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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.

Hao GF, Yang GF - PLoS ONE (2010)

Bottom Line: The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy.As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a "molecular glue".The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, People's Republic of China.

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.

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Chemical structures of IAA and some synthetic auxins.
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pone-0010742-g001: Chemical structures of IAA and some synthetic auxins.

Mentions: As a pivotal plant hormone, auxin controls many aspects of plant growth and development [1]–[7] by modulating gene expression and, thus, leading to changes in cell division, expansion, and differentiation [8], [9]. Indole-3-acetic acid (IAA) is the major naturally occurring auxin. In addition, several synthetic auxins have also been developed, including 2,4-dichlorophenoxyacetic acid (2,4-D), 1-naphthalene acetic acid (1-NAA), 2-methoxy-3,6-dichlorobenzoic acid (dicamba), 4-amino-3,5,6-trichloropicolinic acid (tordon or picloram), α-(p-chlorophenoxy) isobutyric acid (PCIB, an antiauxin), and so on (Figure 1) [10]. These chemically diverse molecules share two common characteristics: a planar aromatic ring and a side chain with a carboxyl group. Although auxin is known as one of the most important “signaling messengers” in the plant kingdom, the detailed action mechanism of auxin with its receptor remains one of the most interesting questions in plant biology.


The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations.

Hao GF, Yang GF - PLoS ONE (2010)

Chemical structures of IAA and some synthetic auxins.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2873998&req=5

pone-0010742-g001: Chemical structures of IAA and some synthetic auxins.
Mentions: As a pivotal plant hormone, auxin controls many aspects of plant growth and development [1]–[7] by modulating gene expression and, thus, leading to changes in cell division, expansion, and differentiation [8], [9]. Indole-3-acetic acid (IAA) is the major naturally occurring auxin. In addition, several synthetic auxins have also been developed, including 2,4-dichlorophenoxyacetic acid (2,4-D), 1-naphthalene acetic acid (1-NAA), 2-methoxy-3,6-dichlorobenzoic acid (dicamba), 4-amino-3,5,6-trichloropicolinic acid (tordon or picloram), α-(p-chlorophenoxy) isobutyric acid (PCIB, an antiauxin), and so on (Figure 1) [10]. These chemically diverse molecules share two common characteristics: a planar aromatic ring and a side chain with a carboxyl group. Although auxin is known as one of the most important “signaling messengers” in the plant kingdom, the detailed action mechanism of auxin with its receptor remains one of the most interesting questions in plant biology.

Bottom Line: The computational simulation results provided a reasonable explanation for the structure-activity relationships of auxin and its synthetic analogues in view of energy.As a result, auxin enhances the TIR1-Aux/IAA interactions by acting as a "molecular glue".The structural and mechanistic insights obtained from the present study will provide valuable clues for the future design of promising auxin analogues.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, People's Republic of China.

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.

Show MeSH