Supplemental Information. Structural and Mechanistic Paradigm. of Leptin Receptor Activation Revealed

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1 Structure, Volume 22 Supplemental Information Structural and Mechanistic Paradigm of Leptin Receptor Activation Revealed by Complexes with Wild-Type and Antagonist Leptins Kedar Moharana, Lennart Zabeau, Frank Peelman, Philippe Ringler, Henning Stahlberg, Jan Tavernier, and Savvas N. Savvides

2 Figure S1. Structural characterization of LRecto (A) Log plot of small angle X-ray scattering intensities from LRecto at three concentrations against the momentum transfer. Inset: Same plot of log I vs. momentum transfer at very low scattering angles, showing absence of any concentration dependency. (B) Superimposed and manually fitted reference ab initio model (as grey surface) onto the rigid body model (as ribbon), both generated from SAXS of 0.9 mg/ml LRecto. The color scheme for the rigid body model is same as in figure 1C: CRH1 in red, Ig domain in violet, CRH2 domain in orange, FNIII domains in green and glycans have been shown as grey sticks. (C) The 33 class averages obtained from 681 particles by negative stain electron microscopy of LRecto. Figure S1, related to Figure 1. 2

3 Figure S2. Size exclusion chromatrography of samples recovered from ITC experiments. Size exclusion chromatography of sample recovered after isothermal titration calorimetry of (A) wt-leptin at 20 µm into LR ecto at 1 µm and (B) wt-leptin at 148 µm into LR ecto at 8.4 µm.. In each case, excess of wt-leptin eluted as a minor peak. Figure S2, related to Figure 2. 3

4 Figure S3. Structural characterization of wt-leptin/lrecto quaternary complex by SAXS (A) Four cluster centers produced by DAMAVER from 20 ab initio models of wt-leptiin/lrecto quaternary complex. The proportion of each cluster in percentage and the corresponding chi square values against the scattering data up to momentum transfer (q) of 0.1 Å-1 has been presented. (B) The SASREF rigid body model in cartoon view has been superimposed and manually fitted onto the DAMMIF bead model (as grey surface) and presented in three different orientations. The coloring scheme for different domains of the rigid body model is same as in Figure 3: : CRH1 in red, Ig domain in violet, CRH2 domain in orange, FNIII domains in green and glycans have been shown as grey sticks. Figure S3, related to Figure 3. 4

5 Figure S4. Structural characterization of LRecto in complex with antagonist leptin variants by SAXS and EM (A) The reference DAMMIF ab initio envelop (as grey surface) determined using DAMAVER has been superimposed and manually fitted onto the SASREF rigid body model of leptina1/lrecto binary complex (as cartoon). The chi square for the DAMMIF model has been calculated against experimental scattering up to momentum transfer (q) of The color scheme for different domains of rigid body model is same as in Figure 4D and 4E : CRH1 in red, Ig domain in violet, CRH2 domain in orange, FNIII domains in green and glycans have been shown as grey sticks. (B) Similar representation of leptina2/lrecto complex as in (A). The chi square fit of the ab initio models is up to momentum transfer (q) values of The color scheme for different domains of rigid body model is as in Figure 4D and 4E. (C) The seven class averages obtained from 391 particles by negative stain EM of leptina2/lrecto binary complex. Figure S4, related to Figure 4. 5

6 Figure S5. Structural characterization of alkylated LR ecto and its complexes (A) SAXS scattering of iodoacetamide treated LR ecto and its complexes: SAXS scattering intensity have been plotted for iodoacetamide treated LR ecto (green), its complex with leptin a2 (purple) and with wt-leptin (orange) in log scale against the momentum transfer. The standard deviation for each curve is shown in grey. (B) Pairwise-distance distribution: The pairwise distance distribution plot for alkylated LR ecto (green), its complex with leptin a2 (purple) and with wt- Leptin (orange). (C) Ab initio modeling: The scattering curves from receptor and its complexes have been used to generate ab initio models using DAMMIF. Figure S5, related to Figure 1, Figure 3, and Figure 4. 6

7 TABLE S1: SAXS analysis of LR ecto, leptin a1 -LR ecto, leptin a2 -LR ecto in the presence of the sulfhydryl alkylating agent iodoacetamide. Table 1 related to Experimental Procedures and Figure 1, Figure 3, and Figure 4. Data collection LR ecto wt-leptin/lr ecto Leptin a2 /LR ecto parameters (+iodoacetamide) (+iodoacetamide) (+iodoacetamide) Beamline ID 14-3, ESRF ID 14-3, ESRF ID 14-3, ESRF Detector PILATUS 1M PILATUS 1M PILATUS 1M Beam Geometry 0.7 x 0.7 mm x 0.7 mm x 0.7 mm 2 Wavelength (Å) Q range (Å -1 ) Exposure Time (sec) 100 (10 x 10) 100 (10 x 10) 100 (10 x 10) Concentration range (mg/ml) Temperature (K) Structural Parameters I(0) (Å -1 ) from P(r) 20.0± ± ±1.6 Rg (Å) from P(r) 72.5± ± ±2.6 I(0) (Å -1 ) from Guinier 20.0± ± ±1.8 Rg (Å ) (from Guinier) 70.6± ± ±3.8 Dmax (Å) 251.2± ± ±13.3 Porod volume estimate, V ρ Excluded volume, V ex(å 3 ) Molecular Mass (kda) From I(0) 187.5± ± ±14.4 From SaxsMOW From Porod volume (Vp/1.7) 181.5± ± ±6.5 From excl. volume (Vex/1.7) Peptide (Protparam) Peptide + n-glycans Modeling Parameters Symmetry P1 P1 P1 χ 2 of reference model # of models averaged DAMAVER NSD (var) 0.78± ± ±0.05 Rigid body modeling Initial χ Final χ Software/Server Data Reduction BSX-CUBE BSX-CUBE BSX-CUBE Data Processing PRIMUS PRIMUS PRIMUS Data Evaluation PRIMUS, GNOM PRIMUS, GNOM PRIMUS, GNOM Structure Modeling DAMMIF DAMMIF DAMMIF 7