Protein Recognition by Functionalized Sulfonatocalix[4]arenes

Abstract

The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.

A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold

“…Alternatively, the reduced entropy may be rationalized by considering that the first sclx 8 can ‘explore’ a larger protein surface, while the second ligand is restricted. The binding affinities of sclx 8 are comparable to the K d ∼2–8 μM for binding of the related ligand, phosphonato‐calix[6]arene ( pclx 6 ), and are much tighter than the K d ∼30 μM for the smaller sulfonato‐calix[4]arene . Interestingly, pclx 6 triggers dimerization of cytochrome c but not in an auto‐regulated fashion, suggesting a fundamentally different assembly mechanism compared to sclx 8 .…”

Calixarene capture of partially unfolded cytochrome c

“…(A) Overlaid C α traces of cyt c (PDB 5t8w , dark grey) and the cyt c – sclx 6 complex (light grey). The displacement of Ω‐loop D (Gly77 specifically) is highlighted by an arrow while disordered Ω‐loop C is signified by a dashed line.…”

“…Yeast cyt c C102T was produced as described . sclx 6 (TCI Europe: Zwijndrecht, Belgium) was prepared in water and the pH adjusted to 6.0.…”

“…) . Although a variety of cyt c structures have been obtained with sclx 8 and calix[4]arene derivatives , cocrystallization of cyt c with sclx 6 yielded just one crystal form that requires the presence of imidazole. This combination of ligands resulted in a substantially altered conformation of cyt c .…”

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

“…Only recently, the interactions of calixarenes 6 and 12 with cytochrome c have been studied in solution and in the crystalline state (PDB IDs: 5KPF (for 6 ) and 5LFT (for 12 )) . Although only unmethylated lysines are available in cytochrome c , the dissociation constant for the complex with 12 is 20 μ m .…”