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The Role of Phe82 and Phe351 in Auxin-Induced Substrate Perception by TIR1 Ubiquitin Ligase: A Novel Insight from Molecular Dynamics Simulations

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  • Ge-Fei Hao
  • Guang-Fu Yang

Abstract

It is well known that Auxin plays a key role in controlling many aspects of plant growth and development. Crystal structures of Transport inhibitor response 1 (TIR1), a true receptor of auxin, were very recently determined for TIR1 alone and in complexes with auxin and different synthetic analogues and an Auxin/Indole-3-Acetic Acid (Aux/IAA) substrate peptide. However, the dynamic conformational changes of the key residues of TIR1 that take place during the auxin and substrate perception by TIR1 and the detailed mechanism of these changes are still unclear. In the present study, various computational techniques were integrated to uncover the detailed molecular mechanism of the auxin and Aux/IAA perception process; these simulations included molecular dynamics (MD) simulations on complexes and the free enzyme, the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) calculations, normal mode analysis, and hydrogen bond energy (HBE) calculations. The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy. In addition, a more detailed model for auxin and Aux/IAA perception was also proposed, indicating that Phe82 and Phe351 played a pivotal role in Aux/IAA perception. Upon auxin binding, Phe82 underwent conformational changes to accommodate the subsequent binding of Aux/IAA. As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a “molecular glue”. Besides, Phe351 acts as a “fastener” to further improve the substrate binding. The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues.

Suggested Citation

  • Ge-Fei Hao & Guang-Fu Yang, 2010. "The Role of Phe82 and Phe351 in Auxin-Induced Substrate Perception by TIR1 Ubiquitin Ligase: A Novel Insight from Molecular Dynamics Simulations," PLOS ONE, Public Library of Science, vol. 5(5), pages 1-9, May.
  • Handle: RePEc:plo:pone00:0010742
    DOI: 10.1371/journal.pone.0010742
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    References listed on IDEAS

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    1. Nihal Dharmasiri & Sunethra Dharmasiri & Mark Estelle, 2005. "The F-box protein TIR1 is an auxin receptor," Nature, Nature, vol. 435(7041), pages 441-445, May.
    2. Stefan Kepinski & Ottoline Leyser, 2005. "The Arabidopsis F-box protein TIR1 is an auxin receptor," Nature, Nature, vol. 435(7041), pages 446-451, May.
    3. Xu Tan & Luz Irina A. Calderon-Villalobos & Michal Sharon & Changxue Zheng & Carol V. Robinson & Mark Estelle & Ning Zheng, 2007. "Mechanism of auxin perception by the TIR1 ubiquitin ligase," Nature, Nature, vol. 446(7136), pages 640-645, April.
    4. William M. Gray & Stefan Kepinski & Dean Rouse & Ottoline Leyser & Mark Estelle, 2001. "Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins," Nature, Nature, vol. 414(6861), pages 271-276, November.
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