4CPF

Wild-type streptavidin in complex with love-hate ligand 3 (LH3)

Summary for 4CPF

• Entry DOI: 10.2210/pdb4cpf/pdb
• Related: 4CPE 4CPH 4CPI
• Descriptor: STREPTAVIDIN, methyl 4-(2-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H- thieno[3,4-d]imidazolidin-4-yl]pentanehydrazido}-3- [4-(methoxycarbonyl)phenyl]phenyl)benzoate (3 entities in total)
• Functional Keywords: biotin-binding protein, avidin, biotin, biotinylated, steric clash, strained, hindered, force, ligand series, affinity
• Biological source: STREPTOMYCES AVIDINII
• Total number of polymer chains: 2
• Total formula weight: 27165.37

Authors

Fairhead, M.,Shen, D.,Chan, L.K.M.,Lowe, E.D.,Donohoe, T.J.,Howarth, M. (deposition date: 2014-02-06, release date: 2014-08-06, Last modification date: 2023-12-20)

Primary citation

Fairhead, M.,Shen, D.,Chan, L.K.M.,Lowe, E.D.,Donohoe, T.J.,Howarth, M.
Love-Hate Ligands for High Resolution Analysis of Strain in Ultra-Stable Protein/Small Molecule Interaction.
Bioorg.Med.Chem., 22:5476-, 2014

PubMed 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 1.1-1.6Å 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.

PubMed: 25128469
DOI: 10.1016/J.BMC.2014.07.029

Experimental method

X-RAY DIFFRACTION (1.14 Å)