The molecular dynamics simulation studies on the 14 auxin perception systems that comprise auxins, receptor TIR1, cofactor InsP₆ and IAA7 substrate peptide are carried out to investigate the interaction mode between receptor TIR1 and the four auxins of IAA, 1-NAA, 2,4-D and 2-NAA, respectively. The importance of cofactor InsP₆ and IAA7 substrate peptide in early auxin perception was also discussed. MD simulations show that the binding intensity between auxins and TIR1 is consistent with auxin activity|the molecular structure has an important impact on auxin activity|multiple center-waters pull auxins to suitable position where auxins can strongly bind with TIR1 through the hydrogen bonds|the hydrogen bonds between InsP₆ and TIR1 make the binding pocket stable to ensure auxins to bind effectly|in addition, IAA7 becomes more active after binding with auxins, which means auxins ignite the activity of IAA7 as the trigger to induce the further gene expression of auxin perception.

Key words: auxin perception, receptor TIR1, IAA7 substrate peptide, MD simulation