A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF

• Published in: Structure (London) 2021-05, Vol.29 (5), p.433-443.e4
• Main Authors: Kröger, Pascal, Shanmugaratnam, Sooruban, Ferruz, Noelia, Schweimer, Kristian, Höcker, Birte
• Format: Article
• Language: English
• Subjects: biogenic amines; isothermal titration calorimetry; molecular dynamics simulation; nuclear magnetic resonance spectroscopy; X-ray crystallography
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2020.12.005

Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by 1H-15N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering. [Display omitted] •Binding analysis utilizing computational, biochemical, and structural techniques•PotF binds several compounds from polyamine biosynthesis•Crystal structures of closed and open apo states emphasize PotF’s plasticity•Binding pocket hydration pattern affects thermodynamic profile for the ligands Kröger et al. dissect PotF’s binding capabilities for different ligands from polyamine biosynthesis utilizing orthogonal techniques. They combine extensive molecular dynamics simulations with in-solution NMR, crystal structures, and calorimetric data.