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

Pascal Kröger; Sooruban Shanmugaratnam; Noelia Ferruz; Kristian Schweimer; Birte Höcker

doi:10.1016/j.str.2020.12.005

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

Structure. 2021 May 6;29(5):433-443.e4. doi: 10.1016/j.str.2020.12.005. Epub 2021 Jan 5.

Authors

Pascal Kröger¹, Sooruban Shanmugaratnam¹, Noelia Ferruz¹, Kristian Schweimer², Birte Höcker³

Affiliations

¹ Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.
² Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany; Northern Bavarian NMR Center, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.
³ Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany. Electronic address: birte.hoecker@uni-bayreuth.de.

PMID: 33406388
DOI: 10.1016/j.str.2020.12.005

Abstract

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.

Keywords: X-ray crystallography; biogenic amines; isothermal titration calorimetry; molecular dynamics simulation; nuclear magnetic resonance spectroscopy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Escherichia coli Proteins / chemistry*
Escherichia coli Proteins / metabolism
Ligands
Periplasmic Binding Proteins / chemistry*
Periplasmic Binding Proteins / metabolism
Polyamines / chemistry
Polyamines / metabolism
Protein Binding
Receptors, Biogenic Amine / chemistry*
Receptors, Biogenic Amine / metabolism

Substances

Escherichia coli Proteins
Ligands
Periplasmic Binding Proteins
Polyamines
Receptors, Biogenic Amine
potF protein, E coli