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Molecular Dynamics simulations of Auxin Binding Protein 1
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Branimir Bertoša, Sanja Tomića and Darko Babić
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Ruđer Bošković Institute, P.O.B. 180, HR-10002 Zagreb, Croatia
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.