Designing Lipid Layers Around Proteins with Molecular Box Builder

Molecular modelers often face the challenge of creating biologically realistic environments, such as embedding proteins within lipid membranes. This task can be time-consuming and involves multiple steps of manual setup. The Molecular Box Builder extension for SAMSON offers a practical solution by allowing you to automate the creation of lipid layers around proteins in just a few steps. In this post, we'll guide you through the process of building a single lipid layer around a protein, using the example of the copper-transporting PIB-ATPase 4BBJ.

Step 1: Aligning the Protein

Before integrating a lipid layer, it is crucial to properly orient the protein for alignment with the layer.

  1. Right-click the protein in the Document view.
  2. From the context menu, select: Move selection > Align with Z axis.
  3. Next, select: Move selection > Center on the origin.

This ensures the protein is centered and aligned, preparing it for surrounding lipids. See the alignment step below:

Align protein

Step 2: Setting the Lipid Molecule

Next, we'll add the lipid molecule to use in the layer. Follow these simple steps:

  1. Import a lipid molecule that you want to use.
  2. Select the lipid and click Set in the Molecular Box Builder app.
  3. For proper orientation, align the lipid's principal axis to the +Z axis.

Here's an example of aligning a molecule along the Z-axis:

Align a molecule with Z-axis

Step 3: Defining the Box

At this stage, you'll create a 3D box that specifies where the lipid layer should be placed.

  1. Center the box around the protein.
  2. Adjust the box dimensions to accommodate a single lipid layer.
  3. If necessary, specify the margin between inserted lipids to avoid overlapping molecules.

Here is a generated box containing a protein, ready to be filled with lipids:

A box with a protein

Step 4: Generating the Lipid Layer

Now, the lipid layer can be generated:

  1. Enable the Consider existing molecules in the box option so that lipids are only placed in free space around the protein.
  2. Click Generate to populate the box with lipids.

The result is a single lipid layer surrounding the protein:

A lipid layer with a protein

Optional: Creating a Lipid Bilayer

If your system requires a full lipid bilayer instead of just a single layer, repeat the steps for generating the first layer, but make minor adjustments:

  1. Generate the first lipid layer with +Z alignment.
  2. Shift the box's center slightly in the Z-direction.
  3. Generate the second layer by aligning the new lipids to the -Z direction.

Once completed, you will have a bilayer that can be further refined and simulated.

For additional details and more advanced options, visit the complete documentation for the Molecular Box Builder.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.

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