Pinpointing the l-phenylalanine binding sites of TyrR using biosensors and computer-aided simulation

  • Danyang Bai
  • Dongqin Ding
  • Jinlong Li
  • Lina CongEmail author
  • Dawei ZhangEmail author
Original Research Paper



To determine the binding sites for l-phenylalanine in TyrR protein via a rational mutation analysis combining biosensors and computer-aided simulation.


TyrR protein of Escherichia coli is the chief transcriptional regulator of several genes essential for the biosynthesis and transport of aromatic amino acids. The identification of ligand-binding sites is often the starting point for protein function annotation and structure-based protein design. Here we combined computer-aided prediction methods and biosensors to identify the ligand-binding sites for l-Phe in TyrR protein.


Residues at positions 160, 173 and 184 of TyrR protein are important for transcriptional activation of target genes tyrP induced by l-Phe, which indicates that they are the bona fide l-Phe binding sites of TyrR protein.


TyrR protein l-Phe binding site Biosensor Computer-aided simulation 



This work was financially supported by National Key R&D Program of China (2018YFD0901001), Tianjin Science Fund for Distinguished Young Scholars (17JCJQJC45300), Nature Science Foundation of Tianjin City (CN) (16JCYBJC23500), Tianjin Science and Technology Project (15PTCYSY00020) and the Science and Technology Service Network (STS) Initiative of Chinese Academy of Sciences.

Supporting information

Supplementary Table 1—Strains and plasmids used in this study.

Supplementary Table 2—Primers used in this study.

Supplementary Figure 1—The effect of 184 site of TyrR on the binding mode of l-phe. The representative conformation of l-phe with 173 and 160 sites is verified by mutation S184L/V. The mutations S184L and S184V would clash with the benzene ring of l-Phe when binds 173 and 160 sites.

Supplementary Figure 2—Representative conformations of three clusters in MD simulations for 15 site of TyrR protein.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10529_2019_2645_MOESM1_ESM.docx (392 kb)
Supplementary material 1 (DOCX 392 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of Biological EngineeringDalian Polytechnic UniversityDalianPeople’s Republic of China
  2. 2.Tianjin Institutes of Industrial Biotechnology, Chinese Academy of SciencesTianjinPeople’s Republic of China
  3. 3.Key Laboratories of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinPeople’s Republic of China
  4. 4.University of Chinese Academy of SciencesBeijingPeople’s Republic of China

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