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. 2015 May 5;108(9):2258–2269. doi: 10.1016/j.bpj.2015.03.053

Figure 1.

Figure 1

(A) The AA (left) and CG (middle) representations of the SNARE bundle are shown. Both models include helices Syb, Syx, SN1, and SN2 with each helix contributing one residue to the ionic layer (beads): R56, Q226, Q53, and Q174 respectively. The C-terminal ends of Syb and Syx play an integral role in the fusion process in that they attach to the vesicle (Syb) and plasma membrane (Syx). The ENM spring network (right) that maintains the individual helical structure is shown for Syb and Syx. (Thick lines) Cα backbones; (thin lines) ENM springs. The Miyazawa and Jernigan (23–25) contacts between Syb and Syx are also represented (dotted lines). (B) The spectra used to compare the fluctuations of the AA and CG models are shown for Syb. Values for ks of 0.0963 N/m and Rc of 20 Å were used for the CG model. (Inset) Ten snapshots of Syb during the corresponding AA simulation. (C) Mean distance for different values of parameter A along with snapshots of the SNARE bundle. (Black line) Original crystal. (Black circle) Version chosen for simulation. To see this figure in color, go online.