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Tutorial
Membrane Builder

The Membrane Builder helps the user generate a series of CHARMM inputs necessary to build a protein/membrane complex for molecular dynamics simulations. A brief description of each step is given below. Among various other building schemes, either the "insertion" or the "replacement" method can be chosen by the user in step 3. (user can choose one of them in step 3, see below).

  • Insertion method
    A protein is inserted into a pre-equilibrated lipid bilayer with a hole whose size is comparable to the protein size (the libraries of lipid bilayers are available in archive)
  • Replacement method
    A protein is first packed by lipid-like spheres whose positions are subsequently used to place randomly chosen lipid molecules from the library (the libraries of lipid molecules are available in archive)
Please note that
  • the protein must be oriented with respect to a membrane bilayer whose normal is parallel to the Z-axis and whose center is located at Z=0
  • RCSB PDB structures are NOT pre-oriented, but can be oriented in step 2 (see below)
  • OPM (http://opm.phar.umich.edu) provides pre-oriented protein coordinates with respect to the membrane normal
  • a homogeneous lipid bilayer can be built with DMPC, DPPC, DOPC, POPC, DLPE, and POPE
  • a heterogeneous lipid bilayer can be built with 32 different lipid molecules (see lipid list)
  • the heterogenous Membrane Builder can be used for a homogeneous lipid bilayer (only using the replacement method)
  • the Membrane-ONLY Builder is now available
  • rectangular and hexagonal geometries are available for a system shape in XY
  • there is an archive of (pre-equilibrated) protein/membrane complexes generated by Membrane Builder
References:

T. Woolf and B. Roux (1996)
Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer Proteins 24:92-114

S. Jo, T. Kim, and W. Im (2007)
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations. PLoS ONE 2(9):e880

S. Jo, J.B. Lim, J.B. Klauda, and W. Im (2009)
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes. Biophys. J. 97:50-58

Protein/Membrane System

Download PDB File: Download Source:

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PDB Format: RCSB CHARMM

Membrane Only System

Next Step:
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A brief explanation of each step:
  • STEP1: Read protein coordinates
    The user can download the coordinates from RCSB (PDB website) or OPM (http://opm.phar.umich.edu). OPM provides pre-oriented protein coordiantes with respect to the membrane normal. The user can upload the PDB (or CHARMM) format coordinates from the user's local machine, once you properly orient the protein in membranes.

  • STEP2: Orient the protein
    If the PDB coordinates from RCSB, it is necessary to properly orient the protein with respect to membranes. There are two options for doing this. It is the step in which the cross-section area of the protein along the Z-axis is calculated and displayed. The maximum top (10<Z<20) and bottom (-20<Z<-10) areas are used to determine the system size in XY.

  • STEP3: Determine the system size
    To determine the system size in XY, there are three options, in the case of homogeneous bilayer generation, based on (1) number of lipid layers around the protein, (2) specific number of lipid molecules in top and bottom, and (3) specific size of the system along X and Y. The system size along Z is determined by the water extent from the top and bottom of the protein. For now, six types of lipids (DMPC, DPPC, DOPC, POPC, DLPE, and POPE) and two types of system shapes in XY (rectangular and hexagonal) are provided.

    In the case of heterogeneous bilayer generation, there are two options to determine the system size: (1) ratio of lipid types to be used and initial (guess) size of the system along X and Y (2) specific number of lipid molecules and ratio of system size along X and Y The system size along Z is determined by the water extent from the top and bottom of the protein. If desired, hydration number (number of water molecules per one lipid molecule) can be used for this purpose.

  • STEP4: Build the components
    Based on the system size determined in the previous step, this step builds individual pieces such as (1) the lipid bilayer around the protein, (2) additional water molecules to fully solvate the protein, and (3) ions (with Monte Carlo sampling) for the given concentrations.

  • STEP5: Assemble the components
    All the pieces (protein, lipid bilayer, additional water, and ions) are assembled together in this step.

  • STEP6: Equilibrate the system
    Due to the their computation time, only the input files for five "suggested" equilibration steps are provided. However, the user can find equilibrated coordinates for some membrnae proteins from the archive.