Designing Protein Denaturants: Synthetic Agents Induce Cytochromec Unfolding at Low Concentrations and Stoichiometries

Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin

Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.

Reading of protein surfaces in the native state at micromolar concentrations by a chirogenetic porphyrin probe

The recognition of some globular proteins was carried out in aqueous solution, at micromolar concentrations, by using an uncharged symmetrical cobalt-porphyrin (Co-P). By means of UV/Vis, induced circular dichroism, and fluorescence spectroscopy techniques, it was ascertained that the interactions between specific amino acid residues and Co-P occurred on the protein surface. In particular, spectroscopic evidence showed the formation of supramolecular complexes without disruption of the native structure of the proteins and, furthermore, that signal changes were characteristic of each Co-P/protein system, so that they could be used as a highly sensitive analytical tool for protein recognition. The relative association constants were proportional to the protein molecular masses (and then to the number of amino acid residues).

Heat-Capacity Changes in Host–Guest Complexation by Coulomb Interactions in Aqueous Solution

Heat-capacity changes (deltaC(p)0) were determined for the complexation of 1-alkanecarboxylates with protonated hexakis(6-amino-6-deoxy)-alpha-cyclodextrin (per-NH3(+)-alpha-CD) and heptakis(6-amino-6-deoxy)-beta-cyclodextrin (per-NH3(+)-beta-CD). DeltaC(p)0 decreased with an increase in the binding constant (K) and plateaued at K = 4000 M(-1). The complexes of 1-pentanoate, 1-hexanoate, and 1-heptanoate with per-NH3(+)-alpha-CD are classified as the host-guest system in which the size of the guest fits the CD cavity well. In such a system, van der Waals interaction is the major force for complexation, leading to a negative deltaH0 value. Simultaneously, the water molecules around the hydrophobic alkyl chain of the guest and inside the CD cavity are released to the aqueous bulk phase, leading to a positive deltaS0 value. The negative deltaC(p)0 value in such complexation is ascribed to dehydration of the hydrophobic alkyl chain of the guest and extrusion of the water molecules inside the CD cavity. Meanwhile, the complexes that show positive deltaC(p)0 values are characterized by complexation in which the guest molecules are significantly smaller than the CD cavities. In such a case, the complexation is endothermic and driven by the entropy gain. When the guest is much smaller than the CD cavity, the main binding force should be Coulomb interaction. To form an ionic bond, dehydration of the charged groups must occur. This process is endothermic and leads to positive deltaH0 and deltaS0 values. As the top of the CD cavity is capped by a small but hydrophobic alkyl chain, the water molecules inside the CD cavity may form the iceberg structure. This process must be accompanied by a positive deltaC(p)0 value. Hence, the complexation of a small guest with the CD with a large cavity through Coulomb interactions shows positive and large deltaC(p)0 values. These conclusions were applied to the electrostatic binding of proteins with an anionic ligand.

Proteo-Dendrimers Designed for Complementary Recognition of Cytochromec: Dendrimer Architecture toward Nanoscale Protein Complexation

"Proteo-dendrimers" in which polyanionic hepta(glutamic acids), fluorescent zinc porphyrinate cores, hydrophilic polyether surfaces, and nonpeptide hydrophobic dendrons are combined, were developed as a new series of synthetic receptors for protein recognition. They have polyanionic "patch" structures on their surfaces and undergo complementary electrostatic interactions with a positively charged cytochrome c patch, as observed in biological protein-protein recognition systems. Stability constants of the resulting supramolecular complexes were determined in phosphate buffer (pH 7) by monitoring the fluorescence quenching of the zinc porphyrinates. These proteo-dendrimer receptors exhibited higher affinities with cytochrome c proteins in aqueous solutions than with biological cytochrome b5. Furthermore, they effectively blocked complexation of biological cytochrome b5 with cytochrome c, indicating that the proteo-dendrimers and cytochrome b5 similarly occupy the polycationic patch of cytochrome c.