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, 1H 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.
| Original language | English |
|---|---|
| Pages (from-to) | 7649-7657 |
| Number of pages | 9 |
| Journal | Journal of the American Chemical Society |
| Volume | 146 |
| Issue number | 11 |
| DOIs | |
| State | Published - Feb 13 2024 |
Funding
This paper is dedicated to the memory of Prof. Michael J. Waring. ARU gratefully acknowledges financial support from the National Institutes of Health (GM141708 and GM126511), the Welch Foundation (W-1640 and W-0031), and Trinity University. PRS and CWB are grateful to the Institute for Basic Science for support (IBS-R019-D1). The NMR and mass spectrometers were funded by grants from the National Science Foundation (CHE-1726441 and CHE-0957839). This work is based upon research conducted in the Structural Biology Core, a part of the Institutional Research Cores at the University of Texas Health Science Center at San Antonio supported by the Office of the Vice President for Research, Greehey Children’s Cancer Research Institute, and the Mays Cancer Center Drug Discovery and Structural Biology Shared Resource (NIH P30 CA054174). The Rigaku HyPix-6000HE Detector, Universal Goniometer, and VariMax-VHF Optic instrumentation are funded by NIH-ORIP SIG Grant S10OD030374. We follow the definition of hydrogen bonding from the 2011 recommendations of the IUPAC. Briefly, in a D–H···A system, the bonding is an attractive interaction stemming from either electrostatics, dispersion, or charge transfer; the donor (D) and acceptor (A) are more electronegative than H; the DHA angle approaches 180° with a minimum of 110°; the H···A distance ranges from ∼1.0 to 2.6 Å, and where there is either spectroscopic or crystallographic evidence for bond formation. †
| Funders | Funder number |
|---|---|
| Trinity University | |
| CHE-1726441, CHE-0957839 | |
| S10OD030374, GM141708, P30 CA054174, GM126511 | |
| W-1640, W-0031 | |
| Institute for Basic Science | IBS-R019-D1 |
Keywords
- Receptors, Artificial
- Dipeptides/chemistry
- Peptides/chemistry
- Crystallography, X-Ray
- Binding Sites