All-Atoms Connexon Model Figure 1. Overview of the connexon model in a membrane patch and dynamical behavior. a) Cartoon of the side view of the connexon. Each connexin is depicted with different colors. The central connexin is additionally colored by structure: pink for helices, white for coils and light pink for b–strands. The phospholipid membrane, embedding the hemi–channel, is represented in gray. Four phospholipids randomly chosen are colored by atom. b) Root mean square deviations (RMSD) calculated over the Ca atoms of the whole connexon (black) and over the sole TM domain of the connexon (red). Individual RMSD traces of each of the six connexin TM domains are practically indistinguishable and remain below 0.17 nm (lower traces). c) Structural superposition between initial (red) and final (blue) conformers. The Tyr151 residues that delineate the maximum constriction point of the channel pore are shown in space filling mode. d) Minimum diameter of the pore measured as the distance between the OH atoms of opposite Tyr151 in different connexins, averaged over the three possible pairs. The nearly horizontal red dotted line corresponds to a linear fit over the entire simulation, with slope of 20.004 and an y-ordinate of 1.45 nm. e) Stereo view of the rigid docking of the Ca models by Fleishman et al. (red tube) and ours (blue tube) onto the electron microcopy map of Cx43 for the TM part of one connexin seen from the membrane side. Ca atoms are also shown. doi:10.1371/journal.pone.0002614.g001 Table 1. Surface complementarities between different orientations of TM2. Model A Interface ASAa % of interface ASA GAP volume indexb Model B Interface ASA % of interface ASA GAP volume index TM 1, 3, 4 712.4 13.1 1.5 701 13 1.2 TM 2 769.6 31.7 832,9 34.2 The model as obtained from the original Ca coordinates ([11] PBD entry code 1TXH) and the one obtained in this work are referred as Model A and B respectively. aAccessible surface area. bDefined as = Gap Volume/Interface ASA doi:10.1371/journal.pone.0002614.t001 hydrogen bonding of Thr86 to the backbone carbonyl of Ile82 causes a 37 degrees bending of the helix that corresponds functionally to the channel open state [23]. The model proposed in ref. [11] was constructed by fitting canonical, i.e. straight, a2helices to the map in ref. [10] and thus shows no sign of a PK in TM2. MD relaxation in our model retrieved the PK early in the simulation, and stabilized around an average bend angle of 1665 degrees (mean6S.D.) (Figure 2c). This more conservative estimate arises as a consequence of the constraints imparted to TM2 by its protein and membrane environment. Obviously, these constraints were not present in the isolated TM2 model [23]. Along the MD trajectory, we observed the formation of H2bond interactions between the Thr86 and the backbone carbonyl of Ile82, as well as between Ser85 and the backbone carbonyl of Leu81 (see Figure S2a), confirming their stabilizing role in TM2 bending. Main determinants of connexon stability associated to electrostatic interactions Inspection of the MD simulation trajectory reveals the formation of four salt bridges within each single connexin chain. PLoS ONE | www.plosone.org 3 July 2008 | Volume 3 | Issue 7 | e2614