Stability of Ligand-induced Protein Conformation Influences Affinity in Maltose-binding Protein

Marco van den Noort, Marijn de Boer, Bert Poolman*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)
115 Downloads (Pure)

Abstract

Our understanding of what determines ligand affinity of proteins is poor, even with high-resolution structures available. Both the non-covalent ligand-protein interactions and the relative free energies of available conformations contribute to the affinity of a protein for a ligand. Distant, non-binding site residues can influence the ligand affinity by altering the free energy difference between a ligand-free and ligand-bound conformation. Our hypothesis is that when different ligands induce distinct ligand-bound conformations, it should be possible to tweak their affinities by changing the free energies of the available conformations. We tested this idea for the maltose-binding protein (MPB) from Escherichia coli. We used single-molecule Förster resonance energy transfer (smFRET) to distinguish several unique ligand-bound conformations of MBP. We engineered mutations, distant from the binding site, to affect the stabilities of different ligand-bound conformations. We show that ligand affinity can indeed be altered in a conformation-dependent manner. Our studies provide a framework for the tuning of ligand affinity, apart from modifying binding site residues.

Original languageEnglish
Article number167036
JournalJournal of Molecular Biology
Volume433
Issue number15
Early online date4-May-2021
DOIs
Publication statusPublished - 23-Jul-2021

Keywords

  • ligand-binding
  • conformational dynamics
  • ligand affinity
  • single-molecule FRET
  • thermodynamics of ligand binding

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