Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints
Fig 4
Models of PfMATE obtained using multilaterated rotamers more closely resemble the inward-facing crystal structure than those obtained using default rotamers.
Deviation between Cα-Cα distances observed between representative pairs of residues on the A) extracellular and B) intracellular sides of the crystal structure (PDB: 6FHZ) and the corresponding distances predicted from each of the best-scoring models. (C and D) Best-scoring inward-facing models of PfMATE obtained using ten restraints either with pseudo-rotamers available by default (left) or with those refined by multilateration (right). Inward-facing crystal structure shown in black. Ribbon thickness corresponds to the Cα root mean squared fluctuation among the top ten models. Bottom: The best-scoring models obtained using default rotamers (left) were less inward-open than those obtained using multilaterated rotamers (right).