Supplementary Figure S1 Domain organization of ASIC1. Side view of the trimeric sodium channel ASIC1 910 in ribbon representation showing the domains

Transcription

1 Supplementary Figure S1 Domain organization of ASIC1. Side view of the trimeric sodium channel ASIC1 910 in ribbon representation showing the domains according to the nomenclature of Jasti et al The view highlights the individual regions in the ASIC1 subunit C in color. The transmembrane helices are depicted in red, the ball in orange, the palm in yellow, the knuckle in blue, the finger in violetpurple and the thumb in green. The gray lines depict the position of the membrane based on the hydrophobicity of the protein surface. In the apo form, protons can readily access the putative ph sensor characterized by an array of acidic residues including Asp346, Asp350, Glu354 (thumb) and Glu236, Glu238, Glu239, Glu243, Asp260 (finger) of one subunit and Glu178, Glu220 and Asp408 (palm) of the adjacent subunit. Protonation causes the formation of H-bonds between the carboxylates of the prominent pairs Asp238/Asp350, Glu239/Asp346 and Glu220/Asp408 and subsequent opening of the channel.

2 Supplementary Figure S2 Electrophysiological experiments. Concentration-response relation for H + -dependent activation of human wt ASIC1(1-528) channels expressed in SF9 cells. a, Superimposed current traces recorded in patch clamp recordings from a single SF9 cell at -80 mv holding potential. The cell was constantly superfused and the sodium concentration reduced to 5mM to avoid excessively large currents corrupting the voltageclamp. The arrow indicates the ph shift for 0.6 s of the superfusing solution from ph 7.4 to the values indicated below the traces. A resting time of 1 min at ph 7.4 was applied between the successive responses. The ph 6.0 stimulus was repeated at end of the series of ph stimuli to monitor the stability of the evoked responses. As expected, the current rise was slowest for the highest ph values (lowest proton concentration, lowest activation). At ph 6.8 the current started to inactivate after reaching peak. b, ph-response relation derived from 10 experiments similar to a. Circles and error bars indicate mean values and standard deviations (S.D.). The

3 function y = 1 / [ n (ph-pk) ] was fitted to each experiment separately and the curve was then calculated with the mean values of the fitted parameters, pk = 6.85 ± 0.06 and n = 7.5 ± 2.1 (mean ± S.D.). The latter value suggests that between 6 and 9 protons bind cooperatively to the channel for activation (pore opening). c, Inhibition of H + -evoked currents in whole-cell patch-clamp experiments on SF9 cells expressing human wt ASIC1(1-528). The ASIC1- mediated current was repeatedly activated by short pulses of ph-6.0-buffered solution before, during and after the addition of 1 nm or 10 nm PcTx1 or 1 µm A Bars indicate the average degree of inhibition, values in parenthesis the number of cells tested and standard error of the mean (SEM) is given by the error bars.

4 Supplementary Figure S3 PcTx1 binding to purified ASIC1 protein. a, Surface plasmon resonance direct binding assay using human ASIC1(25-464). The sensogram presents an overlay of the binding curves demonstrating binding of 6.25 nm PcTx1 (green), 100 µm A (grey) and both molecules in a competition binding experiment (black dashed). The resulting signal height in the competition experiment shows that both substances interact simultaneously with the channel addressing separate binding sites. b,c, Purified chicken ASIC1(26-463) in the presence and absence of PcTx1 was loaded on a size-exclusion chromatography (SEC) column and on an SDS-PAGE to characterize the quality and quantity of the samples. The red and blue curves in the SEC chromatogram depict the apo and PcTx1- bound form of ASIC1. The bands for monomeric ASIC1 and PcTx1 are labeled. Bands with higher apparent molecular weight correspond to higher oligomer species of ASIC1.

5 Supplementary Figure S4 Gating modifier toxin comparison. Structure comparison of Psalmotoxin 1 (PcTx1, a-c) with the inhibitory cysteine knot gating modifier toxins Hanatoxin 1 (HaTx1, d-f) and VSTx1 (g-i) that both bind and modify voltage-gated potassium channels 30. a,d,g, Ribbon representation of the polypeptide chain of PcTx1, HaTx1 (PDB ID 1D1H) and VSTx1 (PDB ID 1S6X). b,e,h, Structure of the three toxins with the polypeptide chain in white ribbon representation and residues in stick. Blue and red depict positively and negatively charged side chains, respectively. Green depicts hydrophobic side chains. c,f,i, Surface representation of the three toxins with color code of b, The view visualizes the structural organization of gating modifier toxins exposing their hydrophobic patch and basic cluster to the surrounding medium. The similar distribution of hydrophobic and positive side chains at the surface of the toxins suggests a common principle of ion channel binding in these ICK toxins.

6 Supplementary Figure S5 Comparison of PcTx1 in the complex and in solution. Superposition of PcTx1 observed in the PcTx1-ASIC1 complex (green) and observed in solution by NMR that were used in docking studies (PDB ID 1LMM, magenta; PDB ID 2KNI, cyan). Significant conformational differences are evident in the beta-hairpin motif featuring the basic cluster and for the side chains Arg26, Arg27, Arg28 as well as Trp7 and Trp24 that likely prevent from correctly docking the toxin onto ASIC1.

7 Supplementary Figure S6 Electron density and crystal lattice. a, Stereo image of the final 2Fo-Fc electron density map contoured at 1σ at helix 5 in the ASIC1-PcTx1 binding interface b, Fo-Fc electron density map contoured at 3 σ after molecular replacement. Unbiased electron density for three PcTx1 molecules is visible at the interface between adjacent subunits of ASIC1 (ribbon representation). c,d Crystal packing in the PcTx1-ASIC1 complex crystals. Neither the PcTx1 molecules nor the ASIC1 transmembrane helices are involved in crystal lattice contacts. Therefore, these regions are unperturbed in the crystal structure.

8 k a [M -1 s -1 ] k d [s -1 ] K D [M] human ASIC1(1-467) 7.92 (±1.47) x (±0.15) x (±0.23) x 10-9 human ASIC1(25-464) 7.99 (±0.60) x (±0.09) x (±0.18) x 10-9 chicken ASIC1(26-463) 9.94 (±1.75) x (±0.32) x (±0.26) x 10-9 Supplementary Table S1 Surface plasmon resonance direct binding assay. Binding affinities (K D ), association (k a ) and dissociation constants (k d ) of PcTx1 for the purified, biotinylated ASIC1 protein constructs human ASIC1(1-467), human ASIC1(25-464) and chicken ASIC1(26-463) immobilized on the streptavidin surface of a CM4 chip. PcTx1 was added into the buffer for analysis. The experiment was repeated 4 times for each construct at 18 C in a buffer containing 20 mm sodium citrate ph 6.3, 300 mm NaCl, 0.05 % n-dodecylβ-d-maltopyranoside (DDM), 0.05 % CHAPS, 0.01 % cholesterol hemisuccinate (CHS), 25 µm of a 7:3 (w/w) mixture of 1,2-dieoleoyl-sn-glycero-3-phosphocholine:1,2-dieoleoylsn-glycero-3-phospho-L-serine (DOPC:DOPS). Numbers in the parenthesis represent the standard deviation. The binding curves were fitted using a one-to-one binding model and the BIAevaluation software 3000 version 3.2 (Biacore). The individual K D, k a and k d values differ only marginally for the three truncated protein constructs indicating the preservation of a single population of binding sites for PcTx1.

9 apo 3S3W PcTx1-bound 3S3X Data collection Space group P C2 Cell dimensions a, b, c (Å) 110.5, 142.7, , 109.4, α, β, γ ( ) 90, 90, 90 90, 119.8, 90 Resolution (Å) * ( ) 49-3 ( ) R sym 0.16 (0.82) 0.11 (0.73) I/σI 8.6 (1.2) 8.5 (1.1) Completeness (%) 99.8 (99.4) 99.7 (99.8) Redundancy 6.7 (6.6) 3.4 (3.5) Refinement Resolution (Å) ( ) ( ) No. reflections R cryst/ R free 21.2 (41.2) / 23.6 (44.0) 21.9 (42.9) / 24.9 (46.2) No. atoms Protein Ligand/ion 3 8 Water Phase error (º) # B-factors Protein / / Ligand/ion / / Water / / R.m.s deviations Bond lengths (Å) Bond angles (º) Both datasets were collected from one single crystal. *Highest resolution shell is shown in parenthesis. # Based on Maximum Likelihood after refinement with PHENIX 43. Supplementary Table S2 Data collection and refinement statistics.

10 PcTx1 ASIC1 Subunit A ASIC1 Subunit B secondary structure element Jasti region Lys6 Tyr317 α4 Thumb 5 Asn321 α4 Thumb 5 Glu343 α5 Thumb 5 Trp7 Tyr317 α4 Thumb 5 Asn321 α4 Thumb 5 Glu343 α5 Thumb 5 Cys344 α5 Thumb 5 Pro347 α5 Thumb 5 Ala348 α5 Thumb 5 Phe351 α5 Thumb 5 Lys8 Glu343 α5 Thumb 5 Trp24 Pro347 α5 Thumb 5 Asp350 α5 Thumb 5 Phe351 α5 Thumb 5 Glu354 α5 Thumb 5 Lys355 α5 Thumb 5 Trp24 Gly177 β3-β4 Ball 3 Glu178 β3-β4 Palm 3 Lys25 Phe174 β3 Palm 3 Gly177 β3-β4 Palm 3 Gln179 β3-β4 Palm 3 Arg26 Phe174 β3 Palm 3 Arg26 Asp238 β6-β7 Ball 4 Lys342 α5 Thumb 5 Asp346 α5 Thumb 5 Pro347 α5 Thumb 5 Asp350 α5 Thumb 5 Arg27 Phe174 β3 Palm 3 Phe175 β3 Palm 3 Arg176 β3-β4 Palm 3 Gly177 β3-β4 Palm 3 Thr215 β6 Palm 4 Gly216 β6 Palm 4 Asn217 β6 Palm 4 Gly218 β6 Palm 4 Glu220 β6 Palm 4 Asp408 Palm 6 Arg27 Glu354 α5 Thumb 5 Arg28 Glu236 β6-β7 Ball 4 Thr237 β6-β7 Ball 4 Asp238 β6-β7 Ball 4 Thr240 β6-β7 Ball 4 Ser241 β6-β7 Ball 4 Phe242 β6-β7 Ball 4 Glu243 β6-β7 Ball 4 Salinas domain

11 Arg28 Gln271 β9 Ball 4 Ser29 Glu236 β6-β7 Finger 4 Thr237 β6-β7 Finger 4 Asp238 β6-β7 Finger 4 Phe30 Glu236 β6-β7 Finger 4 Lys342 α5 Thumb 5 Val32 Pro347 α5 Thumb 5 Val34 Phe351 α5 Thumb 5 Pro35 Tyr317 Thumb 5 Phe351 α5 Thumb 5 Thr37 Phe351 α5 Thumb 5 Lys355 α5 Thumb 5 Pro38 Lys355 α5 Thumb 5 Supplementary Table S3 PcTx1-ASIC1 interface. Mapping of chicken ASIC1 residues interacting with Psalmotoxin 1 to the secondary structure elements and structural domains 9 and to the chimeric construction domains Only ASIC1 residues within 5Å around PcTx1 are listed. Residues involved in charged hydrogen bonds are marked with a *. The structure shows, with one exception, that all interactions are with domains 3,4 and 5 and that the hydrophobic interactions predominantly exist with domain 3 and 5 whereas two of the three important charged arginine interactions are with domain 4. This is in agreement with the experimental observation, that only ASIC1 chimeras 1b/1a and 2a/1a containing simultaneously all the domains 3, 4 and 5 of ASIC1a could still bind PcTx1. However, the authors of the chimera study concluded from their results a binding model where only domains 3 and 5 are directly involved in binding and postulated an indirect role for domain 4.

12 PcTx1 Observed chicken ASIC1 (5Å cutoff) Predicted human ASIC1a (from Table 1 in Pietra 2009 ) Predicted human ASIC1 (from Table S3 in Qadri, Berdiev et al. 2009, 6Å cutoff) Glu1 Arg166 Asp2 Arg121 Arg166 Cys3 Arg121 Arg166 Ile4 Asn120 Arg166 Pro5 Glu113; Asn120 Asp164; Ile165; Asp167; Leu169; Leu170; Ala181 Lys6 Tyr317*; Asn321*; Glu343* Glu344* Leu169; Leu170; Lys393; Phe394; Trp7 Tyr317*; Asn321; Glu343*; Cys344*; Pro347*; Ala348*; Phe351* Lys343*; Glu344*; Cys345*; Pro348* Lys8 Glu343* Glu113,; Asn119, Asn120; Lys343 Gly9 Asn395 Leu169; Leu170; Ser171; Asp223; Leu390; Ala391; Lys392; Lys393; Phe394 ; Asn395; Lys396 Arg166; Leu169; Leu170; Ser171; Cys172; Val178; Cys179; Ser180; Ala181; Gly182; Lys393; Phe394 Leu169; Leu170; Ser171; His173; Val178; Cys179; Ser180 Cys10 His173; Val178 Val11 Leu116; Asn119, Cys172; His173; Phe174; ; Gly176; Glu177; Val178; Cys179; Ser180; Gly182; Asp183;Arg204 Asn12 Pro125; Asp126, Met129 Arg13 Asp126 Gly182 His14 Met129 Val178 Asp16 Gly182 Cys23 Val178 Trp24 Gly177; Glu178; Lys356* Pro347*; Asp350*; Phe351*; Glu354*; Lys355* Lys25 Arg26 Arg27 Phe174; Gly177; Gln179 Phe174; Asp238*; Lys342*; Asp346*; Pro347*; Asp350* Phe174; Phe175; Arg176; Gly177; Thr215; Gly216; Asn217; Gly218; Phe174; Cys179 Phe174; Asn347?, Leu350*; Asp351*; Glu355*; Lys356* Phe174, Arg175; Gly176, Glu177; Val178; Glu129; Glu355* Val178; Ser180; Ala181; ; Gly182 Gly176; Val178; Glu235*; Pro348*; Asp351*; Glu355* His173; Gly234; Glu235*; Thr236*; Asp237*; Thr239*; Phe241*; Tyr389; Lys393 Leu114*; Arg190*; Glu235*; Thr236*; Asp237*; Glu238*; Thr239*; Gln341*; Predicted rat ASIC1 (from Table 3 in Saezet al ) Ala178 Asp349*; Pro346* Asp349*; Glu353*; Asp237*; Glu353*,; Gly176 Glu235*; Thr236*; Asp237*; Thr239* His173; Glu242*; Asp237*; Asp407;

13 Arg28 Ser29 Glu220; Asp408; Glu354* Gln271; Glu236*; Thr237*; Asp238*; Thr240*; Ser241*; Phe242*; Glu243* Glu236*; Thr237*; Asp238* Glu219 Tyr342*; Lys343*; Glu344*; Cys345*; Ala346*; Asp347*; Pro348*; Ala349*; Leu350*; Asp351* Ser171; His173; Arg190; Glu219; Met221; Glu235*; Thr236*; Asp237*; Glu238*; Thr239*; Ser240*; Phe241*; Glu242*; Gln270*; Phe272; Asp351*; Glu355*; Ile381; Val407; Leu408; Asp409 Ser171; His173; Glu219; Met221; Glu235*; Thr236*; Asp237*; Thr239*; Phe241*; Tyr389; Lys393 Phe30 Glu236*; Lys342* Leu116; Lys343* Ser171; Cys172; His173; Phe174; Arg175; Gly176; Glu177; Val178; Cys179; Glu219; Glu235; Glu355*; Lys356* Glu31 Ser171; Cys172; His173; Lys393 Val32 Pro347* Leu170; Ser171; Cys172; His173; Glu235*; Tyr389; Lys393; Phe394 Glu219; His173; Met221; Gln270; Glu235*; Phe241*; Glu235*; Lys391; His173 Lys354* Cys33 Lys393 Val34 Phe351* Pro35 Tyr317*; Phe351* Lys36 Glu342* Thr37 Phe351*; Lys355* Glu342* Pro38 Lys355* Lys39 Asp126* Glu338*; Glu342* Thr40 Lys392; Asn395 Glu338* Supplementary Table S4 Data comparison. Comparison of the observed (PDB ID 3S3X) and predicted interactions between PcTx1 and ASIC1. PcTx1 binds between two adjacent subunits of the ASIC1 trimer and residues that belong to the adjacent subunit are labeled with a *. In summary, the vast majority of predicted inter residual contacts is incorrect (cursive). 17 of the 40 PcTx1 residues predicted to interact with ASIC1 were not observed to interact in the complex structure. Merely 10, 15 and 8 out of 40, 160 and 30 predicted inter residual contacts_enref_7, were among the 58 observed inter residual contacts in the structure (underlined). The results of the 3 modeling studies deviate strongly from each other, and half of the observed contacts were not predicted by any of the studies. Of the ten observed

14 hydrogen bonds that convey the specificity of binding between PcTx1 and ASIC1 none has been explicitly predicted. Notably, none of the three important, occluded, charged hydrogen bonds between the positive cluster residues Arg26, Arg27 and Arg28 and the negatively charged acidic pocket residues Asp350, Glu220 and Glu243 were predicted correctly. Furthermore, no correct prediction exists for the hydrophobic interactions. Phe351, which is one of the ASIC residues with the biggest contribution to the binding surface, was not predicted to be involved in binding by any study. The comparison confirms that the NMRderived conformations of the PcTx1 basic cluster residues used for docking were too different from the conformation observed in the complex to yield correct docking predictions (Supplementary Figure S6). The published docking models therefore represent nonphysiological conformations 29.

15 Supplementary Methods Electrophysiological experiments on human ASIC1(1-528). The optimal harvest point for infection of SF9 cells with ASIC1 for electrophysiological studies was determined using a PatchLiner robot (Nanion, Germany). Frozen cell pellets were thawed and resuspended in the extracellular buffer at ph 7.4 (NaOH) containing 5 mm Hepes, 5 mm MES, 150 mm NaCl, 4 mm KCl, 2 mm CaCl 2, 1 mm MgCl 2.Cells were used within 4 hours after thawing. The intracellular buffer at ph 7.2 (CsOH) contained 10 mm Hepes, 20 mm EGTA, 10 mm NaCl, 2 mm MgCl 2, 60 mm CsF, 50 mm CsCl. The holding potential was set to -80 mv. No current responses were detected at 7 h, a plateau of current amplitudes between 8 na and 64 na (median 29 na, 73 cells) was observed 48 hours post infection. The ph dependence, PcTx1 (Peptanova) and A inhibition of ASIC1-mediated currents were measured in manual whole-cell patch-clamp experiments using an EPC-9 amplifier (HEKA, Germany). In most of the experiments the concentration of NaCl was reduced to 5 mm to avoid H + -evoked currents of very large amplitudes corrupting the voltage clamp. The osmolarity and ionic strength of the buffer was maintained replacing sodium for the membrane impermeable cation N-methyl-D-glucamine. Thus, the extracellular saline contained 5 mm HEPES, 5 mm MES, 5 mm NaCl, 145 mm N-methyl-D-glucamine, 4 mm KCl, 1.2 mm CaCl 2 and 1 mm MgCl 2. The HEPES/MES buffer mix was needed to adjust the extracellular ph with HCl in a range from ph 5.7 to 7.4. The intracellular solution for the recording pipettes contained 10 mm HEPES(KOH) ph 7.2, 10 mm BAPTA, 130 mm KCl, 6 mm MgCl 2 and 5 mm Na 2 -ATP. To monitor the stability of channel function (run-down), a ph 6.0 control stimulus was repeatedly applied during the sequence of stimuli. Current amplitudes evoked by any test stimuli (differing ph or presence of inhibitors) were visualized as a fraction of the control response amplitude estimated by interpolation between the next ph 6.0 stimuli. Experiments were discarded if the run-down exceeded 25 % of decrease from one control response to the next. For all inhibition experiments, the cells were constantly superfused by solutions buffered to ph 7.4 (rest) or 6.0 (activation). The activation solution was applied for 0.6 ms intervals at a rate of 1/min. At least 3 pulses of activation solution were applied before the addition of PcTx1 or A to monitor the stability of the control responses. Inhibitors were then added to the rest and activation solutions and 3 more pulses of activation solution were applied. Thus, the first response in presence of either inhibitor was recorded after 1 min pre-incubation and the last after 3 min presence of the inhibitor. The

16 amplitude of the last response was compared with the control responses to estimate the degree of channel inhibition. Crystallization and structure determination of apo chicken ASIC1. For apo chicken ASIC1, initial crystallization trials were performed in sitting drop vapor diffusion setups at a protein concentration of 2.5 mg/ml. Liquid handling was carried out at 4 C and the plates subsequently incubated at 13 C. A number of crystal hits were observed, mainly from crystallization conditions containing various kinds of polyethylene glycols as precipitating agents. Grid screening in hanging drop in vapor diffusion setups was used to improve the size and quality of the crystals. Elongated prism-shaped crystals were obtained by applying a 1:1 protein to reservoir mix containing 100 mm Tris(HCl) ph 7.5, 100 mm ammonium sulfate, 18 % PEG The crystals appeared within 2 days and matured within two weeks to a final size of 200 x 30 x 30 µm. Diffraction data was collected at 2.6 Å resolution at a wavelength of Å using a PILATUS 6M detector at the beamline X10SA of the Swiss Light Source (Paul Scherrer Institute, Villigen, Switzerland). XDS 45 was used for data processing and SADABS (Bruker) was used for scaling instead of SCALA 44. Initial phase information was obtained by molecular replacement using the coordinates of the 3.0 Å resolution structure of apo chicken ASIC1 (PDB ID: 3IJ4 10 ) as a search model. After placement of the model and initial rigid body refinement using PHASER 46, the model was rebuilt with COOT 47 and refinement was continued with the PHENIX suite 43 including positional, TLS, and individual B-value refinement. TLS groups were identified automatically during refinement and included glycosylation at Asn367 and Asn394. NCS-restrains were applied for the extracellular domains (residues ), except for those regions with clear differences in side-chain conformations due to crystal contacts. The secondary structure of the flexible terminal transmembrane helices (residues and ) was kept helical by restraining their dihedral angles during refinement. The quality of the model was assessed using the Ramachandran plot in COOT (no outliers, 3.2% allowed), the rotamer analysis in COOT (13 outliers) and the Cα deviations in PHENIX (maximum in the model: 0.16 A, target: all residues <0.25A) (Supplementary Table S2). The structure was deposited under the PDB ID 3S3W. Supplementary References 43. Zwart, P. H. et al. Automated structure solution with the PHENIX suite. Methods Mol. Biol. 426, (2008).

17 44. Kabsch, W. Xds. Acta Cryst. D Biol. Cryst. 66, (2010). 45. The CCP4 suite: programs for protein crystallography. Acta Cryst. D Biol. Cryst. 50, (1994). 46. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, (2007). 47. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Cryst. D Biol. Cryst. 60, (2004).