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.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Kristen Procko