Supplementary Material

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1 Gangabadage et al., Structure and Dynamics of Human Apolipoprotein C-III Supplementary Material Table S1. ApoCIII average order parameters of helices from relaxation data measured at two magnetic fields and comparison with lipid affinity as defined via class A and G* and via hydrophobic moment and charge interactions. class 2 S f 2 S s S 2#1 #2 H M #3 C M <H M +C M > H1 $1 G* H2 G* H3 G* H4 A H5 $3 A H6 G* mean std H1a $2 G* H1b G* #1 S 2 is the over all squared order parameter (= S 2 f*s 2 s); #2 H M total hydrophobic moment of each helix in the final structure scaled to 10 residues; Kyte and Doolittle hydrophobicity scale is used (see Materials and Methods); #3 C M, number of anchoring residues per helix (see main text); $1 h1 (8-18), h2 (20-29), h3 (34-43), h4 (47-53); h5 (55-64), h6 (74-79); $2 h1a (9-12) and h1b (13-18). For h1 distinction 1a and 1b is made because its N-terminal contains a cluster of strongly hydrophobic residues. $3 Helix h5 is located next to a highly flexible loop, which affects its C-terminal residues; consequently, the S 2 values of 63 and 64 are lower and have been left out for calculating the average.

2 Table S2a. Structure characteristics for top 10 (0f 100) structures apoc-iii in complex with SDS micelle calculated using all experimental restraints obtained from NMR (noe, cdih,jcoup, rdc) Total number of experimental restraints noe 185 (threshold: 0.5) cdih 154 (threshold: 2.0) jcoup 74 (threshold: 1.0) rdc 70 (threshold: 0.5) Energy Name energy (dev) rmsd (dev) Viols (dev) Total ( 9.6) 0.70 ( 0.04) 84.9 ( 7.3) Bond 17.8 ( 1.3) 0.00 ( 0.00) 0.0 ( 0.0) Angle 92.2 ( 6.9) 0.53 ( 0.02) 16.1 ( 5.9) Impr 33.6 ( 4.4) 0.58 ( 0.04) 10.1 ( 2.5) Vmd 34.4 ( 4.8) 0.40 ( 0.50) Rama ( 9.3) Noe (13.1) 0.19 ( 0.01) 7.5 ( 0.7) Cdih 33.7 ( 8.9) 1.88 ( 0.25) 11.9 ( 2.9) Jcoup (11.5) 1.40 ( 0.06) 33.4 ( 3.5) Rdc 27.6 ( 3.9) 0.28 ( 0.02) 5.5 ( 1.9) Rmsd backbone rmsd (dev) hydmom (dev) helix 1 (8-18) ( 0.23) ( 0.14) helix 2 (20-29) ( 0.43) ( 0.14) helix 3 (34-43) ( 0.28) ( 0.32) helix 4 (46-53) ( 0.46) ( 0.19) helix 5 (55 65) ( 0.64) ( 0.47) helix 6 (74 79) ( 0.21) ( 0.05) residue ( 7.65) Energies in kcal/mole, rmsd in Å or degrees (where applicable); Hydrophobicity scale used: Kyte & Doolittle.

3 Table S2b. Structure characteristics of the top 10 (of 50) global structures of apo-ciii on SDSmicelle calculated using all experimental constraints obtained from NMR measurements (noe, cdih, jcoup, rdc) and positioned on the model of SDS-micelle using additional restraints, physical-theoretical (hydrophobic moments directions) and geometrical (size of the micelle with radius Å). Total number of experimental restraints as in Table 1 Energies (1 structure) name energy (dev) rmsd (dev) Viols (dev) total (20.26) ( 0.009) ( 5.9) bond ( 1.51) ( 0.000) 0.0 ( 0.0) angle ( 4.28) ( 0.011) 24.3 ( 4.6) impr ( 2.26) ( 0.017) 15.7 ( 2.2) vdw ( 3.75) 1.0 ( 0.7) rama (15.71) noe ( 6.13) ( 0.004) 6.8 ( 0.4) Cdih ( 1.79) ( 0.052) 12.4 ( 0.8) jcoup ( 8.03) ( 0.036) 34.0 ( 0.9) rdc ( 1.99) ( 0.010) 6.5 ( 1.2) Rmsd backbone rmsd (dev) hydmom (dev) Helix1 (8-18) ( 0.041) ( 0.084) Helix2 (20-29) ( 0.012) ( 0.070) Helix3 (34-43) ( 0.081) ( 0.113) helix4 (46-53) ( 0.071) ( 0.145) helix5 (55-65) ( 0.032) ( 0.107) helix6 (74-79) ( 0.090) ( 0.021) residue ( 0.316) Energies in kcal/mole, rmsd in Å or degrees (where applicable). Hydrophobicity scale used: Kyte & Doolittle. In refinement the lower bound on noe restraints put uniformly to 2 Å.

4 Table S3. Comparison of amino acids of the LDL receptor-binding sites on RAP (2) with sites on apoe, apob and putative site apoc-iii. Site 1 Sequence 2 Charge 3 G bind 4 R-site (252) Ala Lys Ile Glu Lys His Asn His Tyr (260) 4(2-3) 12(6-9) E-site (142) Arg Lys Leu Arg Lys Arg Leu Leu Arg (150) 6(3-5) 18(9-15) A-site (3147) Lys Ala Gln Tyr Lys Lys Asn Lys His (3155) 5(2-3) 15(6-9) B-site (3359) Arg Leu Thr Arg Lys Arg Gly Leu Lys (3367) 5(3-4) 15(9-12) CIII-site (17) Lys His Ala Thr Lys Thr Ala Lys Asp (25) 3(1-3) 9(3-9) 1 The R- and E-site represent LDL receptor binding sites on RAP and apoe, respectively, the A- and B-sites those on apob100, and the CIII-site represents the putative weak binding on apo CIII. 2 Between brackets, amino acid position of first and last residue of the receptor-binding site. Positively charged amino acids are depicted in bold and Lysine residues that bind or are putatively binding into the Lys-pocket on the receptor are depicted boxed, K-motif; Lys-residues that aid (R-site) or putatively aid in stabilizing the interaction by direct contact are underlined. 3 The net positive charge of each site; between brackets, the number of direct interaction of K- motif and plus aiding residue as derived from R-site. Because the interaction is mostly coulombic, the overall net positive charge is likely to be significant for the strength of the interaction with the negative charged receptor domain. As can be seen the CIII-site has the lowest net positive charge (3), while the E-site has the highest positive charge (6). 4 Taking an average charge-charge distance of 7 Å and 3 negative charges on the receptor domain, the unscreened coulombic free energy of interaction amounts to 3xCharge kt-units per molecule. Between brackets are the numbers for the direct interaction site and plus aiding residue as derived from R-site.

5 Table S4: NMR spectral parameters used for 15 N/ 13 C apoc-iii in SDS micelle complex Experiment a SW b (Hz) SW1 b (Hz) SW2 b (Hz) xt c yt c zt c scans d xcar e (ppm) ycar e (ppm) zcar e (ppm) Processed size f CBCACONH H C N 4096/256/256 HNCACB H C N 4096/256/256 HNCO H C N 4096/256/256 HNHA H H N 4096/256/256 NOESY(1) H H N 2048/256/256 NOESY(2) H N N 2048/256/256 a Name of the experiment. The triple resonance experiments (frequency-labeled nucliei underlined) were recorded on Varian INOVA spectrometer operating at MHz 1 H frequency; the two NOESY experiments were recorded at Varian INOVA spectrometer operating at MHz 1 H frequency. NOESY(1) and NOESY(2) stand for 15 N-NOESY-HSQC, and 15 N- HSQC-NOESY-HSQC, respectively, both recorded with a NOESY mixing time of 120 ms. All the spectra were recorded at 42.7 C. b SW, SW1 and SW2 are the spectral widths (in Hz) for acquisition dimension (x) and indirect dimensions 1(y) and 2 (z), respectively; c xt, yt and zt are number of real points acquired in each dimension, d number of scans, e xcar, ycar and H, C, N zcar are positions of the carrier frequencies in x, y, and z dimensions; the superscripts denote 1 H, 13 C, and 15 N nuclei, respectively; f final size of the data matrix after processing in x, y and z dimensions.

6 Figure S1. Summary of apociii 15 N backbone relaxation data (T1, T1rho and NOE) measured at 42.7 C at 600 and 800 MHz of apociii in complex with SDS micelle Errors in the data are as indicated by the error bars and derived from multiple measurements as described in Materials and methods. Figure S2. Comparison of anchoring residues of the class A and G* helices of human apociii, apocii, and apoci For apociii, the global structure in complex with SDS micelle as derived in this paper is shown and for apocii, the global structure in complex with SDS micelle as derived by Zdunek et al. (3). The micelle is depicted as a green grey sphere. For apoci is shown, the structure of apoci in complex with SDS micelle by Rozek et al., which is based on shortrange (secondary structure) NMR data of (4). Here no global features were derived and therefore the micelle is not shown. The helices are shown as indicated in the respective papers with positively and negatively charged residues highlighted in blue and red, respectively. ApoC-III contains two class A helices (h 4 and 5) and three class G* helices (h 1, 2, and 3); helix 6 is of minor importance. In the class A helices 4 and 5, the positive residues reside at the polar non-polar interface, and all negative residues line the polar face (solvent-exposed). These are termed anchoring residues (see Table S1 and text for definition). H 4 and 5 have 2 to 3 anchoring residues, respectively (Table 2). Class G* helix 3 contains one positive residue at the polar to non-polar face interface (R40). Class

7 G* helices 1 and 2 contain each one anchoring residue (Table 2), H18 (h1) and D25 (h2). This leads to 1 anchoring residue per class G* helix. At the transition between the h1 and h2 three solvent-exposed Lys residues are present (K17, K21, K24). ApoC-II, contains three class A helices (helix 1a/b and 2). In these helices, all positive residues (K,R,H) reside at the polar to non-polar interface and can thus interact with the lipid head groups. The negative residues (D, E) line the polar face (solvent-exposed face). This leads to 3 anchoring residues for helix 1a, 1b and 2 (Table 2). ApoCI contains two long class A helices (helix 1, res 7-30, and helix 2, 37-52/54). For reason of comparison with apo CII and CIII, the helices have subdivided into two ca residues each, helix 1, 7-19, helix 1, 20-30, helix 2, 37-45, and helix 2, 46-54, as also indicated in Table2. Also in apoci the positive residues line the polar to non-polar interface and can interact with the negative lipid head groups, while negative residues line the solvent exposed face. This leads to 5, 6, 4 and 6 anchoring residues for helices 1, 1, 2, and 2, respectively (Table 2).

8 Materials and Methods Expression of 13 C, 15 N-labeled apociii ApoCIII was expressed from a pet23b vector (a kind gift from Dr Philippa Talmud, London, UK), containing the full-length cdna for human apociii including the sequence for a hexa-his tag at the 3 end (C-terminal hexa-his tag) preceded by two additional amino acid residues (Leu and Glu) (5). The vector was transformed into competent E. coli cells (BL 21 (DE 3)-RIL) and used to inoculate an overnight culture in LB medium with carbenicillin (50 µg/ml) at 27ºC. Bacteria from 12.5 ml of this culture were sedimented by centrifugation at 3000 rpm for 5 min at +4ºC and then suspended in 10 ml Silantes E. coli-od2 medium without 13 C and 15 N (Silantes GmbH, München, Germany). The whole suspension was then added to 1 L of the isotope-containing E. coli OD2 CN medium (Silantes) with carb (50 µg/ml) and incubation was carried out under gentle shaking for 3.2 h when the OD 600nm was Expression was induced by addition of IPTG (1 ml of 0.5 M) and incubation was continued at 37ºC for another 30 min. The culture medium was put in ice for 30 min and then centrifuged at 3500 rpm for 20 min. The sedimented bacteria were suspendend in 65 ml 6 M guanidinium chloride, 0.1 M phosphate, 0.01 M Tris, ph 8. After 4 h in room temperature, the suspension was frozen (-20ºC) until further processing. Extraction and purification of recombinant apociii The extracted bacteria were thawed in room temperature and briefly sonicated before centrifugation at rpm for 30 min (20ºC). The supernatant was recovered and mixed with 4 ml Ni-NTA-agarose (Qiagen GmbH) equilibrated in 6 M guanidinium chloride,

9 0.1 M NaH 2 PO 4, 0.01 M Tris, ph 8, at room temperature overnight. The remaining pellet was in the mean time extracted in 5 ml buffer containing 6 M guanidinium chloride and the supernatant was recovered and stored frozen until later. The Ni-NTA-agarose gel was packed in a small column and was first washed with the equilibration buffer until the OD 280 was less than 0.06 and the column was then eluted with 8 M urea in 0.1 M NaH 2 PO 4, 0.01 M Tris, ph 4.5. Fractions of 2 ml were collected and fractions with an OD 280 > were pooled. The efficiency of the expression and the purification on the Ni-NTA-agarose column was analyzed by electrophoresis on SDS-Tricine gels stained by Gel Code blue stain reagent (Pierce) or Invision His-tag in gel stain (Invitrogen), or by transfer to Bio Trace NT membranes (Pall Gelman Science) and Western blotting with a rabbit antiserum raised against human apociii 2 isolated from plasma (6). For further purification, especially for removal of a previously identified His-rich E-coli protein (7), the pooled fractions were dialyzed against 6 M urea, 10 mm Tris-Cl, ph 8.2 at +9ºC for 20 h with 3 changes of buffer. The final sample (23 ml) had an OD 280 of 0.43 and was applied on a 10 ml column of DEAE-Sephacel (Amersham Biosciences) equilibrated in the same buffer (with urea). The unbound material was recycled once through the column and after this the binding efficiency was about 75 %. The column was eluted with a linear gradient of Tris from 50 mm to 110 mm in 6 M urea, ph 8.2 (40 ml +40 ml). Fractions containing apociii (analyzed by Western blotting) corresponding to the second protein peak eluted from the column, were pooled (total volume 24 ml) and dialyzed for 60 h at +4ºC against a total volume of 5 L 10 mm ammoniumbicarbonate in tubing with a cut off at 3.5 kda (Spectram Laboratories Inc., Canada). The sample was then lyophilized for 96 h and resulted in about 1.5 mg dry powder. The second extract from the bacteria pellet

10 processed in the same way did not result in significant additional material and was therefore discarded. For this study, two batches of ca. 1.5 mg isotope-labeled apoc-iii were prepared as described above. References 1. Segrest, J. P., Jones, M. K., Deloof, H., Brouillette, C. G., Venkatachalapathi, Y. V. & Anantharamaiah, G. M. (1992) J. Lipid Res. 33, Fisher, C., Beglova, N. & Blacklow, S. C. (2006) Mol. Cell 22, Zdunek, J., Martinez, G. V., Schleucher, J., Lycksell, P. O., Yin, Y., Nilsson, S., Shen, Y., Olivecrona, G. & Wijmenga, S. (2003) Biochemistry 42, Rozek, A., Sparrow, J. T., Weisgraber, K. H. & Cushley, R. J. (1999) Biochemistry 38, Liu, H. Q., Talmud, P. J., Lins, L., Brasseur, R., Olivecrona, G., Peelman, F., Vandekerckhove, J., Rosseneu, M. & Labeur, C. (2000) Biochemistry 39, Bengtsson-Olivecrona, G. & Olivecrona, T. (1991) Methods Enzym. 197, Shen, Y., Lookene, A., Nilsson, S. & Olivecrona, G. (2002) J. Biol. Chem. 277,