Contacts from the SASREF model of the TPR domain dimer were used

Modeling of the barley SGT1 dimer was performed using the CORAL program from the ATSAS package, and the scattering curve was obtained from the MCR-ALS analysis. CORAL combines two algorithms, rigid body modeling from SASREF and multidomain protein modeling using rigid body and ab-initio modeling from BUNCH, to model multiple chain and domain proteins. With the CORAL program, it is possible to model multichain protein complexes without imposing any symmetry. In the CORAL runs, contacts from the SASREF model of the TPR domain dimer were used as an additional constraint, and no symmetry was imposed. The use of ab-initio modeling was QS11 necessary because there is no structural model of the barley SGT1 protein. The structure of the three domains of the barley SGT1 protein was modeled using the ab-initio modeling platform QUARK and meta-threading approach approach implemented in I-TASSER, which were chosen because are ranked as the best platform in the free-modeling and protein prediction competition in CASP9. The structural model of the TPR domain of barley SGT1 is very similar to the known structures of other TPR domain-containing proteins. The model of the TPR domain has a typical fold consisting of three helix-turn-helix motifs, with a solvating helix at the C terminus. The model of the CS domain is similar to the structure of the CS domains from human and Arabidopsis SGT1 homologs and has a typical beta sandwich structure. The structure of the barley SGS domain consists of a three-helix bundle and regions with no secondary structures at the C terminus; this structure corroborates NMR spectroscopic results showing only a limited a-helical secondary structure content in the NMR spectrum of the isolated human SGS domain. The predicted dimer has a open topology, as shown in Figure 3E, and is distinct from the crystal structure of the CTPR3Y3-engineered TPR domain, which forms open superhelical oligomers. The interface between TPR domains are formed only by residues from B3 and B39 helices.In Figure 3F are also 5-hydroxymethyl-2-furaldehyde presented the results of direct comparison of theoretical scattering curves for TPR dimer and monomer with experimental SAXS data. A high ionic strength environment can influence these interactions and prevent SGT1 dimer formation, which substantiates our SAXS measurements, as well as the results of the Kleanthous and Shirasu laboratories.