Summary of effects of SDS on ataxin-3 aggregation.

<p>Schematic summarizing the effects of micellar and non-micellar SDS on both stages of ataxin-3 aggregation.</p

Native Page analysis of M and Z α₁AT under HDX conditions.

<p>M and Z α₁AT were incubated in D₂O buffered with 10 mM Tris (pD 8) at 25°C for up to 2500 seconds. Samples of the proteins were then analyzed by 10% Native PAGE. (A): M α₁AT t = 0 seconds; (B) M α₁AT t = 2500 seconds; (C) Z α₁AT t = 0 seconds; (D) Z α₁AT t = 2500 seconds and (E) Z α₁AT polymers purified directly from <i>P. Pastoris</i> 10].</p

Summary of differences in HDX between M and Z α₁AT.

<p>The structure of α₁AT (PDB: 1QLP) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102617#pone.0102617-Elliott1" target="_blank">[24]</a> with Red spheres: regions showing increased HDX in Z. Dark blue: regions showing decreased HDX in Z. Cyan: regions showing no significant difference between M and Z. Grey: regions for which no peptides were analyzed.</p

Details of the peptides derived from pepsin digestion and tandem mass spectrometry experiments.

<p>The relative masses used in this study were determined using Sequest.</p><p>Details of the peptides derived from pepsin digestion and tandem mass spectrometry experiments.</p

Aggregation of ataxin-3 in the presence of SDS monitored by SDS-insolubility.

<p>Formation of SDS-insoluble fibrils was followed by taking aliquots from a 30 µM ataxin-3(Q64) timecourse assay at 37°C, pH 7.4. (A) A representative filter-trap membrane of ataxin-3(Q64) with 0–10 mM SDS is shown. QBP1 was added to a ataxin-3(Q64) containing 5 mM SDS as indicated. (B) Analysis of the filter trap membrane by densitometry. Ataxin-3(Q64) is shown with the addition of 0 mM SDS(-▪-), 1 mM SDS(-▴-), 5 mM SDS (-♦- ), 5 mM SDS with QBP1 (-◊-) and 10 mM SDS (-•-). Results from three independent experiments were fit to an exponential curve.</p

Far-UV CD spectra of ataxin-3 variants in increasing concentrations of SDS.

<p>The far-UV CD spectra for (a) ataxin-3(Q64), (b) ataxin-3(Q15) and (c) Josephin were measured at 37°C with increasing concentrations of SDS; 0 mM SDS (<i>black solid line</i>), 1 mM SDS (<i>black dotted line</i>), 5 mM SDS (<i>grey solid line)</i> or 10 mM SDS (<i>grey dashed line</i>). The final protein concentration was 30 µM and the spectra measured with a path length of 0.1 mm.</p

Regions in α₁AT that are affected by the Z mutation.

<p>(A) Peptides that displayed decreased exchange in Z α₁AT (Red) compared to M α₁AT (Black); (B) Peptides that displayed enhanced exchange in Z α₁AT (Red) compared to M α₁AT (Black) at 10 sec. (C) The structure of α₁AT (PDB: 1QLP) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102617#pone.0102617-Elliott1" target="_blank">[24]</a> indicating residues with an increased D₂O uptake in Z (red) and decreased D₂O uptake in Z (Blue) after 10 seconds of incubation in D₂O.</p

Peptic fragments derived from α₁AT that show comparable exchange kinetics in M and Z α₁AT.

<p>(A) The kinetics of deuterium incorporation into M α₁AT (black) and Z α₁AT (red) by individual peptic fragments which show comparable exchange are shown. The individual data points are the average of three independent experiments for clarity the error bars are not shown. (B) Crystal structure of M α₁AT (PDB: 1QLP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102617#pone.0102617-Elliott1" target="_blank">[24]</a>) indicating the location of peptic fragments with comparable exchange highlighted in red.</p

Midpoints of ataxin-3(Q64) aggregation.

<p>Midpoints of ataxin-3(Q64) aggregation.</p

Differences in hydrogen exchange at 2000 seconds between M and Z α₁AT.

<p>The amino acid sequence of α₁AT is shown with secondary structure highlighted above the sequence. The 18 peptides used in the study are noted, as double headed arrows. The peptides for both M and Z α₁AT are colored according to the percentage deuterium incorporation at 2000 seconds: class 1 80–100% (red), class 2 30–80% (yellow) and class 3 0–30% (blue).</p