Graduation Year

2026

Date of Submission

4-2026

Document Type

Open Access Senior Thesis

Degree Name

Bachelor of Arts

Department

Biology

Second Department

Chemistry

Reader 1

Bethany Caulkins

Reader 2

Patrick Ferree

Abstract

Ubiquitin is a highly conserved 76-residue protein central to proteasomal degradation, DNA repair, and immune regulation. Its dysfunction underlies neurodegenerative diseases and cancer, so it is important to understand how synthetic molecules recognize ubiquitin’s surface at residue level as it has implications for biosensor design and therapeutic targeting. This study performs a quantitative analysis of ubiquitin-cavitand binding interacting using four 1H-15N HSQC NMR titration spectra collected across increasing tetracarboxylate cavitand concentrations (apo, 1:15, 1:2, and 1:3 cavitand:ubiquitin). Using CCPNMR AnalysisAssign, all 73 non-proline backbone amide resonances were assigned against published BMRB reference shifts.The chemical shift perturbations (CSPs) were calculated at each titration point using the formula: Δδ=√(ΔδH)2 +(0.2×ΔδN)2. At the highest cavitand concentration, five lysine residues (K6, K11, K29, K33,K48) and four arginine residues (R42, R54, R72, R74) exhibited the largest CSPs, consistent with direct electrostatic and cation-π interactions at the negatively charged rim of the cavitand. Structural mapping of perturbations onto a three-dimension ubiquitin structure using PyMol revealed that the significantly perturbed residues clustered on the β-sheet face encompassing the β3, β4, and β5 strands asymmetrically while the α-helix and opposing surface remained largely unperturbed. The Ile44 hydrophobic patch showed no significant perturbation, demonstrating that cavitand engages ubiquitin’s electrostatic surface rather than its hydrophobic interface. Synthetic host molecules provide a controlled chemical environment which are used to probe protein surface recognition. Understanding how hosts are able to interact with protein surfaces can provide insights into molecular recognition and interaction mechanisms for protein-ligands.

Download

Share

COinS