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. 2023 Nov 6;14:7152. doi: 10.1038/s41467-023-42601-y

Fig. 2. All-atom molecular dynamics simulations with native VpOmpM1.

Fig. 2

a The AlphaFold2 prediction for the stalk (grey) was grafted onto the N-terminus of the first residue (L100) modelled into the experimental density of native VpOmpM1 (in colour). R64 (bottom of SLH domain) and R113 are shown as space filling models. b Bird’s-eye-view of the β-barrel region from outside the OM (left) and a plot of the stalk end projection (centre of mass of the R64 Cα atoms) over the 1 μs simulation (right). The observation point in the left and right panels is equivalent. c Frequency distribution of stalk lengths (R64-R113 Cα-Cα) observed throughout the simulation. d Distances between the R113 sidechain and interacting sidechain atoms throughout the simulation. The dotted line denotes an inter-atomic distance of 3 Å. The equivalent plots for a replicate simulation and a simulation without the AlphaFold2 graft are presented in Supplementary Fig. 5.