Paper Citing NAMD - Abstract
Wang Teng; Sun Hong-Wei; Chen Lan; Shen Rong-Xin; Lai Cheng-Ming
Docking and Molecular Dynamics Simulation Studies of Interaction Between Arabidopsis TIR1 and Auxin IAA
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 30:1835-1838, SEP 10 2009
On the basis of the complex crystal structure of transport inhibitor response 1 (TIR1) and indole-3-acetic acid(IAA) obtained recently, systematic docking and molecular dynamics studies of interaction between auxin IAA and TIR1 have been performed using autodock 3.0 and NAMD 2.5 packages. The clocking results indicate that the co-factor InsP(6) and central water molecule play important roles in binding to the TIR1 pocket for auxin IAA correctly. The complex of TIR1 and auxin IAA was stable during the MD simulation, and stable hydrogen bond interaction had been formed between two water molecules which acted as central water molecule one after the other with auxin IAA. The interaction between auxin IAA and active residues around binding site was a little different from that in crystal structure.
