Jmol/Visualizing membrane position

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. 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). 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 Image:5lil opm2.pdb.