engleski

Molecular Dynamics Simulations of Auxin Binding Protein1

Auxins are the first identified plant hormones that regulate plant growth and affect many processes such are, cell division and elongation, apical dominance, autumnal loss of leaves, formation of buds, roots, flowers and fruit. Auxin Binding Protein 1 (ABP 1) has been known for decades as the protein that binds auxin-like molecules, but it's role in auxin signalling pathway has not been identified yet. Recently determined crystal structures of ABP1 (pdb code 1LR5) and of its complex with NAA (pdb code 1LR5) enable structural investigation of an auxin binding to ABP1. We performed a series of 5 ns long Molecular Dynamics (MD) simulations on ABP1 alone as well as on the complexes of ABP1 with an auxin, ABP1 with an antiauxin and on ABP1 with the compound that has auxin-like structure, but does not have any auxin activity. Results clearly show a pathway that enables water molecules to enter and leave the ABP1 active site. When there is no auxin-like molecule in the active site, water molecules coordinate the zinc ion, the central part of the ABP1 binding site. An auxin-like molecule replaces two water molecules from the Zn2+ coordination sphere and they are released. MD simulations also indicate some other roles that water molecules might have in binding of auxin-like molecules to the ABP 1 active site.

Auxin; Molecular Dynamics; Amber

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