Tomographic docking suggests the mechanism of auxin receptor TIR1 selectivity.
We study the binding of plant hormone IAA on its receptor TIR1, introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest that selectivity is related to constraints that potential ligands encounter on their way from the surface of the protein to their final position at the pocket bottom. Tomographic docking helps develop specific hypotheses about ligand binding, distinguishing binders from non-binders, and suggests that binding is a three-step mechanism, consisting of engagement with a niche in the back wall of the pocket, interaction with a molecular filter which allows or precludes further descent of ligands, and binding on the pocket base. Only molecules that are able to descend the pocket and bind at its base allow the co-receptor IAA7 to bind on the complex, thus behaving as active auxins. Analysing the interactions at different depths, our new method helps in identifying critical residues that constitute preferred future study targets and in the quest for safe and effective herbicides. Also, it has the potential to extend the utility of docking from ligand searches to the study of processes contributing to selectivity.
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
Veselina V
VV
Uzunova
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
Mussa
M
Quareshy
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
Charo I
0000-0001-9958-017X
CI
Del Genio
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK Richard.Napier@warwick.ac.uk.
Richard M
0000-0002-0605-518X
RM
Napier
D001665:Binding Sites; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010937:Plant Growth Regulators / Q000737:chemistry* / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism*; D010944:Plants / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011956:Receptors, Cell Surface / Q000737:chemistry* / Q000378:metabolism*
D010937:Plant Growth Regulators; D010940:Plant Proteins; D011956:Receptors, Cell Surface; C046131:auxin receptor, plant
auxin; molecular filter; receptor selectivity; tomographic docking