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

Mockler, Niamh M.; Ramberg, Kiefer O.; Crowley, Peter B.

doi:10.1107/s2059798323003832

Cited by 4 publications

(17 citation statements)

References 43 publications

(62 reference statements)

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“…The 6-bladed β-propeller RSL binds sclx 8 with low affinity, cocrystallizing in at least four forms. , These structures involve six different protein–calixarene interfaces, and the macrocycle is engaged to varying degrees as a molecular glue. In contrast, the 5-bladed β-propeller Pent binds sclx 8 with high affinity at one well-defined site.…”

Section: Discussionmentioning

confidence: 99%

“…Both techniques reveal multivalent protein−calixarene binding, 24,25 in which the protein is clearly the host and the macrocycle is the guest. 26 Contrary to previous studies with the 6-bladed β-propeller, 21,22…”

Section: ■ Introductionmentioning

confidence: 95%

“…The β-propeller, with 4–12 blades, is a widespread toroidal fold with diverse functions ranging from ligand binding to catalysis and protein–protein interactions. − Moreover, the repeat structure is amenable to multivalent interactions. , Previously, we characterized the 6-bladed β-propeller Ralstonia solanacearum lectin (RSL) in complex with sclx 8 . − The acidic RSL binds anionic sclx 8 at pH 4, as evidenced by solution NMR spectroscopy. Co-crystallization of RSL and sclx 8 is pH-dependent also, and at least four cocrystal forms are known. , Here, we investigated sclx 8 complexation with a designed 5-bladed β-propeller (PDB 5C2N), based on tachylectin-2. Each blade of this β-propeller is a 47-residue monomer of ∼5.2 kDa (yielding a pentamer of ∼26 kDa) that binds one equivalent of N-acetylglucosamine (GlcNAc).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

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Multivalent Calixarene Complexation of a Designed Pentameric Lectin

Flood,

Cerofolini,

Fragai

et al. 2024

Biomacromolecules

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“…In the course of RSL−sclx 8 cocrystallization trials, we observed that sodium citrate pH 4−6 leads to calixarene crystallization. 18 In this sodium salt structure (CCDC 2298745), the calixarene is again in the pleated loop conformation and has a staggered packing arrangement (Figure 3). The sclx 8 dimer and trimer assemblies in protein cocrystals (Figure 2) are essentially identical to the structural arrangement of sclx 8 in the sodium salt.…”

Section: ■ Discussionmentioning

confidence: 99%

“…Poor packing at this site may have contributed to an overall increase in disorder for this structure (and hence the 2.6 Å resolution). This result is also interesting in that a C 2 symmetric protein–calixarene–protein interface at Lys25/Lys83 occurs in the H 32 crystal form …”

Section: Discussionmentioning

confidence: 99%

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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Host–Guest Complexes of p-Sulfonato-calix[4]arene and Benzamidine: A Matter of Counterion and Aging in the Mother Liquor

Kravets,

Danylyuk

2024

Crystal Growth & Design

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p-Sulfonato-calix [4]arene is commercially available either as a sodium salt or as a sulfonic acid. We aimed to clarify the complexation and crystallization pathways of p-sulfonato-calix[4]arene with benzamidine ligand employing these two commercial forms of macrocyclic host. The additional aspect that we considered is what happens when initially formed crystals are kept in the mother solution simply over passing of time, allowing slow evaporation. This seems to be not as innocent as it intuitively appears. The "aging" of multicomponent crystals exposed to concentration changes of the dissolved components during crystal growth and partial evaporation of the mother solution can embrace different scenarios, including dissolution−recrystallization transformations. Our findings highlight the need of taking into account psulfonato-calix[4]arene counterion and crystal aging in the mother liquor as important variables for supramolecular and crystal design of host−guest complexes.

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

Cited by 4 publications

References 43 publications

Multivalent Calixarene Complexation of a Designed Pentameric Lectin

Multivalent Calixarene Complexation of a Designed Pentameric Lectin

Supramolecular Synthons in Protein–Ligand Frameworks

Host–Guest Complexes of p-Sulfonato-calix[4]arene and Benzamidine: A Matter of Counterion and Aging in the Mother Liquor

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