An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions

D. Molodenskiy; H. Mertens; D. Svergun

To test the modelling components of the AMPP, we performed an automatic structural characterization of a tetrameric α-helical membrane channel Aquaporin0 in DDM solution. The AMPP was utilized in all three pipeline regimes: i) with the high resolution model available ii) with detergent composition and the protein primary structure (FASTA sequence) known iii) plain ab initio modelling (no a priori information). The models generated from these three modelling trajectories are displayed in Figure 6 (as the protein was known to be tetrameric, P4 symmetry was utilized in MONSA and DAMMIF). Figure. 6. Examples of automatically reconstructed Aquaporin0 PDC models by the AMPP pipeline utilizing MEMPROT (hybrid modeling with known protein model (PDB:2B6P) and unknown detergent belt) (A), MONSA (multi-phase ab initio, the model was built from precalculated searching volume; fourfold symmetry around z-axis is imposed) (B) and DAMMIF(C) (single phase ab initio also with P4 symmetry applied). The first row shows the side view cross-section of the PDC components that is represented with a section inside the detergent corona; protein beads are green for ab initio models and colored according to atom type for the hybrid model, detergent tails and heads are blue and red, respectively. The second and third rows represent the top and the side view of the models.