Structural features of carrot α-tubulin predetermining the natural resistance to dinitroaniline herbicides

  • O. G. Melnyk Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine, 04123, Kyiv, Baidy Vyshnevetskoho str., 2A; Educational and Scientific Center "Institute of Biology and Medicine" of Taras Shevchenko National University of Kyiv, Ukraine, 03022, Kyiv, acad. Glushkova ave., 2 https://orcid.org/0000-0002-4249-9175
  • S. P. Ozheredov Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine, 04123, Kyiv, Baidy Vyshnevetskoho str., 2A https://orcid.org/0000-0003-4710-0706
  • Y. B. Blume Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine, 04123, Kyiv, Baidy Vyshnevetskoho str., 2A https://orcid.org/0000-0001-7078-7548
  • P. A. Karpov Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine, 04123, Kyiv, Baidy Vyshnevetskoho str., 2A https://orcid.org/0000-0002-6876-642X
DOI: https://doi.org/10.7124/FEEO.v35.1678
Keywords: α-tubulin, dinitroanilines, herbicides, resistance, trifluralin, microtubules

Abstract

Aim. To explain the natural resistance of Daucus carota L. to dinitroaniline herbicides. To clarify features of the carrot α-tubulin that may affect formation of the ligand-protein complex based on the structural and electrostatic analysis of the ligand-binding site. Methods. Reconstruction of the spatial structure of α-tubulin from D. carota and Toxoplasma gondii using profile (Swiss-Model) and de-novo (AlphaFold2) modeling. Molecular dynamics (MD) simulations of the built 3D-models in Gromacs. Analysis of the molecular electrostatics with PDB2PQR/APBS tools. Visualization and analysis of molecular structures in PyMOL. Results. It has been shown that along with the typical positive charge of the dinitroaniline-binding pocket, all isotypes of carrot α-tubulin demonstrate negatively charged regions that may cause conflicts with the nitro-groups of the ligands. Also, the MD-stable negatively charged "bridge" between Cys316 and the aryl-fragment of Phe255 was observed in all α-tubulin isotypes. In our opinion, it not only competes with the cyclic fragment of dinitroanilines, but overall prevent the opening of the site pocket in carrot α-tubulin. Conclusions. It was clarified that natural resistance of D. carota to dinitroaniline herbicides may be associated with steric and electrostatic conflicts observed in in all α-tubulin isotypes. In our opinion, it prevents interaction with dinitroaniline compounds at the stage of primary site recognition on the early stages of protein-ligand complex formation.

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