An Integrated Framework Advancing Membrane Protein Modeling and Design
Fig 6
MPrelax for high-resolution refinement of a membrane protein.
(A) FoldTree representation for the MPrelax protocol with the residue closest to the center-of-mass of the protein being at the root of the FoldTree (circled X). The membrane residue (M) is attached via a flexible jump edge (dashed arrow). Protein chains are shown as gray boxes with N- and C- termini marked and peptide edges shown as solid arrows. (B) Rosetta total score vs. backbone RMSD to the crystal structure for 1000 models of meta-rhodopsin. Models in blue are created with the original membrane relax protocol of RosettaMembrane; models in red are created with MPrelax. (C) Crystal structure of meta-rhodopsin in gray (PDB 3pxo) superimposed with the lowest scoring models from both the original RosettaMembrane protocol (blue) and the MPrelax protocol (red).