Alpha solenoid

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An example of an alpha solenoid structure composed of 15 HEAT repeats. The protein phosphatase 2A regulatory subunit is shown with the N-terminus in blue at bottom and the C-terminus in red at top. A single helix-turn-helix motif is shown in the center with the outer helix in pink, the inner helix in green, and the turn in white. From PDB: 2IAE​.[1]

An alpha solenoid (sometimes also known as an alpha horseshoe or as stacked pairs of alpha helices, abbreviated SPAH) is a

protein-protein interactions with their binding partners.[2][4] Examples of alpha solenoid structures binding RNA and lipids have also been described.[2]

Terminology and classification

The term "alpha solenoid" has been used somewhat inconsistently in the literature.

peridinin-chlorophyll binding protein.[4]

Structure

Alpha solenoid proteins are composed of repeating structural units containing at least two

tetratricopeptide (TPR) repeats, leucine-rich repeats, and ankyrin repeats.[2][4][5]

Alpha solenoids have unusual elasticity and flexibility relative to

protein-protein interaction surfaces or to form deep concave areas for binding globular proteins.[2]

Because they are composed of repeating relatively short subunits, alpha solenoids can acquire additional subunits relatively easily, resulting in new interaction surface properties.[2] As a result, known alpha solenoid proteins vary substantially in length.[4]

Function

Nuclear pore complex components

Alpha solenoids feature prominently in the proteins making up the

planctomycetes.[10]

Vesicle coat proteins

The structure of the clathrin heavy chain leg segment showing helical repeats, with the N-terminus in blue at left and the C-terminus in red at right.[11]

Vesicle coat proteins frequently contain alpha solenoids and share common domain architecture with some NPC proteins.

anterograde transport.[12]

Transport proteins

Due to their propensity for forming large interaction surfaces well-suited to

exportin-5[14] or pentatricopeptide-repeat-containing RNA-binding proteins, which are particularly common in plants.[15][16]

Regulatory proteins

The assembled heterotrimer of protein phosphatase 2A. Subunit A, consisting of 15 HEAT repeats, is shown in rainbow color with the N-terminus in blue at bottom and the C-terminus in red at top. The regulatory subunit B, consisting of irregular pseudo-HEAT repeats, is shown in light blue. The catalytic subunit C is shown in tan. (All from PDB: 2IAE​.) Superposed is the unbound form of the regulatory subunit B in gray (from PDB: 1B3U​), illustrating the flexibility of this alpha solenoid protein. Conformational changes in HEAT repeat 11 result in flexing the C-terminal end of the protein to accommodate binding of the catalytic subunit.[1][17]

The protein-protein interaction capacity of alpha solenoid proteins also makes them well suited to function as

regulatory proteins. For example, regulatory subunit A (also known as PR65) of protein phosphatase 2A is a HEAT-repeat alpha solenoid whose conformational flexibility regulates access to the enzyme binding site.[18][1]

Taxonomic distribution

Alpha solenoid proteins are found in all

planctomycetes, which have unusually complex intracellular compartmentalization relative to most prokaryotes.[2]

Evolution

Evolutionary relationships between different alpha solenoid proteins are difficult to trace due to the low sequence homology of the repeats. Convergent evolution of similar protein structures from ancestrally unrelated proteins is thought to be significant in the evolutionary history of this fold class.[2]

Nuclear pore complexes and vesicle transport

The

beta propeller and a C-terminal alpha solenoid has been detected in both NPC and coat proteins, suggesting a possible common origin.[7][8] An ancestral "protocoatomer" that diversified to acquire derived characteristics of all four modern complexes has been proposed.[4][19][20][21]

Examination of the genome of

archaeal relatives to eukaryotes, did not reveal any examples of the beta propeller/alpha solenoid domain architecture, although homologs of other proteins involved in eukaryotic membrane trafficking were identified. However, it is unclear whether this observation means that the propeller/solenoid architecture evolved later or was lost from modern lokiarchaea.[22]

Membrane coat proteins in prokaryotes

A survey of the sequenced genomes of complex prokaryotes from the PVC superphylum (Planctomycetota-Verrucomicrobiota-Chlamydiota) identified examples of proteins with homology to eukaryotic membrane trafficking proteins, including examples of the distinctive beta-propeller/alpha-solenoid domain architecture previously believed to be unique to eukaryotes.[10] The PVC superphylum is known for containing bacteria with unusually complex membrane morphology, and this discovery has been cited as evidence in favor of these organisms' status as an intermediate form between prokaryotes and eukaryotes. The planctomycete Gemmata obscuriglobus has exceptionally complex membrane architecture and has been a source of controversy in the literature regarding the possibility that it has a membrane-bound "nucleoid" compartment enclosing its DNA.[23][24][25][26][27][28] The identification of proteins with sequence similarities to HEAT repeats in the G. obscuriglobus proteome has been interpreted as support for the membrane-bound nucleoid hypothesis;[29] however, this has been disputed.[24]

Bioinformatics

Low sequence similarity among alpha solenoid proteins of similar structure has impeded their identification using

amino acid sequence.[2][30][31]

External links

References

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  5. ^
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  6. ^ "CATH Topology "Alpha Horseshoe"".
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  23. ^ Fuerst, John A. (2010). "Beyond Prokaryotes and Eukaryotes : Planctomycetes and Cell Organization". Nature Education. 3 (9): 44.
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