<i>P</i>-Sulfonatocalix[8]arene coordinates sodium cations and forms host-guest complex with berberine: insight from crystal structure

Kravets, Kateryna; Kravets, Mykola; Kędra-Królik, Karolina; Danylyuk, Oksana

doi:10.1080/10610278.2022.2161901

Cited by 5 publications

(9 citation statements)

References 57 publications

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“…50 Re-cently, Danylyuk and co-workers reported crystals that were obtained by slow diffusion of ethanol into an aqueous solution of the sclx 8 sodium salt. 54 In this structure, sclx 8 is in the pleated loop conformation and forms columnar stacks. The stacks are almost perfectly superposed calixarenes, yielding tubes with a solvent-filled core and an outer layer of sodium cations coordinating the sulfonates.…”

Section: ■ Resultsmentioning

confidence: 99%

“…In both structures, the calixarene occurs as oligomeric stacks, assembled from the regular pleated loop conformation. This conformation is amenable to columnar stacking (with a central solvent channel) 54 or staggered stacking (Figure 3A). The latter arrangement is essentially identical to that found in the protein cocrystal (Figure 2D,F).…”

Section: ■ Discussionmentioning

confidence: 99%

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Supramolecular Synthons in Protein–Ligand Frameworks

Flood,

Mockler,

Thureau

et al. 2024

Crystal Growth & Design

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Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein−calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene−calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.

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Section: ■ Resultsmentioning

confidence: 99%

Section: ■ Discussionmentioning

confidence: 99%

Supramolecular Synthons in Protein–Ligand Frameworks

Flood,

Mockler,

Thureau

et al. 2024

Crystal Growth & Design

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“…While sclx 8 is a well-established host macrocycle in supramolecular chemistry, ,, it behaves as a guest sitting in the host Pent. This hosting action of the protein is emphasized in crystal form II, where a Pent dimer encapsulates one sclx 8 (Figures S3B and ).…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, the NMR data suggest simple complex formation, rather than macrocycle-mediated oligomerization as occurs for monomeric cytochrome c (∼13 kDa). 45 While sclx 8 is a well-established host macrocycle in supramolecular chemistry, 26,46,47 it behaves as a guest sitting in the host Pent. This hosting action of the protein is emphasized in crystal form II, where a Pent dimer encapsulates one sclx 8 (Figures S3B and 4).…”

Section: ■ Discussionmentioning

confidence: 99%

Multivalent Calixarene Complexation of a Designed Pentameric Lectin

Flood,

Cerofolini,

Fragai

et al. 2024

Biomacromolecules

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We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonatocalix[8]arene (sclx 8 ), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and 15 N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein− calixarene interface observed to date. This system provides a platform for investigating multivalency.

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“…Calix [n]arenes are macrocyclic polyphenols with extensive crystal-engineering applications (Atwood et al, 2002;Kravets et al, 2021;Les ´niewska et al, 2019;Pasquale et al, 2012). The sulfonato-calixarenes are versatile receptors for protein surfaces (with millimolar to micromolar binding affinities), acting as molecular glues with pronounced co-crystallization properties akin to 'silver bullets' (Alex et al, 2019;McPherson & Cudney, 2006).…”

Section: Introductionmentioning

confidence: 99%

Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex

Mockler

Ramberg

Crowley

2023

Acta Crystallogr D Struct Biol

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Controlled protein assembly and crystallization is necessary as a means of generating diffraction-quality crystals as well as providing a basis for new types of biomaterials. Water-soluble calixarenes are useful mediators of protein crystallization. Recently, it was demonstrated that Ralstonia solanacearum lectin (RSL) co-crystallizes with anionic sulfonato-calix[8]arene (sclx8) in three space groups. Two of these co-crystals only grow at pH ≤ 4 where the protein is cationic, and the crystal packing is dominated by the calixarene. This paper describes a fourth RSL–sclx8 co-crystal, which was discovered while working with a cation-enriched mutant. Crystal form IV grows at high ionic strength in the pH range 5–6. While possessing some features in common with the previous forms, the new structure reveals alternative calixarene binding modes. The occurrence of C 2-symmetric assemblies, with the calixarene at special positions, appears to be an important result for framework fabrication. Questions arise regarding crystal screening and exhaustive searching for polymorphs.

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P-Sulfonatocalix[8]arene coordinates sodium cations and forms host-guest complex with berberine: insight from crystal structure

Cited by 5 publications

References 57 publications

Supramolecular Synthons in Protein–Ligand Frameworks

Supramolecular Synthons in Protein–Ligand Frameworks

Multivalent Calixarene Complexation of a Designed Pentameric Lectin

Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex

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