shaped conformation, with the antiparallel strands aligned in close register and interstrand hydrogen bonds spanning across the motif to enforce planarity and rigidity.^[33] The loop exhibits directionality that influences overall tightness: tight hairpins feature short, structured loops that minimize solvent exposure and enhance strand pairing, while meander loops involve longer, more flexible segments that allow the chain to curve back gradually.^[34] This geometry promotes amphipathicity, with hydrophobic residues often clustering on one face to facilitate packing within protein cores.^[33] Beta hairpins are ubiquitous in the beta sheets of globular proteins, occurring in approximately 49,000 unique instances across structures in the Protein Data Bank.^[33] A prominent example is the C-terminal beta hairpin in the B1 domain of streptococcal protein G (residues 41-56; PDB: 2GB1), where the motif contributes to the twisted beta sheet that stabilizes the protein's immunoglobulin-like fold.^[35] Similarly, in immunoglobulin domains, beta hairpins connect successive beta strands in the characteristic beta-sandwich architecture, as seen in variable regions that enable antigen recognition. The total length of a beta hairpin typically spans 10 to 25 residues, with significant variability arising from loop extensions or strand adjustments that accommodate functional diversity.^[33] Short loops, such as those featuring an Asn-Gly dipeptide sequence, are particularly common and stabilize the motif through specific hydrogen bonding patterns in type I' beta turns, where the asparagine side chain often forms an additional hydrogen bond to the glycine backbone.^[36] In terms of function, beta hairpins build the structural cores of beta sheets by providing preformed antiparallel strand pairs that propagate sheet extension through edge-to-edge associations.^[33] They also play a key role in protein folding kinetics, frequently forming as early intermediates that nucleate the assembly of larger beta-sheet domains and lower the energy barrier for chain collapse.^[37]

Beta Corner

The beta corner, also referred to as the β-β-corner or 3β-corner, is a supersecondary structure motif characterized by two anti-parallel β-strands connected by a short loop, forming a sharp approximately 90° bend in the polypeptide chain direction.^[2]^[38] This arrangement creates a compact, Z-like β-sheet configuration where the triple-stranded sheet folds onto itself in a right-handed manner, with the central strand facilitating the orthogonal packing of the two β-β-hairpins in distinct layers.^[39] The inner strand of the bend typically includes a glycine residue to accommodate the required φ/ψ angle flexibility (often around φ = -90° ± 30°, ψ = 0° ± 30°), while the outer strand frequently exhibits a β-bulge—a two-residue insertion that disrupts regular hydrogen bonding—to enable the abrupt turn without steric clashes.^[2]^[38] Hydrogen bonds between the strands preserve the integrity of the local β-sheet network despite the directional shift.^[40] In terms of geometry, one β-strand generally continues the overall chain trajectory, while the adjacent strand deviates sharply to introduce curvature, allowing the motif to serve as a hinge in three-dimensional β-architectures.^[39] This 90° right-handed twist, viewed from the concave side, distinguishes the beta corner from straighter connections like the beta hairpin, which extends planarly rather than curving for spatial compaction.^[2] The motif's design ensures stability through hydrophobic interactions in the core and maintains sheet hydrogen bonding patterns, even at the bend.^[38] Beta corners occur frequently in β-barrels, β-sandwiches, and up-and-down β-sheets, appearing in over 12,000 protein structures in the Protein Data Bank, particularly within all-β class proteins (about 54.5% of cases) and mixed α/β folds.^[38] A representative example is the SH3 domain from Saccharomyces cerevisiae (PDB: 1SSH), where the motif contributes to the compact β-barrel core.^[38] The motif typically encompasses 12-18 residues, including the two short β-strands (3-5 residues each) and the intervening loop (2-5 residues), though variability arises from differences in strand lengths and loop conformations.^[2]^[38] The glycine at the corner position is essential for conformational flexibility, often conserved across homologous structures to support the tight turn.^[41] Functionally, the beta corner enables efficient compact folding of β-sheets into higher-order architectures like barrels, acting as a stable building block that promotes hydrophobic core formation and overall protein stability.^[38] By introducing precise angular bends, it facilitates the closure of β-sheet edges into closed structures, reducing solvent exposure and enhancing thermodynamic favorability during folding.^[39]

Greek Key Motif

The Greek key motif is a prevalent supersecondary structure in proteins, consisting of four antiparallel β-strands connected in a specific topology denoted as 1-2-4-3, or equivalently +3, -1, -1 in standard nomenclature.^[42] This arrangement features two tight loops connecting strands 1 to 2 and 3 to 4, alongside a longer crossover loop linking strands 2 to 3, which imparts a meandering pattern reminiscent of the interlocking design on ancient Greek pottery.^[43] The motif was first systematically identified as a recurring β-sheet topology in protein structures. In terms of geometry, strands 1 and 2 form an adjacent antiparallel pair stabilized by hydrogen bonds, creating one β-hairpin, while strands 3 and 4 similarly form a second adjacent β-hairpin. The crossover connection between strands 2 and 3 arches over the sheet, enabling the non-sequential pairing of strands 2 and 4 via hydrogen bonds, which closes the motif into a compact, twisted β-meander.^[44] This configuration contrasts with simpler β-hairpins by incorporating the crossover to enforce the distinctive 1-2-4-3 connectivity.^[45] The Greek key motif commonly occurs in β-sandwich folds, contributing to the architecture of many all-β proteins, and is a topological signature in a majority of such structures.^[44] Representative examples include the β-sandwich domain of plastocyanin (PDB: 1PLC), where strands 3–6 adopt the motif to form part of a Greek key β-barrel, and the immunoglobulin domains, which feature tandem Greek keys in their β-sheets for domain stability.^[46] Typically spanning 30–40 residues, the motif exhibits variability in the long crossover loop, which often exceeds 10 residues and adopts irregular conformations without fixed secondary structure.^[47] Functionally, it provides structural compactness and intrinsic stability to β-sheet topologies, and is frequently observed in extracellular proteins where robust β-sandwiches resist environmental stresses.^[48]

Mixed Supersecondary Structures

Beta-Alpha-Beta Motif

The beta-alpha-beta motif is a fundamental supersecondary structure consisting of two parallel beta-strands connected by an intervening alpha-helix, where the strands form hydrogen bonds across the helix-mediated crossover connection.^[2] This arrangement positions the alpha-helix atop the plane of the beta-strands, facilitating the formation of parallel beta-sheets.^[49] In terms of geometry, the motif predominantly adopts a right-handed crossover configuration, with the helix crossing over the strands in a right-handed sense, accounting for over 95% of observed instances.^[49] Left-handed variants are rare and typically require glycine residues at key positions to alleviate steric clashes due to the unusual backbone conformation. The right-handed form aligns with the inherent right-handed twist of L-amino acid beta-strands, promoting stable packing.^[50] This motif frequently recurs in larger folds such as Rossmann-like domains and TIM barrels, where multiple units stack to create extended parallel beta-sheet cores.^[51] A representative example is found in triosephosphate isomerase (PDB: 1TIM), an enzyme featuring eight repeating beta-alpha-beta units arranged in a cylindrical TIM barrel structure. Each beta-alpha-beta unit typically spans 15-25 residues, with individual beta-strands comprising 5-7 residues, the connecting alpha-helix encompassing about one turn (roughly 4 residues), and short loops at the junctions providing flexibility.^[52] Variability arises mainly in loop lengths and helix tilt angles, allowing adaptation to specific protein contexts without disrupting the core topology.^[4] Functionally, the motif serves as a structural scaffold for parallel beta-sheet cores in nucleotide-binding enzymes, where the helix positions conserved loops for cofactor recognition and binding, as exemplified in dehydrogenases utilizing the Rossmann fold.^[53]

Rossmann Fold

The Rossmann fold represents an extended mixed supersecondary structure characterized by six parallel β-strands alternating with six α-helices, forming a central β-sheet flanked by helical layers on both sides. This arrangement creates a three-layered α/β/α sandwich topology, where the β-strands adopt a 321456 connectivity. The fold emerges from two repeated β-α-β-α-β units, providing a modular framework for ligand binding.^[54] Geometrically, the structure begins with the first three β-strands connected in a β-α-β pattern, followed by a crossover loop that mirrors the motif in the subsequent three strands, enabling the parallel sheet formation. While the full fold encompasses approximately 150-200 residues, the essential core motif requires about 100 residues, with common variations arising from extensions or shortening of the α-helices and insertions in connecting loops. This modularity allows adaptation across diverse proteins while preserving the overall architecture.^[54] The Rossmann fold occurs in over 38,000 structures within the Protein Data Bank as of 2020, predominantly in dehydrogenases and oxidoreductases involved in metabolic pathways. A classic example is lactate dehydrogenase (PDB: 1LDM), where the fold facilitates NAD⁺ cofactor binding essential for catalysis. This prevalence underscores its evolutionary success as a versatile domain in nucleotide-dependent enzymes.^[54]^[55] Functionally, the Rossmann fold specializes in dinucleotide binding, such as NAD⁺ or NADP⁺, with the pyrophosphate linkage gripped by hydrogen bonds from backbone amides in inter-strand loops, particularly near the conserved GXGXXG motif in the first β-α connection. The adenine ring is stabilized through hydrophobic interactions and hydrogen bonds with residues in the adjacent α-helices, positioning the cofactor for efficient electron transfer in enzymatic reactions.^[54]

Identification and Prediction

Experimental Determination

X-ray crystallography remains the primary experimental method for determining the atomic-resolution structures of protein supersecondary motifs, achieving resolutions typically between 1 and 2 Å that allow precise visualization of hydrogen bonding patterns and side-chain interactions in elements like beta hairpins and helix-turn-helix motifs.^[56] For instance, the beta-hairpin motif in a designed peptide has been resolved at 2.08 Å, revealing the tight turn and antiparallel strand alignment essential to its stability (PDB: 5W4J).^[57] Historically, the technique's application to proteins began in the 1950s with pioneering work by John Kendrew and Max Perutz, who determined the structure of myoglobin at 2 Å resolution in 1959 and hemoglobin at 5.5 Å shortly thereafter, marking the first glimpses of alpha-helical bundles as supersecondary units.^[58]01423-8.pdf) Subsequent advancements, particularly the adoption of synchrotron radiation sources in the 1980s and 1990s, dramatically improved data quality by providing brighter, more coherent X-ray beams, enabling resolutions down to sub-atomic levels (below 1 Å) and facilitating the study of larger, more complex motifs with reduced radiation damage to crystals.^[59]^[60] Nuclear magnetic resonance (NMR) spectroscopy complements X-ray by providing structures in solution, where supersecondary motifs can be identified through characteristic nuclear Overhauser effect (NOE) patterns that report on spatial proximities between atoms, such as inter-helix distances in helix-loop-helix motifs or sequential NOEs in beta hairpins.^[61]^[62] For example, NOE data have confirmed the helical packing and loop flexibility in a designed three-helix bundle protein (PDB: 2A3D), highlighting short-range (i to i+3) and medium-range NOEs diagnostic of alpha-helical continuity across the motif.^[63] NMR is particularly valuable for smaller proteins (up to ~50 kDa) and dynamic regions, as it captures ensemble averages without the need for crystallization, though it requires isotopic labeling and extensive assignment of resonances for accurate motif delineation.^[64]^[65] Cryo-electron microscopy (cryo-EM), a more recent development surging post-2010 with direct electron detectors, has enabled the resolution of supersecondary structures within large protein complexes at near-native conditions, often achieving 3-4 Å for helical bundles or beta-sheet motifs where traditional methods falter.^[66]^[67] For instance, cryo-EM has visualized four-helix bundle motifs in the whole photosynthetic reaction center apparatus from Chlorobaculum tepidum at 2.5 Å, revealing motif packing without crystallization artifacts.^[68] This technique excels for assemblies exceeding 100 kDa, preserving flexibility in loops connecting motifs, but its resolution for isolated supersecondary elements remains coarser than X-ray or NMR due to sample heterogeneity.^[66]^[67] Despite these advances, experimental determination of supersecondary structures faces significant limitations, particularly with dynamic or flexible motifs like connecting loops in helix-loop-helix or beta corners, which often disorder in crystals and yield poor electron density in X-ray maps or broadened signals in NMR spectra.^[4] Cryo-EM also struggles with such flexibility, leading to averaged or blurred densities in reconstructions.^[69] Moreover, all methods require prior knowledge of the protein sequence for initial modeling and interpretation, as raw data alone cannot assign specific motifs without atomic coordinates.^[70]

Computational Methods

Computational methods for identifying and predicting supersecondary structures have evolved from sequence-based empirical approaches to sophisticated AI-driven structure prediction and database scanning techniques. Early sequence-based methods, such as the Chou-Fasman algorithm developed in the 1970s, initially focused on secondary structure prediction by assigning propensity values to amino acids for forming alpha-helices, beta-sheets, and turns, which were later extended to detect supersecondary motifs like beta-hairpins through pattern recognition in predicted secondary elements. These approaches laid the groundwork for more advanced sequence-based predictors using position-specific scoring matrices (PSSMs) derived from multiple sequence alignments. Modern sequence-based predictors build on neural networks and machine learning to target specific supersecondary motifs. For instance, PSIPRED, a widely used tool employing PSI-BLAST profiles and feed-forward neural networks, has been adapted for beta-hairpin detection by integrating multiple alignment information to predict turn positions and strand pairings with improved accuracy over single-sequence methods.^[71] A 2024 review highlights 32 such sequence-based supersecondary structure (SSS) predictors, predominantly focusing on coiled coils and beta-hairpins, with five recent methods achieving per-residue accuracies exceeding 70% through ensemble learning and deep neural networks trained on curated datasets from the Protein Data Bank (PDB).^[72] Structure-based methods rely on scanning known protein structures in databases like the PDB to identify supersecondary motifs via geometric matching. The ARCH (or ArchDB) library, introduced in the early 2000s and updated through 2014, classifies loops and supersecondary structures such as alpha-alpha hairpins and beta-alpha-beta units by clustering hydrogen-bonded elements, enabling motif searches that reveal architectural patterns across protein families.^[73] Similarly, the SMOTIF database, comprising over 466,000 supersecondary fragments (Smotifs) from non-redundant PDB structures, facilitates loop-connected pair identification by indexing secondary structure types (e.g., helix-loop-helix) and geometries, supporting homology modeling and de novo design.^[74] AI-driven approaches, particularly deep learning models, have revolutionized supersecondary structure analysis by predicting full atomic models from sequences, from which motifs emerge naturally. AlphaFold2 (2020) and its successor AlphaFold3 (2024) use attention-based neural networks to generate high-confidence 3D structures, allowing post-prediction annotation of supersecondary motifs via per-residue confidence scores (pLDDT), which highlight regions like beta-hairpins with scores above 90 indicating near-experimental accuracy.^[75]^[76] RoseTTAFold (2021), a trRosetta-inspired model, extends this capability for motif insertion by fine-tuning on scaffold-motif complexes, enabling the design of proteins with embedded supersecondary elements while preserving overall fold stability. Tools for comparative analysis further aid in supersecondary structure identification across homologs. Dali, a seminal algorithm from the 1990s, performs exhaustive 3D alignments to detect structural similarities, including conserved supersecondary motifs in distant homologs, while Foldseek (2022 onward) accelerates this process using sequence-like encodings of structural features for rapid database searches, integrating machine learning for substructure queries up to 2025. These methods support de novo motif design by combining predicted structures with evolutionary constraints. Overall, computational prediction accuracies for common supersecondary motifs reach approximately 80% at the residue level, as benchmarked in recent evaluations, though challenges persist with rare configurations like left-handed crossovers due to limited training data and conformational flexibility.^[72]

References

[1]
The Anatomy and Taxonomy of Protein Structure - ScienceDirect.com
1981, Pages 167-339. Advances in Protein Chemistry. The Anatomy and Taxonomy of Protein Structure. Author links open overlay panelJane S. Richardson. Show ...
[2]
2 Super-secondary structure - SWISS-MODEL
Secondary structure elements are observed to combine in specific geometric arrangements known as motifs or super-secondary structures.
[3]
Supersecondary Structure - an overview | ScienceDirect Topics
Super-secondary structure is defined as a combination of secondary structures that results in more complex formations, such as β-barrels or motifs like helix- ...
[4]
Current Approaches in Supersecondary Structures Investigation - PMC
Nov 2, 2021 · Supersecondary structures (SSS) are a transitional bridge between the secondary and tertiary levels of protein structural organization.
[5]
The anatomy and taxonomy of protein structure - PubMed - NIH
The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981:34:167-339. doi: 10.1016/s0065-3233(08)60520-3. Author. J S Richardson. PMID: 7020376; DOI ...
[6]
[PDF] DNA structure reminder
Most common DNA-binding motif and is typically ~20 amino acids in length ... conserved residues ... The other helix of the helix-turn-helix motif is colored blue.<|control11|><|separator|>
[7]
II. Basic Elements of Protein Structure - Kinemage
The commonest domain size is between 100 and 200 residues, but it now appears that there is no strict and definite upper limit on practical folding size: domain ...
[8]
https://doi.org/10.1590/S0100-879X2001000400001
[9]
PSSNet—An Accurate Super-Secondary Structure for Protein ... - NIH
Nov 26, 2022 · A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape ...
[10]
Creative destruction: New protein folds from old - PNAS
Other models suggest that fold evolution occurs by preadaptation, combinatorial shuffling of supersecondary structures and transfer of isolated folding ...
[11]
A Self-Organizing Algorithm for Modeling Protein Loops
Protein loops play an important role in protein function, such as ligand binding, recognition, and allosteric regulation. ... supersecondary structure ...<|control11|><|separator|>
[12]
De novo design and characterization of a helical hairpin eicosapeptide
De novo design of supersecondary structures is expected to provide useful molecular frameworks for the incorporation of functional sites as in proteins.
[13]
A Three-Dimensional Model of the Myoglobin Molecule Obtained by ...
In 1958, J. C. Kendrew et al. applied Perutz–s technique to produce the first three-dimensional images of any protein - myoglobin, the protein used by ...
[14]
A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution ... - Nature
Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis. Nature 185, 416–422 (1960).
[15]
Three-dimensional Structure of Tosyl-α-chymotrypsin | Nature
A model is proposed for the structure of an inhibited derivative of an enzyme which hydrolyses proteins. It is based on a map of the electron density ...Missing: paper | Show results with:paper
[16]
The structure of carboxypeptidase A: III. Molecular structure at 6 Å ...
The structure of carboxypeptidase Aα at 6 Å resolution has been obtained from X-ray diffraction data from native protein crystals and crystals of four ...
[17]
The structure of proteins: Two hydrogen-bonded helical ... - PNAS
Two hydrogen-bonded helical structures for a polypeptide chain have been found in which the residues are stereochemically equivalent.
[18]
Growth of novel protein structural data - PNAS
In the 15 years from 1960 to 1974, 10 additional protein structures were solved and by 1976 it was possible to use the 31 known structures to define a ...
[19]
John Kendrew and myoglobin: Protein structure determination ... - NIH
The essay reviews John Kendrew's pioneering work on the structure of myoglobin for which he shared the Nobel Prize for Chemistry in 1962.
[20]
https://doi.org/10.1016/0022-2836(73)90388-4
[21]
[PDF] Analysis Of Torsion Angles Between Helical Axes in Pairs of Helices ...
Apr 30, 2018 · It is shown that the distribution of all the helical pairs having the crossing helix projections has a maximum at 20° < Ω < 25°. ... Helix to ...<|separator|>
[22]
4 Tertiary Protein Structure and Folds - SWISS-MODEL
Jane Richardson (1981) describes the globin fold as a "Greek key helix bundle", due to the topological similarity with the Greek key arrangement of ...
[23]
1CGO: CYTOCHROME C - RCSB PDB
The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very ...
[24]
https://swissmodel.expasy.org/course/text/chapter4.htm
[25]
https://www.rcsb.org/structure/1CGO
[26]
https://doi.org/10.1016/0014-5793(84)80039-3
[27]
An overview of the basic helix-loop-helix proteins - PubMed Central
The basic helix-loop-helix proteins are dimeric transcription factors that are found in almost all eukaryotes. In animals, they are important regulators of ...
[28]
Structural Aspects and Prediction of Calmodulin-Binding Proteins
Each motif consists of a canonical helix-loop-helix (HLH) structure. The EF-hand motif, exhibiting pentagonal-bipyramidal geometry, includes a highly ...
[29]
https://pmc.ncbi.nlm.nih.gov/articles/PMC463060/
[30]
3CLN: STRUCTURE OF CALMODULIN REFINED AT ... - RCSB PDB
The four Ca2+-binding domains in calmodulin have a typical EF hand conformation (helix-loop-helix) and are similar to those described in other Ca2+-binding ...
[31]
A systematic analysis of the beta hairpin motif in the Protein Data Bank
Beta hairpins, one of the simplest stable protein structural elements, consist of two antiparallel beta‐sheets joined by a short loop region. Despite their ...
[32]
β-Hairpin families in globular proteins - Nature
Jul 11, 1985 · β- Hairpins, one of the simplest supersecondary structures, are widespread in globular proteins, and have often been suggested as possible ...
[33]
Transition-path sampling of β-hairpin folding - PNAS
The β-hairpin system was prepared by extracting the C terminus (residues 41–56) from the Protein Data Bank structure of protein G-B1 (PDB ID code 2gb1).Sign Up For Pnas Alerts · Tps · Rate Constants
[34]
Analysis of the factors that stabilize a designed two-stranded ... - NIH
L-Asn-Gly (NG) is the most common sequence for residues i+1 and i+2 of a type I` β-turn in natural proteins of known structure (Hutchinson and Thornton 1994), ...
[35]
β-hairpin-forming peptides; models of early stages of protein folding
Formation of β-hairpins is considered the initial step of folding of many proteins and, consequently, peptides constituting the β-hairpin sequence of proteins ( ...
[36]
Biological Role of the 3β-Corner Structural Motif in Proteins - MDPI
The 3β-corner is often found as a building block in protein structures, such as β-barrels, -sandwiches, and -sheets/-layers.
[37]
https://pmc.ncbi.nlm.nih.gov/articles/PMC2906654/
[38]
Favoured structural motifs in globular proteins - ScienceDirect.com
These αα-corners are widespread in proteins in which α -helices are packed in a predominantly orthogonal fashion [6] ; examples include, globins, parvalbumin, ...
[39]
[PDF] Supersecondary Structures (structural motifs)
Large supersecondary structures can be domains. Simple supersecondary structures are typically composed of two secondary structures (ie. strands or helices) and ...
[40]
The Greek key motif: extraction, classification and analysis - PubMed
The Greek key is a common protein motif, traditionally defined as four beta-strands with '+3,-1,-1' topology, and classified into three groups.
[41]
Greek key motif: extraction, classification and analysis
The Greek key is a very common structural motif in proteins. It has been traditionally defined as four β-strands with ' +3,–1,–1' topology.
[42]
A comprehensive analysis of the Greek key motifs in protein beta ...
Greek key motifs are the topological signature of many beta-barrels and a majority of beta-sandwich structures. Beta-barrels can have 12 possible topologies.
[43]
Equilibrium folding intermediates of a greek key β-barrel protein
The Greek key motif was recognized as a super-secondary structure by Richardson in 1977 (Richardson, 1977). It is composed of four antiparallel β-strands with + ...
[44]
1PLC: ACCURACY AND PRECISION IN PROTEIN ... - RCSB PDB
The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10,500 Da) from poplar leaves, has been refined at 1.33 A ...
[45]
Structural Integrity of the Greek Key Motif in βγ-Crystallins Is Vital for ...
Motif 1 covers the sequence 1–40, motif 2 is between residues 42–83, motif 3 is in the sequence 88–128 while the last Greek key is found in the stretch 129–171 ...
[46]
Function of the Greek key connection analysed using circular ...
Interest in the function of the Greek key motif and Greek key connections arose from the discovery that they occur in many β‐strand proteins (Richardson, 1977).
[47]
[PDF] Super secondary structure (Motif)
Beta-alpha-beta (βαβ) motif allows two parallel beta strands. – There is a long crossover between the end of the first strand and the beginning of the second ...
[48]
Supersecondary structure - Wikipedia
A supersecondary structure is a compact three-dimensional protein structure of several adjacent elements of a secondary structure that is smaller than a ...Examples · Helix supersecondary structures · Beta sheet supersecondary...
[49]
Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites
Feb 20, 2015 · The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (β) and ...Missing: et al. 1974 nucleotide-
[50]
βαβ Super-Secondary Motifs: Sequence, Structural Overview, and ...
Length distribution (number of amino acids) of (a) βαβ motifs, ( · Representative βαβ units from TIM barrelTIM barrels proteins depicting the interactions ...<|control11|><|separator|>
[51]
Rossmann fold: A beta‐alpha‐beta fold at dinucleotide binding sites
Feb 20, 2015 · (2) The βαβ fold motif that is common to both FAD and NAD(P) binding enzymes accommodates the common ADP component of these two coenzymes.
[52]
Rossmann-like proteins as an evolutionarily successful structural unit
The Rossmann-like fold is the most prevalent and diversified doubly-wound superfold of ancient evolutionary origin. Rossmann-like domains are present in a ...Missing: 1960s | Show results with:1960s
[53]
Rossmann fold - Proteopedia, life in 3D
### Summary of Rossmann Fold from Proteopedia
[54]
1LDM: Refined crystal structure of dogfish M4 apo-lactate ...
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase ; Deposited: 1987-11-25 ; Released · 1989-07-12 ; Deposition Author(s): Griffith, J.P., Rossmann, ...
[55]
Methods for Determining Atomic Structures - PDB-101
For example, X-ray crystallography is an excellent method for determining the structures of rigid proteins that form nice, ordered crystals.
[56]
5W4J: X-ray crystallographic structure of a beta-hairpin peptide ...
Nov 22, 2017 · RCSB PDB - 5W4J: X-ray crystallographic structure of a beta-hairpin peptide mimic. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.Missing: code immunoglobulin
[57]
Progress in protein crystallography - PMC - NIH
Some recently introduced improvements are specifically addressed for refinement of structures against low resolution data, such as, for example, the 'jelly body ...
[58]
A new era of synchrotron-enabled macromolecular crystallography
May 7, 2021 · Time-resolved macromolecular crystallography at the synchrotron can provide atomic resolution structures at microsecond temporal resolution ...
[59]
Synchrotron Radiation as a Tool for Macromolecular X-Ray ...
Synchrotron beamlines have been used to determine over 70% of all macromolecular structures deposited into the Protein Data Bank (PDB). These structures were ...
[60]
CSI 3.0: a web server for identifying secondary and super-secondary ...
May 15, 2015 · In protein NMR, secondary structures are traditionally identified and assigned using NOE-based (Nuclear Overhauser Effect) methods. By manually ...
[61]
Protein structure determination by NMR | Biophysics Class Notes
Secondary Structure Determination. The presence of characteristic NOE patterns aids in the identification of secondary structure elements (strong HN-HN NOEs ...Missing: supersecondary examples
[62]
Solution structure and dynamics of a de novo designed three-helix ...
Here, the NMR solution structure of a complex 73-residue three-helix bundle protein, α3D, is reported. The structure of α3D was not based on any natural protein ...
[63]
NMR-Based Methods for Protein Analysis | Analytical Chemistry
Jan 13, 2021 · NMR spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states.Structural Analysis of Proteins... · Analysis of Protein... · Perspectives · ReferencesMissing: supersecondary | Show results with:supersecondary
[64]
Protein structure determination from NMR chemical shifts - PNAS
Jun 5, 2007 · NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules.Missing: supersecondary | Show results with:supersecondary
[65]
Integrated NMR and cryo-EM atomic-resolution structure ... - Nature
Jun 19, 2019 · We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods.
[66]
Resolving individual atoms of protein complex by cryo-electron ...
Nov 2, 2020 · Cryo-EM has resolved over four thousand structures at near-atomic resolutions (2–4 Å). It is rapidly becoming the method of choice for structure ...Missing: supersecondary | Show results with:supersecondary
[67]
Sub-3 Å resolution protein structure determination by single-particle ...
Oct 2, 2025 · We report sub-3 Å resolution structures using the 100 keV Tundra cryo-TEM, equipped with the Falcon C direct electron detector (DED).
[68]
High-resolution structure determination of sub-100 kDa complexes ...
Mar 4, 2019 · We show that conventional defocus-based cryo-EM methodologies can be used to determine high-resolution structures of specimens amassing less than 100 kDa.
[69]
Three-Dimensional Graph Matching to Identify Secondary Structure ...
NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution ...
[70]
Detection of secondary and supersecondary structures of proteins ...
Our paper focuses on the computational interpretation and detection of secondary and supersecondary structures of intermediate (6–10 Å) and coarse (10–15 Å) ...Missing: crystallography | Show results with:crystallography
[71]
Assessing the Quality of 3D Structures - RCSB PDB
Oct 27, 2023 · For example, the resolution of PDB entry 7s98 is 1.9 Å, R-value is 0.186, and the R-free value is 0.216 (see Figure 1). Based on these measures ...
[72]
prediction of β-hairpins in a protein from multiple alignment ...
Jul 1, 2005 · Abstract. This paper describes a method for predicting a supersecondary structural motif, β-hairpins, in a protein sequence.
[73]
Recent Advances in Computational Prediction of Secondary and ...
We also review 32 sequence-based SSS predictors, which primarily focus on predicting coiled coils and beta-hairpins and which include five methods that were ...
[74]
ArchDB 2014: structural classification of loops in proteins - PMC - NIH
Based on that classification of loops, we have developed ArchDB 2014, which includes super-secondary structures with 310 helices, and a new clustering method ...
[75]
Modeling proteins using a super-secondary structure library ... - NIH
Building the Smotif database. The Smotif database currently consists of 466,939 Smotifs obtained from 28,012 sequentially non-redundant protein structures ...
[76]
Highly accurate protein structure prediction with AlphaFold - Nature
Jul 15, 2021 · We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein ...Missing: supersecondary | Show results with:supersecondary