Fine-tuning spermidine binding modes in the putrescine binding protein PotF

J Biol Chem. 2021 Dec;297(6):101419. doi: 10.1016/j.jbc.2021.101419. Epub 2021 Nov 19.


A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research, such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study, we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins, PotF and PotD. Building on a previously designed construct, modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design but also our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria.

Keywords: adaptability; ligand specificity swap; periplasmic binding proteins; protein engineering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli K12 / chemistry*
  • Escherichia coli K12 / genetics
  • Escherichia coli K12 / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Membrane Transport Proteins / chemistry
  • Membrane Transport Proteins / genetics
  • Membrane Transport Proteins / metabolism
  • Periplasmic Binding Proteins / chemistry*
  • Periplasmic Binding Proteins / genetics
  • Periplasmic Binding Proteins / metabolism
  • Protein Binding
  • Receptors, Biogenic Amine / chemistry*
  • Receptors, Biogenic Amine / genetics
  • Receptors, Biogenic Amine / metabolism
  • Spermidine / chemistry*
  • Spermidine / metabolism


  • Escherichia coli Proteins
  • Membrane Transport Proteins
  • Periplasmic Binding Proteins
  • PotD protein, E coli
  • Receptors, Biogenic Amine
  • potF protein, E coli
  • Spermidine