Supporting Information Oxaliplatin binding to human copper chaperone Atox1 and protein dimerization Benny D. Belviso, 1 Angela Galliani, 2 Alessia Lasorsa, 2 Valentina Mirabelli, 1,3 Rocco Caliandro, 1 Fabio Arnesano, 2 and Giovanni Natile 2 1 Institute of Crystallography, Consiglio Nazionale delle Ricerche, via Amendola 122/o, 70126 Bari, Italy. 2 Department of Chemistry, University of Bari A. Moro, via E. Orabona 4, 70125 Bari, Italy. 3 Department of Economics, University of Foggia, Via A. Gramsci 89/91, 71122 Foggia, Italy. Contents Figure SI1. Size exclusion chromatograms of Atox1 treated with cisplatin Figure SI2. ESI-MS spectra of elution fractions obtained by SEC analysis of Atox1 treated with cisplatin Figure SI3. ESI-MS spectra of Atox1 treated with oxaliplatin and then with GSH Figure SI4. 1 H, 15 N-SOFAST HMQC spectra of 15 N-Atox1 apo, monomer and dimer, and 1 H, 15 N-HSQC spectra of 15 N-cisplatin incubated with 15 N-Atox1 Figure SI5. Superposition of the crystal structures containing dimers of Atox1 Figure SI6. H-bond inter dimer interactions Figure SI7. Supramolecular motif of Atox1 monomer superimposed to those of chains A and B of Atox1 dimers Table SI1. Diffraction data statistics of dimeric Atox1-platinum adduct Table SI2. Bond distances for Pt-binding sites in dimeric Atox1-platinum adduct Table SI3. Bond angles for Pt-binding sites in dimeric Atox1-platinum adduct Table SI4. H-bond distances below 3.5 Å between the two chains forming the Atox1 dimer Table SI5. Ionic radii for metal ions present in the tetrahedral cage 1
Figure SI1. Size exclusion chromatograms (SEC) of Atox1 treated with an equimolar amount of cisplatin, recorded at time zero (dashed line) and after 24 h incubation (solid line) (A). SDS-PAGE (4-20%) of monomeric (RV 13.1 ml) and dimeric (RV 11.6 ml) SEC fractions isolated after 24 h incubation of Atox1 with cisplatin. Bands corresponding to monomeric and dimeric protein adducts are indicated by arrowheads showing the molecular weight (B). Figure SI2. ESI-MS spectra and corresponding deconvoluted spectra of elution fractions, having retention volumes of 13.1 ml (A and B) and 11.6 ml (C and D), obtained by SEC analysis after 24 h incubation of Atox1 with cisplatin. 2
Figure SI3. ESI-MS spectra (+8 multiply charged state) of Atox1 incubated with oxaliplatin for 24 h (A) and then treated with 10-fold molar excess of GSH for additional 24 h (B). Figure SI4. 2D 1 H, 15 N-SOFAST HMQC and 2D 1 H, 15 N-HSQC spectra of Atox1 monomeric (B and E) and dimeric (C and F) samples obtained from SEC analysis performed after 48 h incubation of 15 N-Atox1 with 15 N-cisplatin. 2D 1 H, 15 N-SOFAST HMQC spectrum of apo 15 N-Atox1 (A) and 2D 1 H, 15 N-HSQC spectrum of 15 N-cisplatin (D) are also reported. In the spectra of panels D-E, cross-peaks are assigned to 15 NH3 trans to O, Cl, or S donor atoms. Cross-peaks belonging to the same species are connected by a straight line. 3
Figure SI5. Superposition of the crystal structures containing dimers of Atox1. Protein molecules are in ribbon representation while metal ions appear as sphere. Previously published 1FE0, 1FEE, 1FE4, and 3IWX are in red color, whilst the present crystal structure 4QOT is shown in green. The straight lines in the figure result from the linear interpolation of the Cα coordinates of each chain and are shown in the same color code of the protein molecules. Metal ions are Cd for 1FE0, Cu for 1FEE, Hg for 1FE4, Pt for 3IWX and 4QOT. Figure SI6. H-bond inter dimer interactions (H-acceptor/donor maximum distance = 3.5 Å). Interactions are shown as dashed lines between the H-acceptor and H-donor atoms. (a) Interactions between chains A (green) of three different dimers related by symmetry operations (marked by * and **). (b) Interactions between chains B (cyan) of three different dimers related by symmetry operation (marked by *** and ****). The central chains A and B which are partners in a dimer are shown in the same orientation to highlight the differences in orientation of the interacting, symmetry related, chains in the two cases. Platinum ions Pt1 are shown as violet spheres while oxygen, nitrogen, and sulfur atoms are shown in red, blue, and yellow, respectively. Water and sulfate molecules at a distance 3.5 Å from the chain interfaces are shown as red and yellow spheres. Helices, beta-strand, and beta-turn are labeled α, β, and β-turn with a preceding number that indicates their order in the protein chain. 4
Figure SI7. The supramolecular motif found in the crystal structure of the Atox1 monomer (only one chain in the asymmetric unit, PDB code 3IWL) is superimposed (blue cartoon) to the supramolecular motifs formed by chains A (green cartoon) and B (cyan cartoon) of Atox1 dimers. A nearly perfect match is found only for Atox1 monomer and chain B of Atox1 dimer. In order to show the primary metal-binding site for Atox1, the Cys12 and Cys15 are shown as sticks. 5
Table SI1. Diffraction data statistics of crystals obtained from co-crystallization of Atox1 and [Pt(R,R-1,2-DACH)(H2O)(SO4)] in 1:1 ratio (Atox12-platinum adduct). Wavelength (Å) 1.072 Resolution range (Å) 42.5-2.2 Space group P65 Unit cell parameters (Å) a b c 78.055 78.055 54.628 Total number of reflection 37806 Total number of unique reflection 9647 <I/ (I)> 6.5 Rmerge 12.8% Completeness 99.5% Multiplicity 3.9 Table SI2. Bond distances for Pt-binding sites in Atox12-platinum crystals. For atoms involved in platinum binding, the atom name in PDB format, the residue number, and the protein chain are indicated. Distance (Å) Pt1-SG/Cys12/A 2.3±0.2 Pt1-SG/Cys15/A 2.3±0.3 Pt1-SG/Cys12/B 2.3±0.3 Pt1-SG/Cys15/B 2.3±0.3 Pt2-SG/Cys41/B 2.4±0.3 Pt2-O1/SO498/B 1.9±0.3 Pt2-NZ/Lys3/B 2.1±0.4 Pt2-OE1/Glu5/B 2.1±0.4 6
Table SI3. Bond angles for Pt-binding sites in Atox12-platinum crystals. For atoms involved in platinum binding, the atom name in PDB format, the residue number, and the protein chain are indicated. Angle ( ) SG/Cys12/A - Pt1 - SG/Cys12/B 106.4 SG/Cys12/A - Pt1 - SG/Cys15/A 120.4 SG/Cys15/B - Pt1 - SG/Cys15/A 103.9 SG/Cys15/B - Pt1 - SG/Cys12/B 117.1 SG/Cys15/B - Pt1 - SG/Cys12/A 106.5 SG/Cys15/A - Pt1 - SG/Cys12/B 103.2 O1/SO498/B - Pt2 - SG/Cys41/B 95.8 SG/Cys41/B -Pt2-OE1/Glu5/B 87.4 OE1/Glu5/B -Pt2-NZ/Lys3/B 87.0 NZ/Lys3/B - Pt2 - O1/SO498/B 88.2 O1/SO498/B - Pt2 - OE1/Glu5/B 172.0 SG/Cys 41/B -Pt2-NZ/Lys3/B 165.6 Table SI4. H-bond distances below 3.5 Å between the two chains forming the Atox1 dimer in Atox12-platinum crystals. For atoms involved in H-bond interactions, the atom name in PDB format, the residue number, and the protein chain are indicated. Interactions shown in Atom1 Atom2 Distance (Å) Figure 6a NH1/Arg21/B O/Gly59/A 2.7±0.2 OG1/Thr11/A SG/Cys12/B 2.9±0.2 O/Gly14/B O/wat77/A 3.1±0.2 O/Asp9/A O/wat77/A 3.2±0.3 NH2/Arg21/B OG1/Thr61/A 3.5±0.2 Figure 6b OD2/Asp9/B O/wat83/B 2.6±0.3 O/Asp9/B O/wat91/B 2.7±0.3 NH1/Arg21/A O/wat83/B 2.8±0.3 SG/Cys12/A OG1/Thr11/B 2.8±0.3 NH1/Arg21/A O/Gly59/B 2.8±0.3 OG1/Thr61/B O/wat83/B 2.9±0.3 O/wat91/B OG1/Thr11/B 3.1±0.3 N/Thr61/B O/wat83/B 3.2±0.2 NH2/Arg21/A O/wat83/B 3.3±0.3 NH2/Arg21/A OG1/Thr61/B 3.4±0.3 OD2/Asp9/B O/wat91/B 3.5±0.3 Figure 6c O/Thr58/A O/wat70/A 2.6±0.3 O/Thr58/B O/wat70/A 2.9±0.3 NZ/Lys60/A O/wat70/A 3.0±0.3 NZ/Lys60/A NZ/Lys60/B 3.0±0.3 NZ/Lys60/B O/wat70/A 3.4±0.3 7
Table SI5. Ionic radii of metal ions present in the tetrahedral cage of sulfur atoms found in crystal structures of Atox1 dimers, and volumes of the tetrahedron having at the vertices the four sulfur atoms. a Metal ion Ionic radius (Å) Cd 2+ 1.55 7.66 Hg 2+ 1.50 7.02 Cu + 1.35 6.41 Pt 2+ 1.35 6.37 Tetrahedron volume (Å 3 ) a Ionic radii were taken from J.C. Slater (1964) J Chem Phys 41:3199 and from J.C. Slater (1965) Quantum Theory of Molecules and Solids. Symmetry and Bonds in Crystals. Vol 2. McGraw-Hill, New York. 8