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Published Erratum
. 2022 Apr 19;121(8):1576-1579.
doi: 10.1016/j.bpj.2022.03.035. Epub 2022 Apr 8.

Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data

Francesco Pesce, Kresten Lindorff-Larsen
Published Erratum

Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data

Francesco Pesce et al. Biophys J. .
No abstract available

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Figures

Figure 1
Figure 1
Reweighting ensembles using SAXS data calculated using different values for the parameters that effect the contribution from the hydration layer and displaced solvent. The grids show the results from the iBME ensemble optimization with different combinations of δρ and r0/rm, where rm is the average atomic radius (Table S2). The top row (a–c) shows Hst5, the second row (d–f) shows Sic1, the third row (g–i) shows Tau, and the last row (j–l) shows results for TIA1. For each protein, we show in the first column (a, d, g, and j) χr2, we show in the second column (b, e, h, and k) φeff, and we show in the third column (c, f, i, and l) γ=ln(χr2φeff). White spots correspond to ensembles in which the iBME reweighting failed. To see this figure in color, go online.
Figure 2
Figure 2
Comparing ensembles relative to the optimum. For each protein (a: Hst5, b: Sic1, c: Tau and d: TIA1) we calculated the effective fraction of frames (shown here as φeff) between the weights obtained using the parameters in Table 1 and the weights obtained at all other combinations of r0/rm and δρ. White spots correspond to ensembles in which the iBME reweighting failed. Purple spots correspond to the minima for γ. To see this figure in color, go online.
Figure 3
Figure 3
Effect of the δρ and r0 parameters on reweighted probability distributions of Rg. We use Sic1 as an example and show p(Rg) from both the optimal (lowest γ) parameters (blue) as well as three other choices of r0 and δρ in the low-γ region (orange, green, and red). The insert shows the parameters used in each case and the results of the reweighting on the Rg distribution. To see this figure in color, go online.
Figure 5
Figure 5
Reweighting α-Synuclein ensembles using SAXS data calculated using different values for the parameters that effect the contribution from the hydration layer and displaced solvent. The grids show the results from the iBME ensemble optimization with different combinations of δρ and r0/rm. The top row (a–c) shows the results from the flexible-meccano ensemble, the second row (d–f) shows the results using a99SB-disp as the prior, and the third row (g–i) shows the results from a03ws as the prior. For each ensemble we show in the first column (a, d, and g) χr2, in the second column we show (b, e, and h) φeff, and in the third column (c, f, and i) we show γ=ln(χr2φeff). White spots correspond to ensembles in which the iBME reweighting failed. Purple spots in the third column correspond to the minima for γ. To see this figure in color, go online.
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