MECHANISM OF AUXIN INTERACTION WITH AUXIN BINDING PROTEIN (ABP1): A MOLECULAR DYNAMICS SIMULATION STUDY

Branimir Bertoa ¹, Biserka Kojic-Prodic; ¹, Rebecca Wade ² and Sanja Tomic ^1*

¹ Rudjer Bokovic Institute
² EML

^* To whom correspondence should be addressed. E-mail: sanja.tomic{at}irb.hr.

Submitted on March 20, 2007
Revised on June 5, 2007
Accepted on 27 July 2007

	Abstract

Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. In order to understand the proposed receptor function of ABP1 we carried out a detailed molecular modelling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilised by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site.

Key Words: auxin, binding protein 1 (ABP1), molecular dynamics, random acceleration molecular dynamics (RAMD), signalling pathway