engleski

MOLECULAR MODELLING STUDY OF AUXIN BINDING PROTEIN 1

Auxins are the first identified plant hormones that regulate plant growth and affect many processes such as, cell division and elongation, apical dominance, autumnal loss of leaves, formation of buds, roots, flowers and fruit, and many others. Although their physiological function is well known, their molecular mechanisam of work is still a puzzle. Auxin Binding Protein1 (ABP1) binds auxins with high affinity and it is a strong candidate for an auxin receptor. In order to understand molecular mechanism of auxin binding to ABP1 series of molecular dynamics (MD) simulations of ABP1 and it's complexes with auxin-related compounds have been made. Results of simulations pointed to the differences between conformations in which ABP1 exists with and without auxin molecule bound. Possible routes by which auxin-related compounds enter and leave ABP1 active site have been investigated by random expulsion molecular dynamics (REMD) simulations in which small, artificial, randomly orientated force is applied to the ligand center of mass. Since smaller expelling force enhances larger protein reorganization during the ligand exit and gives more reliable results, but also extends simulation time, different accelerations of random force have been tried with the most common auxin molecules (NAA and IAA). Two main routes have been found. Considering assumed orientation of ABP1 to the membrane, one of them leads into the membrane and the other to the lumen of endoplasmic reticulum or citosol, depending on the ABP1 location.

auxin; ramd; molecula simulations; signal transduction

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