Supplemental Information. Structural Basis for the Regulation. of Cysteine-Protease Activity by a New Class. of Protease Inhibitors in Plasmodium

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1 Structure 19 Supplemental Information Structural Basis for the Regulation of Cysteine-Protease Activity by a New Class of Protease Inhibitors in Plasmodium Guido Hansen, Anna Heitmann, Tina Witt, Honglin Li, Hualiang Jiang, Xu Shen, Volker T. Heussler, Annika Rennenberg, and Rolf Hilgenfeld

2 Figure S1, related to Fig. 1

3 Figure S2, related to Fig. 2

4 Supplemental Figures Legends Figure S1. Details on the extended loop L3 of PbICP-C and chemical structure of E64 (A) L3 covers a cluster of hydrophobic residues of the front sheet of PbICP-C. PbICP-C is shown in ribbon representation as in Fig. 1A. Side chains of hydrophobic residues in L3 and front sheet are shown as brown sticks. (B) Interaction of L3 with FP-2. L3 residues form a ridge in vicinity of Phe158p of FP-2 (gray). Contacts between Lys256i, Leu257i, and Phe158p might further stabilize the protease:inhibitor complex. (C) The moieties of the inhibitor E64 that occupy the S1, S2, and S3 subsites of FP-2 are labeled P1, P2, and P3, respectively. The active-site residue Cys42p of FP-2, which is covalently bound to the inhibitor, is highlighted in red. Figure S2. Comparison of FP-2:inhibitor complexes. PbICP-C (ribbon representation) in complex with FP-2 (surface representation, gray) superimposed on FP-2 complexes with chagasin (upper panel, PDB code: 2OUL), cystatin (middle panel, PDB code: 1YVB), and E64 (lower panel, PDB code: 3BPF). Loop regions of chagasin (brown) and cystatin (yellow) are shown in ribbon representation, E64 is shown in stick representation (carbon: yellow, oxygen: red, nitrogen: blue). For clarity, regions of the macromolecular inhibitors not involved in interactions with FP-2 are omitted.

5 Supplemental Experimental Procedures Inhibition studies Prior to inhibition studies, FP-2 was activated by preincubation with 10 mm DTT for 30 min at 37 C, and the concentration of catalytically competent FP-2 was determined by active-site titration with E-64 as described by Abrahamson (1994) using Z-Phe-Arg-(7-amino-4-methylcoumarin) (AMC) (Bachem) as substrate and 100 mm sodium acetate, 10 mm DTT, ph 5.5 as reaction buffer. Subsequently, the molar enzyme inhibitory concentration of Plasmodium ICPs and chagasin was determined by active-site titration with FP-2 under identical conditions. Design of inhibition assays for tight-binding inhibitors was optimized according to Murphy (2004). Briefly, maltose-binding protein (MBP)-tagged PbICP, PbICP-C, PfICP, PfICP-C, and chagasin (8 nm nm) were incubated with FP-2 (110 nm) in reaction buffer for 10 min at 20 C. The assay was started by the addition of Z-Phe-Arg-AMC (30 µm) and product formation was measured for 60 min at 30 C. To evaluate the influence of the MBP-tag, PbICP-C and PfICP-C were assayed after removal of the purification tag by incubation with factor Xa (New England Biolabs). Release of AMC was measured every 10 seconds using a spectrofluorometer (Infinite 200, Tecan) at excitation/emission wavelengths of 340 nm/430 nm. Assays were performed in triplicate. K i values based on initial reaction velocities were determined by nonlinear regression analysis using the quadratic equation describing tight-binding behavior (Morrison equation; Morrison, 1969) as implemented in PRISM (GraphPad Software, San Diego, California, United States). Corrections for substrate competition were made using a K M value of 12 µm determined from six independent measurements (150 nm FP-2, 5-40 µm Z-Phe-Arg-AMC, reaction buffer as above). The determined K M value (12.05 ± 2.30 µm) is identical with previous reports (12.1 µm; Sijwali et al., 2002). As the MBP-tag did not affect the inhibitory activity of PbICP-C or PfICP-C, it was not cleaved prior to inhibition experiments described below.

6 To determine the effect of PbICP-C Mut1-Mut5, papain (Sigma) or FP-2 were incubated with 125 µm Z-Phe-Arg-pNA substrate in the presence of 1 μm PbICP- C Mut1-Mut5. Cathepsin B (Sigma) and E. histolytica lysate (Irmer et al., 2009) were incubated with 145 µm Z-Arg-Arg-pNA (Bachem) in the presence of 1 μm PbICP- C Mut1-Mut5. Assay buffers were 100 mm KH 2 PO 4, 2 mm EDTA, 1 mm DTT, ph 7.0 (papain and E. histolytica lysate), 100 mm KH 2 PO 4, 2 mm EDTA, 10 mm DTT, ph 6.0 (cathepsin B), or 100 mm sodium acetate, 10 mm DTT, ph 5.5 (FP-2). Final concentrations of enzymes with corresponding molar inhibitor:enzyme ratios (I:E) were: ~300 nm, I:E: ~3.3 (FP-2); 180 nm, I:E: 5.6 (papain); 355 nm, I:E: 2.8 (cathepsin B). For assays with E. histolytica lysate, 2-5 µl of a 20 mg/ml stock solution were used per 210 µl reaction volume. All assays were performed in triplicate. Product formation after 10 min incubation was used to calculate the residual protease activity relative to a control sample without protease inhibitor. The effect of 1 µm ICP, ICP-C, or ICP-N from P. berghei or P. falciparum on the activity of FP-2, papain, cathepsin L (V. Turk, Jozef Stefan Institute, Ljubljana), cathepsin B (Sigma), calpain-1 (Calbiochem), caspase-8 (Calbiochem), and caspase- 3 (Calbiochem) was determined using suitable AMC, 7-amino-4- trifluoromethylcoumarin (AFC), or carboxyfluorescein (FAM)-linked peptide substrates in a fluorimetric protease assay. Proteolytic substrates were Z-Phe-Arg- AMC (30.8 µm; FP-2, papain, cathepsin L, cathepsin B), H-Lys(FAM)-Glu-Val-Tyr- Gly-Met-Met-Lys(Dabcyl)-OH (2.5 µm; Calbiochem; calpain-1), Z-Ile-Glu-Thr-Asp- AFC (Calbiochem; caspase-8), and Ac-Asp-Glu-Val-Asp-AMC (25 µm; Calbiochem; caspase-3). Assay buffers were 100 mm sodium acetate, 10 mm DTT, ph 5.5 (FP-2, papain, cathepsin L), 100 mm KH 2 PO 4, 2 mm EDTA, 10 mm DTT, ph 6.0 (cathepsin B), 50 mm Hepes, 250 mm NaCl, 5 mm EDTA, 20 mm CaCl 2, 1 mm DTT, ph 7.0 (calpain-1), or 50 mm Hepes, 100 mm NaCl, 0.1% CHAPS, 100 mm EDTA, 10% glycerol, 10 mm DTT, ph 7.4 (caspases). Final concentrations of enzymes with

7 corresponding molar inhibitor:enzyme ratios (I:E) were: 150 nm, I:E: 6.6 (FP-2); 33 nm, I:E: 30.3 (papain); 64 nm, I:E: 15,6 (cathepsin L); 4 nm, I:E: 250 (cathepsin B); 10 nm, I:E: 100 (calpain-1); 5 nm, I:E: 200 (caspases). Release of AMC, AFC, or FAM was measured as described above with excitation/emission wavelengths of 340 nm/430 nm (AMC), 360 nm/485 nm (AFC), and 485 nm/535 nm (FAM). Assays were performed in triplicate. Protease activity in the presence of the control protein MBP was set to 100% and residual activity in the presence of recombinant ICP variants was calculated. Determination of the angle of approach of PbICP-C relative to FP-2 For comparison of PbICP-C:FP-2 with previously reported chagasin-like inhibitor:protease complexes, the angle of approach (τ) of PbICP-C relative to FP-2 was determined according to Redzynia et al. (2009). The angle of approach was defined as the dihedral angle between two planes, (a) and (b). Plane (a) divides FP-2 into R and L lobes and is defined by Cα atoms of Ile57p, Leu84p, and Trp206p of FP- 2. Plane (b) is defined by Cα atoms of residues in L4 (Gly311i) and L6 (R336i) and residue Thr352i at the C-terminus of PbICP-C. τ was determined with the program GEOMCALC of the CCP4 suite (CCP4, 1994). Supplemental References Abrahamson, M. (1994). Cystatins. Methods Enzymol. 244, Collaborative Computational Project, Number 4 (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, Irmer, H.,Tillack, M., Biller, L., Handal, G., Leippe, M., Roeder, T., Tannich, E., and Bruchhaus, I. (2009). Major cysteine peptidases of Entamoeba histolytica are required for aggregation and digestion of erythrocytes but are dispensable for phagocytosis and cytopathogenicity. Mol Microbiol 72,

8 Morrison, J.F. (1969). Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors, Biochim. Biophys. Acta 185, Murphy, D.J. (2004). Determination of accurate K I values for tight-binding enzyme inhibitors: an in silico study of experimental error and assay design. Anal Biochem 327, Sijwali, P.S., Shenai, B.R., Rosenthal, P.J. (2002). Folding of the Plasmodium falciparum cysteine protease falcipain-2 is mediated by a chaperone-like peptide and not the prodomain. J Biol Chem 277,