Cucurbit[7]uril‐Dimethyllysine Recognition in a Model Protein

Guagnini, Francesca; Antonik, Paweł M.; Rennie, Martin L.; O'Byrne, Philomena; Khan, Amir R.; Pinalli, Roberta; Dalcanale, Enrico; Crowley, Peter B.

doi:10.1002/anie.201803232

Cited by 59 publications

(79 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, simulated EPR spectra at high CB [7] concentrations showed better agreement with experimental ones when a 2:1 complex was considered (with two CB [7]). Previous reports mentioned the possibility for cucurbiturils to aggregate in water [28][29][30][31][36][37][38][39][40], but there is only a slight improvement in the agreement between simulated spectra and experimental ones (regression coefficient of 0.9955) assuming this model; other techniques would be necessary to confirm this possibility. As mentioned above, a decrease in a N was associated with a more hydrophobic surrounding for the nitroxide group, while the observed decrease in a C also indicated a redistribution of spin densities on the corresponding ring, together with a probable freeze in dihedral angles due to the inclusion.…”

Section: Complexation Between Tempone and Cb[7]mentioning

confidence: 81%

EPR Spectroscopy: A Powerful Tool to Analyze Supramolecular Host•Guest Complexes of Stable Radicals with Cucurbiturils

et al. 2020

View full text Add to dashboard Cite

Stable organic free radicals are increasingly studied compounds due to the multiple and unusual properties imparted by the single electron(s). However, being paramagnetic, classical methods such as NMR spectroscopy can hardly be used due to relaxation and line broadening effects. EPR spectroscopy is thus better suited to get information about the immediate surroundings of the single electrons. EPR has enabled obtaining useful data in the context of host•guest chemistry, and a classical example is reported here for the stable (2,2,6,6-tetramethyl-4-oxo-piperidin-1-yl)oxyl or 4-oxo-TEMPO nitroxide (TEMPONE) inside the macrocycle host cucurbit [7]uril (CB[7]). Generally and also observed here, a contraction of the spectrum is observed as a result of the reduced nitrogen coupling constant due to inclusion complexation in the hydrophobic cavity of the host. Simulations of EPR spectra allowed determining the corresponding binding constant pointing to a weaker affinity for CB [7], compared to TEMPO with CB [7]. We complement this work by the results of EPR spectroscopy of a biradical: bis-TEMPO-bis-ketal (bTbk) with cucurbit[8]uril (CB[8]). Initial investigations pointed to very weak effects on the spectrum of the guest and incorrectly led us to conclude an absence of binding. However, simulations of EPR spectra combined with NMR data of reduced bTbk allowed showing inclusion complexation. EPR titrations were performed, and the corresponding binding constant was determined. 1 H NMR spectra with reduced bTbk suggested a shuttle mechanism, at nearly one equivalent of CB[8], for which the host moves rapidly between two stations.Molecules 2020, 25, 776 2 of 10 wealth of information, which, correctly extracted, can give users access to crucial information such as stability, structure, or dynamics, in various liquid or solid environments [8]. Supramolecular chemistry principally features diamagnetic compounds, but paramagnetic ones are expected to enable access to new types of applications including molecular magnetic switches [9], dynamic covalent systems [10], or tracers for imaging by stabilizing free radicals in reducing conditions. In the context of host•guest chemistry, the guests are almost exclusively [11] the radicals, and they are included in macrocyclic hosts. Several reviews [12][13][14] have already documented host•guest complexes featuring free radicals and several families of hosts including calixarenes, cyclodextrins, and cucurbiturils. This latter family of pumpkin-shape macrocycles [15][16][17][18][19] possess unique properties, in a broader context, such as ultrahigh binding [20,21], gas adsorption [22], or drug encapsulation and release [23,24]. With cucurbit[n]urils (CB[n]), the main radicals studied are nitroxides [25], in the majority of cases stable ones. In a seminal work, Lucarini and coworkers studied the cucurbit [7]uril (CB[7]) cavity by EPR spectroscopy using several nitroxides [26]. Later, Kaifer and coworkers showed how CB[n] could modulate the extent of spin exchange between covalently linked ...

show abstract

Section: Complexation Between Tempone and Cb[7]mentioning

confidence: 81%

EPR Spectroscopy: A Powerful Tool to Analyze Supramolecular Host•Guest Complexes of Stable Radicals with Cucurbiturils

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Recently, Crowley and co‐workers described the complex of dimethylated Ralstonia solanacearum lectin with 39 (PDB IDs: 6F7W and 6F7X) . In the X‐ray structure, they found three different modes of binding, suggesting an incompletely filled host cavity (Scheme ), which could also explain the rather low affinity in solution ( K d ≈1000 μ m ).…”

Section: Cucurbiturilsmentioning

confidence: 99%

“… Details of the complex of 39 and dimethylated R. solanacearum lectin (PDB ID: 6F7W) . (Only one host/guest entity is shown.…”

Section: Cucurbiturilsmentioning

confidence: 99%

Synthetic Receptors for the Recognition and Discrimination of Post‐Translationally Methylated Lysines

Gruber

2018

ChemBioChem

View full text Add to dashboard Cite

Post-translational modifications (PTMs) describe the chemical alteration of proteins after their biosynthesis in ribosomes. PTMs play important roles in cell biology, including the regulation of gene expression, cell-cell interactions and the development of different diseases. A prominent class of PTMs is the side-chain methylation of lysine. For the analysis and discrimination of differently methylated lysines, antibodies are widely used, although methylated peptide and protein targets are known to be particularly difficult to differentiate by antibody-based affinity reagents; an additional challenge can be batch-to-batch reproducibility. The application of mass spectrometry techniques for methyllysine discrimination requires a complex sample preparation procedure and is not suited for working in cells. The desire to overcome the above-mentioned challenges has promoted the development of synthetic receptor molecules that recognise and bind methyllysines. Such "artificial antibodies" are of interest for a number of applications, for example, as reagents in biochemical assays, for the isolation and purification of post-translationally methylated proteins and for the tracking of signalling pathways. Moreover, they offer new approaches in diagnostics and therapy. This review delivers an overview of the broad field of methyllysine binding and covers a wide range of synthetic receptors used for the recognition of methylated lysines, including calixarenes, resorcinarenes, pillararenes, disulfide cyclophanes, cucurbiturils and acyclic receptors.

show abstract

“…Synthetic host–guest systems have shown relevant orthogonality to proteins. Especially the synthetic donut‐shaped cucurbituril class of host molecules has proven to be a strong and selective protein binding element, capable of inducing the assembly of proteins into well‐defined dimers and larger oligomers . The cucurbit[8]uril variant can simultaneously bind two N‐terminal phenylalanine‐glycine‐glycine (FGG) peptide elements .…”

Section: Introductionmentioning

confidence: 99%

Cucurbit[8]uril Reactivation of an Inactivated Caspase‐8 Mutant Reveals Differentiated Enzymatic Substrate Processing

et al. 2018

View full text Add to dashboard Cite

Caspase‐8 constructs featuring an N‐terminal FGG sequence allow for selective twofold recognition by cucurbit[8]uril, which leads to an increase of the enzymatic activity in a cucurbit[8]uril dose‐dependent manner. This supramolecular switching has enabled for the first time the study of the same caspase‐8 in its two extreme states; as full monomer and as cucurbit[8]uril induced dimer. A mutated, fully monomeric caspase‐8 (D384A), which is enzymatically inactive towards its natural substrate caspase‐3, could be fully reactivated upon addition of cucurbit[8]uril. In its monomeric state caspase‐8 (D384A) still processes a small synthetic substrate, but not the natural caspase‐3 substrate, highlighting the close interplay between protein dimerization and active site rearrangement for substrate selectivity. The ability to switch the caspase‐8 activity by a supramolecular system thus provides a flexible approach to studying the activity of a protein at different oligomerization states.

show abstract

Cucurbit[7]uril‐Dimethyllysine Recognition in a Model Protein

Cited by 59 publications

References 59 publications

EPR Spectroscopy: A Powerful Tool to Analyze Supramolecular Host•Guest Complexes of Stable Radicals with Cucurbiturils

EPR Spectroscopy: A Powerful Tool to Analyze Supramolecular Host•Guest Complexes of Stable Radicals with Cucurbiturils

Synthetic Receptors for the Recognition and Discrimination of Post‐Translationally Methylated Lysines

Cucurbit[8]uril Reactivation of an Inactivated Caspase‐8 Mutant Reveals Differentiated Enzymatic Substrate Processing

Contact Info

Product

Resources

About