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Love–Hate ligands for high resolution analysis of strain in ultra-stable protein/small molecule interaction

DOI: 10.1016/j.bmc.2014.07.029 DOI Help
PMID: 25128469 PMID Help

Authors: Michael Fairhead (University of Oxford) , Di Shen (University of Oxford) , Louis K.m Chan (University of Oxford) , Ed D. Lowe (University of Oxford) , Timothy J. Donohoe (University of Oxford) , Mark Howarth (University of Oxford)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Bioorganic & Medicinal Chemistry , VOL 22 (19) , PAGES 5476 - 5486

State: Published (Approved)
Published: October 2014

Abstract: The pathway of ligand dissociation and how binding sites respond to force are not well understood for any macromolecule. Force effects on biological receptors have been studied through simulation or force spectroscopy, but not by high resolution structural experiments. To investigate this challenge, we took advantage of the extreme stability of the streptavidin–biotin interaction, a paradigm for understanding non-covalent binding as well as a ubiquitous research tool. We synthesized a series of biotin-conjugates having an unchanged strong-binding biotin moiety, along with pincer-like arms designed to clash with the protein surface: ‘Love–Hate ligands’. The Love–Hate ligands contained various 2,6-di-ortho aryl groups, installed using Suzuki coupling as the last synthetic step, making the steric repulsion highly modular. We determined binding affinity, as well as solving 1.1–1.6 Å resolution crystal structures of streptavidin bound to Love–Hate ligands. Striking distortion of streptavidin’s binding contacts was found for these complexes. Hydrogen bonds to biotin’s ureido and thiophene rings were preserved for all the ligands, but biotin’s valeryl tail was distorted from the classic conformation. Streptavidin’s L3/4 loop, normally forming multiple energetically-important hydrogen bonds to biotin, was forced away by clashes with Love–Hate ligands, but Ser45 from L3/4 could adapt to hydrogen-bond to a different part of the ligand. This approach of preparing conflicted ligands represents a direct way to visualize strained biological interactions and test protein plasticity.

Journal Keywords: Protein crystallization; Biotin; Avidin; Mechanobiology; Chemical biology

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I02-Macromolecular Crystallography , I04-Macromolecular Crystallography