Here are two ways of visualizing the position of a lipid bilayer membrane around the integral membrane portion of a trans-membrane protein.
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Outside
Inside
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- 1. represent the water-lipid boundaries. Red pseudoatoms represent the extracellular boundary, and blue pseudoatoms represent the cytoplasmic boundary.[1]
- 2. A represents membrane near the protein. If desired, .
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[1]. 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).
