Setting Up an Implicit Membrane

The Prime implicit membrane model is intended for proteins embedded in a membrane. The implicit membrane is a low-dielectric slab-shaped region, which is treated in the same way as the high-dielectric implicit solvent region. Hydrophobic groups, which normally pay a solvation penalty for creating their hydrophobic pocket in the high dielectric region, do not have to pay that penalty while in the membrane slab. Also, hydrophilic groups lose any short-ranged solvation energy from the high dielectric region when placed in the low dielectric region.

The implicit membrane model is intended for use with proteins that span the membrane. The slab is trimmed for efficiency, so that any structure that is too small or too far away from the membrane is likely to result in too much trimming and might not produce useful results.

Setting up a membrane is done in the Prime Membrane Setup Panel, which you open by clicking Set Up Membrane in the Options dialog box for any of the Prime refinement panels. See the Prime Membrane Setup Panel topic for information on the panel.

The basic procedure for setting up a receptor membrane is as follows. This procedure uses the Calculate Energy Panel just to set up the membrane. You can of course vary this procedure as needed.

  1. Include the receptor in the Workspace and also select it in the Entry List or Project Table.

  2. Click the Tasks button and browse to Protein Preparation and Refinement → Calculate Energy.

    The Calculate Energy Panel opens. If you are performing a Prime refinement task, you can open the desired panel instead.

    For membrane setup, the only important setting is the structure source, which should be Workspace (included entry).

  3. Click Options.

    The Options dialog box for the Prime task opens.

  4. Select Implicit membrane and click Set Up Membrane.

    The Prime Membrane Setup Panel opens.

  5. Click Place by ASL, with the default value all in the ASL text box.

    The entire protein is embedded in the membrane. If you want some of the protein in the solvent you can use other settings to control where the membrane is placed.

  6. Click Save to Selected Entries and close the panel.

The receptor should now show membrane properties in the Project Table.