Effortlessly Build Lipid Layers Around Proteins

Creating lipid layers around proteins can be a time-consuming challenge for molecular modelers. From aligning your structure to meticulously placing lipids, it’s often a painstaking process. Thankfully, Molecular Box Builder in SAMSON streamlines this, making it easier and faster to create uniform lipid layers—or even a lipid bilayer—around your protein of interest.

Reorienting the Protein: A Critical First Step

Before generating a lipid layer, properly orienting your protein ensures accurate placement of lipids. Start by centering and aligning your protein in SAMSON:

  1. Right-click the protein in the Document view.
  2. Select Move selection > Align with Z axis from the context menu.
  3. Then, choose Move selection > Center on the origin.

This alignment simplifies the process of ensuring that the lipid layer will uniformly surround your protein.

Align protein

Step 2: Assigning the Lipid Molecule

A well-oriented lipid molecule is the foundation of your lipid layer. Here’s how to set it up:

  1. Import a lipid molecule into SAMSON.
  2. Select the lipid and click Set in the app.
  3. Align its principal axis to the +Z direction. This alignment ensures a structured organization of the lipid molecules in the layer.

Align a molecule with Z-axis

Step 3: Configuring the Lipid Layer Box

Now comes the part where your pocket of imagination takes shape around the protein:

  1. Center the box around your protein using the app’s Center function.
  2. Adjust the box’s size to encapsulate a single lipid layer. This ensures the protein is embedded comfortably within the lipid layer.
  3. If needed, specify a margin between lipid molecules to refine packing density or address potential clashes. Aim for uniformity to create a stable configuration.

A box with a protein

Step 4: Generating the Lipid Layer

The most gratifying step of the process is the generation of the lipid layer itself. Before proceeding:

  1. Toggle Consider existing molecules in the box within the app. This feature ensures lipids are only added where space permits, avoiding overlaps with the protein or existing molecules.
  2. Click Generate. In seconds, you’ll witness a perfectly aligned lipid layer around your protein.

A lipid layer with a protein

Creating a Lipid Bilayer (Optional)

To generate a full lipid bilayer around your protein, repeat the following steps:

  1. Add the first layer with lipids aligned to +Z.
  2. Shift the box’s center slightly along the Z axis.
  3. Add the second layer of lipids, this time aligned to -Z.

Within minutes, you’ll create not just a single lipid layer, but an entire bilayer that dynamically interacts with your protein during further simulations.

Next Steps

After constructing your lipid-protein system, you’re ready to minimize, equilibrate, and simulate. Use the GROMACS Wizard for energy minimization and simulations, ensuring realistic behavior of your system.

For a more detailed step-by-step breakdown of this workflow, visit the official documentation.

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

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