Molecular recognition of the plant hormone auxin is still a puzzle

The plant hormone auxin is involved in almost every aspect of plant development; auxin homeostasis and auxin signaling are thus of crucial importance. The wider auxin family includes endogenous growth promoters, such as indole-3-acetic acid (IAA), and chemically diverse synthetic analogues; minor structural modifications afford growth inhibitors (antiauxins). As proper classification is of technological relevance (growth regulators, herbicides) we developed a classification by interaction similarity indices, based on the evaluation of two distinctive molecular conformations (planar and tilted) of indole-3-acetic acid in comparison with the optimized conformations of 50 compounds. Then we extended the method to a larger set of compounds using similarity of molecular interaction fields and lipophilicity predictions (log P). In addition to theoretical approaches based on the evaluation of molecular conformations of possible relevance for binding to the auxin receptor(s), we used experimental methods, such as X-ray structure analysis and spectroscopic methods to characterize the molecules of interest: alkylated IAAs, halogenated IAAs (F, Cl, Br), and dihalogenated IAAs. Systematic analysis of physico-chemical and structural properties provided indirect insight into the topology of the substrate-binding site of the, so far hypothetical, common auxin receptor. Our findings are in reasonable accord with the models proposed by previous researchers. The question of molecular fit to the receptor active site will, however, remain open until the coordinates of the first structurally characterized auxin binding protein, ABP1, will be in the public domain.