Intrinsic disorder and conformational coexistence in auxin coreceptors

Significance This paper shows the most detailed and complete view to date of a canonical Aux/IAA auxin coreceptor protein. Molecular dynamics simulation, coupled with nuclear magnetic resonance analysis shows that, although nominally disordered, the N-terminal half of the Aux/IAA AXR3 appears to show a propensity toward adoption of a small number of specific conformations. The conformational coexistence in auxin coreceptors provides an insight into a protein family that is so crucial for plant life on earth.

The structure is shown in ribbon representation, with a colouring that passes continuously from pure blue at the N terminal to pure red at the C terminal, for ease of inspection.

Figure S5.
The N-terminal half of Aux/IAA17 does not behave like a pure random coil or self-avoiding walk.The average gyration radius computed over the simulation trajectory for a fragment of the peptide with increasing number of residues does not follow a power-law of the number of residues using, indicating that the first half of the protein does not fall into one of the two classic categories of intrinsically disordered proteins.

Figure S6.
The simulation trajectory of the N-terminal half of Aux/IAA17 contains more than one structural cluster.The SWRMSD of the trajectory separates a first cluster of frames (lower band) from the rest.Repeating the procedure on the remaining frames until the whole trajectory is separated allows us to identify 12 total clusters of structures, of which 2 are the most significant, accounting for more than 90% of total occupancy.

Movie legends
Supplemental Movie 1. Minimum-energy poses of the full AXR3-TIR1 models constructed using Cluster 1. AXR3 is in solid surface representation (pink); TIR1 is in semi-transparent surface/ribbon representation (cyan); also shown are the molecular surfaces of auxin (green) and the structural co-factor inositol hexakisphosphate (InsP6) (red).

Figure S3 .
Figure S3.Extended region propensities of the N-terminal half of Aux/IAA17.

Figure S2 .
Figure S2.Alpha helix propensities of the N-terminal half of Aux/IAA17.

Figure S1 .
Figure S1.Starting conformation for MD simulations of the N-terminal half of AXR3, obtained via DMPfold.The structure is shown in ribbon representation, with a colouring that passes continuously from pure blue at the N terminal to pure red at the C terminal, for ease of inspection.

Table S1 .
Parameters for heteronuclear single-quantum correlation (HSQC) experiment.HSQC experiments to study the auxin co-receptor complex were performed at 4˚C and 950 MHz.All other HSQC experiments were performed at 16.5 ˚C and either 950 or 750 MHz.

Table S3 .
Parameters for assignment experiments in the analysis of 13 C and 15 N isotopically labelled AXR3 DI/DII protein.All experiments were performed at 16.5˚C, 600 MHz and with recycling delays of 1 second.Four scans were collected.

Table S4 .
References to software used in the NMR assignment of AXR3 DI/DII protein.