Calixarene capture of partially unfolded cytochrome <i>c</i>

Engilberge, S.; Rennie, Martin L.; Crowley, Peter B.

doi:10.1002/1873-3468.13512

Cited by 12 publications

(14 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This result complements previous data that indicated that macrocyclic glues facilitate crystallization of proteins even with significant disorder. [44] Q7 capture of the Nup peptide is a promising development in host-guest chemistry within protein-macrocycle frameworks. [9] The RSL*-Q7 sheet assembly is evidently amenable to customization, with previous studies demonstrating Lys or His enrichment as a means of modulating the packing with increased cucurbituril content or Zn-binding sites.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons

Ramberg

Guagnini

Engilberge

et al. 2021

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

One approach to protein assembly involves watersoluble supramolecular receptors that act like glues. Bionanoarchitectures directed by these scaffolds are often systemspecific, with few studies investigating their customization. Herein, the modulation of cucurbituril-mediated protein assemblies through the inclusion of peptide tectons is described. Three peptides of varying length and structural order were N-terminally appended to RSL, a β-propeller building block. Each fusion protein was incorporated into crystalline architectures mediated by cucurbit[7]uril (Q7). A trimeric coiled-coil served as a spacer within a Q7-directed sheet assembly of RSL, giving rise to a layered material of varying porosity. Within the spacer layers, the coiled-coils were dynamic. This result prompted consideration of intrinsi-cally disordered peptides (IDPs) as modulatory tectons. Similar to the coiled-coil, a mussel adhesion peptide (Mefp) also acted as a spacer between protein-Q7 sheets. In contrast, the fusion of a nucleoporin peptide (Nup) to RSL did not recapitulate the sheet assembly. Instead, a Q7-directed cage was adopted, within which disordered Nup peptides were partially "captured" by Q7 receptors. IDP capture occurred by macrocycle recognition of an intrapeptide Phe-Gly motif in which the benzyl group was encapsulated by Q7. The modularity of these protein-cucurbituril architectures adds a new dimension to macrocycle-mediated protein assembly. Segregated protein crystals, with alternating layers of high and low porosity, could provide a basis for new types of materials.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons

Ramberg

Guagnini

Engilberge

et al. 2021

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

show abstract

“…In particular, both sclx 6 (pdb entry 6rgi) and sclx 8 (pdb entry 6gd6, Table 1) induce highly porous assemblies of cytochrome-c (Table 1). While sclx 4 shows a normal protein crystal packing (~45% solvent content), sclx 6 yielded a honeycomb arrangement (~65% solvent content) [97] and sclx 8 mediated a high-porosity framework (~85% solvent content) [98]. Owing to their 'floppiness', sclx 6 and sclx 8 can reshape to the protein surface and form large interfaces.…”

Section: Calixarene Moleculesmentioning

confidence: 99%

Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins

Costanzo

Geremia

2020

Molecules

View full text Add to dashboard Cite

Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.

show abstract

“…13 In that realm, functionalized calixarenes, notably para-sulfonato-calix-[n]-arenes have demonstrated their high potential in biochemistry thanks to their abilities to bind positively charged protein surface to form protein oligomers. [14][15][16][17] They offer tremendous perspective in the field of high-resolution X-ray of unfolded protein loops 18 or small cationic proteins 19,20 .…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Approach for Capturing Calixarene–Protein Interactions: The Case of Cytochrome C

et al. 2020

View full text Add to dashboard Cite

Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant protein and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies (comparison between the molecular mechanics Poisson-Boltzmann surface 1 area (MM-PBSA) analysis and the isothermal titration calorimetry (ITC) measurements).The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically-driven association and notably the role of the arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way towards an automated procedure to predict the supramolecular protein-cages association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.

show abstract

Calixarene capture of partially unfolded cytochrome c

Cited by 12 publications

References 43 publications

Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons

Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons

Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins

Molecular Dynamics Approach for Capturing Calixarene–Protein Interactions: The Case of Cytochrome C

Contact Info

Product

Resources

About