Using a novel SAXS data analysis method, we were able to extract the pure scattering function of the monomeric and dimeric forms and to create low-resolution models using ab-initio methods. Two independent programs, DAMMINv51 and GASBOR v22, were used to determine the low-resolution structures of the monomeric and dimeric forms of full-length barley SGT1 in solution. In total, 15 independent DAMMIN bead models were calculated to check the stability of the solution. The models obtained from DAMMIN were averaged to determine the most typical shapes of the SGT1 monomer and dimer forms, using the programs DAMAVER and SUPCOMB. Another program used for the reconstruction of the low-resolution structure of SGT1 was GASBOR. The procedure for the determination of the structural models in GASBOR is based on a similar strategy as in DAMMIN, but the models are built as a chain-compatible spatial arrangement of the dummy atom residues. The number of dummy residues was equal to the number of C atoms. To estimate the degree of the dynamics and conformational heterogeneity of the monomeric and dimeric forms of SGT1, we analyzed the SAXS data using an ensemble optimization method. This method randomly generates a large number of models of multidomain proteins using the rigid body approach. In the next step, the fraction of the models that creates an ensemble with the best fit to the experimental data is selected using a genetic algorithm. To confirm the barley SGT1 models obtained from ab initio modeling, we also applied rigid body modeling, using the program BUNCH from the ATSAS package. SGT1 domains were modeled using the protein structure prediction servers QUARK and I-TASSER. In the rigid body modeling, the flexible regions between the rigid domains were represented as dummy residues, with no structural Trimethadione constraints. Modelling of the TPR dimer against SAXS data was performed in SASREF 6.0 from ATSAS package with imposed P1 or P2 symmetry using the structural model of TPR domain Acetylcimigenol-3-O-alpha-L-arabinopyranside generated by Quark and SAXS data.The data set of 15 independent TPR domain dimer models was generated. All models have almost the same structure. Molecular contacts calculated from SASREF model were further used in rigid body modelling program CORAL.
The procedure for the determination of the structural models
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