Fig. 4. Molecular dynamics simulations.
a, b Representative frames from a 1000-ns MD trajectory overlaid with the model of OX2R bound to full-length OxB (sand). OX2R and OxB ensembles from the simulation are colored gray and yellow, respectively. The amino-terminal α-helix and ECL2 of OX2R are highlighted in cyan and light blue, respectively. Note, in a, OxB was omitted for clarity. c MD-derived density map (orange mesh) of OxB defining the space occupied by the peptide during the simulations, showing that the amino-terminal portion of OxB remains α-helical, but is more flexible than the extended carboxy-terminal portion buried in the OX2R core. d, e Root mean square fluctuation (RMSF) values of α-carbons of OX2R and OxB, respectively, during a representative simulation. f–h Distances between α-carbons of pairs of residues in OxB and OX2R monitored over the course of the same representative simulation. Residue pairs are: Q12(OxB)–F197 (ECL2 of OX2R), Q12(OxB)–E46 (amino-terminal helix of OX2R), and I25(OxB)–F3467.35 (core of OX2R), respectively. A central moving average (window length: 10 ns) of the α-carbon distance for each pair is indicated by a dark blue line. Source data are provided as a Source Data file.