Volume 110, Issue 1, Pages 85-94 (January 2016) Apolipoprotein C-II Adopts Distinct Structures in Complex with Micellar and Submicellar Forms of the Amyloid-Inhibiting Lipid-Mimetic Dodecylphosphocholine  Timothy M. Ryan, Michael D.W. Griffin, Duncan J. McGillivray, Robert B. Knott, Kathleen Wood, Colin L. Masters, Nigel Kirby, Cyril C. Curtain  Biophysical Journal  Volume 110, Issue 1, Pages 85-94 (January 2016) DOI: 10.1016/j.bpj.2015.11.007 Copyright © 2016 Biophysical Society Terms and Conditions

Figure 1 Aggregation of apoC-II. (A) Measurement of the aggregation of apoC-II (2mg/mL) in the absence (circles) and presence of submicellar (0.25 mM, squares) or micellar DPC (10 mM, triangles) was conducted using a point-based ThT fluorescence assay. (B) The ThT measurement of the final point of the time course (solid bars) was confirmed using a pelleting assay, where the protein concentration of the supernate (gray bars) and pellet (open bars) was measured after centrifugation at 100,000 × g, via BCA assay. Biophysical Journal 2016 110, 85-94DOI: (10.1016/j.bpj.2015.11.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 2 SAXS analysis of the apoC-II/DPC complex. (A) SAXS data acquired at the Australian Synchrotron for apoC-II in complex with submicellar DPC (circles). The solid lines represent the DAMMIN fit of the data. (B) the Kratky plot of the data in (A) is consistent with a globular structure. (C) Guinier plot of the data in (A), indicating an Rg of 32.1 Å. (D) P(r) generated from the data in (A), indicating a Dmax of ∼100 Å and an Rg of ∼31.8 Å. (E and F) The de novo structure of apoC-II in complex with DPC generated by DAMMIN (long axis, E; short axis, F). To see this figure in color, go online. Biophysical Journal 2016 110, 85-94DOI: (10.1016/j.bpj.2015.11.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 3 SANS analysis of the apoC-II/DPC complex. (A) SANS data acquired at ANSTO for apoC-II in complex with submicellar DPC (circles). The solid lines represent the GNOM fit (red) and the MONSA fit (blue) of the data. (B) The Kratky plot of the data in (A) is consistent with a globular structure. (C) Guinier plot of the data in (A), indicating an Rg of 32.4 Å. (D) P(r) generated from the data in (A), indicating a Dmax of ∼98 Å and an Rg of ∼31.2 Å. (E and F) The de novo structure of apoC-II in complex with DPC generated by MONSA (long axis, E; short axis, F). To see this figure in color, go online. Biophysical Journal 2016 110, 85-94DOI: (10.1016/j.bpj.2015.11.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 4 SANS analysis of DPC micelles in 40% D2O. (A) SANS data for DPC micelles alone (black circles) and DPC micelles in the presence of apoC-II (blue circles). Solid lines indicate the GNOM fits generated during calculation of P(r) (Red: DPC alone, orange: DPC + apoC-II). (B) P(r) for DPC micelles alone (red line), and for DPC micelles + apoC-II (black line). (C) Guinier analysis for DPC micelles alone (black circles, red line) and in the presence of apoC-II (blue circles, orange line). The two data sets are offset for clarity, but otherwise overlay. (D) Fit of DPC micelles to a BODIES model indicating that the data is consistent with a sphere with a diameter of 40 Å. (E) CRYSON fit to a MD simulation of a DPC micelle containing 54 individual DPC molecules. (F) DPC micelle structure used for CRYSON fit in (E). To see this figure in color, go online. Biophysical Journal 2016 110, 85-94DOI: (10.1016/j.bpj.2015.11.007) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 5 SANS analysis of apoC-II structure in association with DPC micelles. (A) Data acquired for apoC-II in nondeuterated buffers. Solid line represents the MONSA fit (red line) and the CRYSON fit (blue line). (B) Kratky plot of the data in (A). (C) Guinier analysis, indicating an Rg of 20.6 Å. (D) P(r) calculated using GNOM, representing the ensemble of apoC-II structures likely to be present in the sample. (E–G) indicate various views of the top 10 NMR structures (various colors in cartoon format) represented in PDB: 1SOH superimposed with the de novo scattering envelope for apoC-II calculated using MONSA (gray transparent spheres). To see this figure in color, go online. Biophysical Journal 2016 110, 85-94DOI: (10.1016/j.bpj.2015.11.007) Copyright © 2016 Biophysical Society Terms and Conditions