Jmol/Visualizing membrane position

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Here are two ways of visualizing the position of a lipid bilayer membrane around the integral membrane portion of a trans-membrane protein. Outside Inside 1. Pseudoatoms represent the water-lipid boundaries. Red pseudoatoms represent the extracellular boundary, and blue pseudoatoms represent the cytoplasmic boundary. 2. A translucent cylinder represents membrane near the protein. If desired, the ends of the cylinder can be colored similarly to the pseudoatoms. When we apply a hydrophobic vs. polar color scheme, the protein within the lipid bilayer is seen to have a largely hydrophobic surface. The example used here is 5lil. Methods: Pseudoatoms Any protein structure that includes an integral membrane domain can have pseudoatoms added to the PDB file by the Orientations of Proteins in Membranes Server.

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Eric Martz, Kristen Procko