Membrane models for molecular simulations of peripheral membrane proteins

Figures & data

Figure 1. Membrane models and their respective compatible protein description. Membranes from left to right: all-atom, HMMM, MARTINI, SBCG, implicit. Proteins (Pleckstrin Homology (PH) domain, 2DA0) from left to right: all-atom, all-atom, half-MARTINI/half-RBCG, SBCG, all-atom. Rendered with 3DProteinImaging [12]

Figure 2. Tyrosine-choline π-cation interactions in Bacillus thurigiensis phosphatidylinositol-specific phospholipase C anchored at the surface of a PC lipid bilayer. Reprinted from [3], with permission from ACS Publications

Figure 3. Phenol-tetramethylammonium potential energy surface obtained with quantum mechanics calculations, the CHARMM36 force field and the CHARMM-WYF modification of the Lennard-Jones potential. Reprinted from [56], with permission from ACS Publications

Figure 4. Regular atomistic bilayer (right) and HMMM bilayer (left) model. Figure inspired by the Ohkubo et al. 2012 [49] and Vermaas et al. 2015 [85]

Figure 5. Schematic atomistic representation of the α-tocopherol transfer protein interacting with a DOPC/DOPE phospholipid bilayer (grey). The mobile gate (purple) at the entrance of the cavity interacts with the PIP₂ headgroup (red) and the lipids. The neighbouring motif is coloured in blue, and the α-tocopherol molecule bound to the protein in yellow. The head of PIP₂ facilitates anchoring of α-TTP to the membrane. Rendered with 3DProteinImaging [12]. PDB ID: 3W67 [95]

Figure 6. Bar domains structures (N-BAR:1ZWW [134], F-BAR:2V0O [135], I-BAR:1Y20 [136]) coloured by subunit. Rendered with 3DProteinImagning [12]

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