engleski

Investigation of Auxin Binding to ABP1 by Computational Methods

Auxins are the first identified plant hormones that regulate plant growth and development. Auxin Binding Protein 1 (ABP 1) has been known for decades as the protein that binds auxin-related compounds with high affinity. Crystal structures of ABP1 and ABP1 complex with an auxin molecule were used to prepare starting structures for molecular dynamics (MD) and random expulsion molecular dynamics (REMD) simulations. Polar hydrogens were added using WHATIF program and series of minimizations and equilibration were performed in order to obtain stabile system for 5 ns long MD simulations. Simulations were performed with Amber 8 program package, using explicit solvent model and Periodic Boundary Conditions. Beside standard MD simulations at room temperature, simulations at temperature shortly increased at 500 K were also made (altogether 70 ns of MD simulations were accomplished). Two different conformations of ABP1 are identified, one of which is stabilized by auxin binding. In all simulations the same network of water molecules leading from the bulky water to the ABP1 active site was formed. REMD simulations revealed two main routes by which auxin molecules enter and leave ABP1 binding site.

Auxin; ABP1; Molecular dynamics

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