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. Structures in the Protein Data Bank are pre-processed; other structures may be uploaded to the server. The server removes hydrogen atoms from the model. You can download the pseudoatom-enhanced PDB file from the server, and then upload it to Proteopedia for use in a Molecular Scene. In the case of 5LiL, I had difficulty getting the pseudoatoms to show from a green link (even though they displayed in the SAT). In the PDB file, the pseudoatoms followed a MASTER record. I deleted the MASTER record and all CONECT records, and then I got the results shown above with File:5lil opm2.pdb.

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Eric Martz, Kristen Procko