The formation mechanism of the abscisic acid transport channel in PYL2 protein: A molecular dynamics study

Abstract

In this paper, the formation mechanism of the abscisic acid (ABA) transport channel in protein PYL2 was studied by the molecular dynamics (MD) method. MD simulations suggested that CL2, CL3 and CL4 loops in PYL2 are more flexible than other loops after the PYL2 activation. ABA binding induces dramatic conformational changes in loops CL2, CL2 and CL3, which indicates that the three loops may play key roles in the activation of the channel for the ABA entry into the pocket of the PYL2 protein. Simulations also showed that residue Arg120 in CL3 plays an essential role in the formation of the ABA transport channel. In SMD simulations, a steady increase of the applied force during the first 400 ps of the ABA egress process was shown. It rose to approximately 680 pN that was the maximum rupture force of the ABA unbinding along this pathway. The large rupture force may contribute to the breaking of hydrogen bonds between ABA and PYL2.