Paper Citing NAMD - Abstract
Jia Xuebing; Zhang Jun; Sun Hongwei; Chen Lan; Shen Rongxin; Lai Chengming
Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception
ACTA CHIMICA SINICA, 68:2500-2508, DEC 28 2010
The molecular dynamics simulation studies on the 14 auxin perception systems that comprise auxins, receptor TIR1, cofactor InsP(6) 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 InsP(6) 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 InsP(6) 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.
