Cucurbit[8]uril Binds Nonterminal Dipeptide Sites with High Affinity and Induces a Type II β-Turn
Year: 2024
Type: article
Abstract: In an effort to target polypeptides at nonterminal sites, we screened the binding of the synthetic receptor cucurbit[8]uril (Q8) to a small library of tetrapeptides, each containing a nonterminal dipeptide binding site. The resulting leads were characterized in detail using a combination of isothermal titration calorimetry, 1 H NMR spectroscopy, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS), and X-ray crystallography. The equilibrium dissociation constant values determined for the binding of Q8 to nonterminal dipeptide sites Lys-Phe (KF) and Phe-Lys (FK) were 60 and 86 nm, respectively. These are to the best of our knowledge the highest affinities reported to date for any synthetic receptor targeting a nonterminal site on an unmodified peptide. A 0.79 Å resolution crystal structure was obtained for the complex of Q8 with the peptide Gly-Gly-Leu-Tyr-Gly-Gly-Gly (GGLYGGG) and reveals structural details of the pair-inclusion motif. The molecular basis for recognition is established to be the inclusion of the side chains of Leu and Tyr residues, as well as an extensive network of hydrogen bonds between the peptide backbone, the carbonyl oxygens of Q8, and proximal water molecules. In addition, the crystal structure reveals that Q8 induces a type II β-turn. The sequence-selectivity, high affinity, reversibility, and detailed structural characterization of this system should facilitate the development of applications involving ligand-induced polypeptide folding.
DOI: 10.1021/jacs.3c14045
Language: English
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
Funders: National Science Foundation, Cancer Research Institute, Welch Foundation, Institute for Basic Science, National Institutes of Health, University of Texas Health Science Center at San Antonio, National Cancer Institute, National Institute of General Medical Sciences, Division of Chemistry, Office of Research Infrastructure Programs, National Institutes of Health
Awards: Mays Cancer Center at UT Health SA, MRI-R2: Acquisition of a 500 MHz NMR spectrometer by Trinity University, Minimal Protein Affinity Tags, G2354648889, G2463882546, MRI: Acquisition of an ESI-TOF Mass Spectrometer by Trinity University, G3874765150, G548137992, G6008590551, G6475442570, G6867218680, Supramolecular Strategies for the Controlled Release of Protein Drugs, G785582795, Upgrade of a Core Laboratory Macromolecular X-ray Diffraction System, G9000324485, G95984179
OpenAlex ID: W4391780714