Computational protocol: Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP

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[…] Y2H analysis was carried out by Hybrigenics Services S.A and described in SI Materials and methods. Identified partners were analyzed with IUPred (disorder level) and classified using GO annotation (biological process). [...] ID3 was injected into a size-exclusion column equilibrated with buffer of physiological salt concentration and SAXS data were collected continuously, selected frames corresponding to the main protein elution peak were averaged using FOXTROT (buffer scattering subtracted), following data processing/analysis using ATSAS suite and calculation of the radius of gyration by PRIMUS QT. For further details, cf. SI Materials and methods. [...] Secondary structure propensity analysis was calculated from C′, Cα, Cβ and N chemical shifts (95% assigned) by using the neighbor-corrected structural propensity calculator (ncSP) tool. For further details, cf. SI Materials and methods. [...] Ensemble models of ID3 were based on the combination of SAXS data and ncSP derived from experimental chemical shift values. Flexible-Meccano and SCCOMP were used to generate a pool of 9876 semi-random conformations (with side-chains modeled). Then, CRYSOL and the GAJOE algorithm were employed to select subsets of the random pool that that agreed with the experimental SAXS data. For further details, cf. SI Materials and methods. […]

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