Pseudopeptidic host adaptation in peptide recognition unveiled by ion mobility mass spectrometry

Abstract

The complexation of the glutamic-tyrosine-glutamic tripeptide (EYE) with a series of pseudopeptidic cages has been thoroughly investigated using different analytical techniques. Stoichiometry and affinities of the supramolecular host : guest...

Molecular Recognition of Tyrosine-Containing Polypeptides with Pseudopeptidic Cages Unraveled by Fluorescence and NMR Spectroscopies

“…On the other hand, the Tyr inclusion within the cage cavity is additionally modulated by the secondary interactions between the amino acids surrounding the Tyr in the peptide and the side chains decorating the pseudopeptidic cages (as also illustrated by Figure C,D and values in Table ). This last conclusion agrees with the results obtained in previous studies with peptides of different lengths and sequences. ,, Overall, these findings pave the way toward the selective molecular recognition of solvent-exposed Tyr residues in macromolecular PPs since the side chains of the cages establish noncovalent attractive/repulsive contacts with the amino acids in close proximity to the Tyr, thus mapping its chemical environment. The singular case of CyHis is noteworthy: despite it generally showing the strongest binding to the measured peptides, the amphoteric nature of the imidazole side chains reduces any potential sequence selectivity.…”

“…CyHis (entry 3) shows the strongest interaction with polyE 4 Y, as a result of the amphoteric nature of the imidazole ring, with a p K a value close to neutrality that allows it to act as both an acid and a base at the pH used for the titrations. These results agree with the trends observed in the molecular recognition of Ac-EYE-NH 2 by the same cages . This tripeptide can be considered the simplest Tyr binding epitope within polyE 4 Y. Titrations with the PP bearing basic residues (polyK 4 Y, Table , entries 6–10) rendered complementary trends with a more efficient interaction with CyAsp and CyGlu cages, again pivoting on the amphoteric CyHis.…”

“…The molecular recognition of PPs by pseudopeptidic cages comprises the inclusion of Tyr residue within the cage cavity, , which strongly affects the fluorescence emission spectrum of the peptides upon excitation at 276 nm. , These spectral changes can be used to detect and characterize the binding. The titration of aqueous solutions (Tris-HCl buffer) of the PPs with increasing amounts of the cages led to different spectral variations depending on both PP and cage nature (Figure ).…”

“… 15 , 16 More recently, we have reported a thorough structural analysis of the supramolecular complexes between these cages and the minimal Ac-EYE-NH 2 binding epitope, both in buffered aqueous solution and in the gas phase. 17 Additionally, we have shown that pseudopeptidic cages efficiently protect substrates from the action of the c-Src PTK, precluding the corresponding Tyr phosphorylation by selective Tyr encapsulation. In some of these studies and in line with previous reports, 18 we used a synthetic random copolymer (polyE 4 Y) as a protein proxy.…”

“…These specific PPI sites are usually located in disordered regions of the regulated proteins, complicating the rational design of receptors due to the lack of reliable structural information on many of these epitopes. , However, Tyr recognition in proteins is appealing as a PTK-modulation mechanism alternative (or complementary) to targeting catalytic or ATP-binding sites, which is the most common one for PTK inhibitors. − The ATP-binding site in PTKs is highly conserved, which makes their putative ligands suffer from modest selectivity . Regarding that, in previous work, our group designed pseudopeptidic cages as efficient receptors for short peptides in organic or aqueous–organic solvents, showing a good selectivity for the Ac-EYE-NH 2 sequence. , More recently, we have reported a thorough structural analysis of the supramolecular complexes between these cages and the minimal Ac-EYE-NH 2 binding epitope, both in buffered aqueous solution and in the gas phase . Additionally, we have shown that pseudopeptidic cages efficiently protect substrates from the action of the c-Src PTK, precluding the corresponding Tyr phosphorylation by selective Tyr encapsulation.…”