Preparation and simulation of membrane and membrane-protein systems

Overview

Teaching: 30 min
Exercises: 5 min

Questions

• How to prepare a membrane simulation system?

• How to pack a protein in a lipid bilayer?

Objectives

• Learn how to prepare a membrane simulation system?

• Learns to pack a protein in a lipid bilayer?

Creating simulation systems with packmol-memgen

AMBER Lipid force fields

Amber currently includes Lipid21 as its main membrane force field. In this modular force field, lipids are modeled as polymers composed of a headgroup and acyl tails. Essentially, this means that each headgroup and tail are independent modules, analogous to protein residues. Each lipid molecule is composed of a tail analogous to an “N-terminal”, a central headgroup and another tail analogous to a “C-terminal”. You can combine any headgroup with any pair of tails in this force field. Ok, now you should have an idea how the lipids are represented in the Lipid21 force field, and what lipids you can include in a simulation.

• There is a great deal of information provided in Dickson, 2022 regarding best practices when using AMBER for lipid simulations.
• Full list of supported lipids is in Section 3.4 of Amber22 manual

Known Issues: Using MC barostat with hard LJ cutoff is known to cause bilayer deformation. It is recommended to use an LJ force switch when running simulations with the MC barostat.Gomez, 2021

• To see all available lipids use --available_lipids_all, but the list will have thousands of items!

Creating a membrane-only simulation system

• What lipids are available?

ml StdEnv/2020 gcc cuda/11.4 ambertools/22
packmol-memgen --available_lipids 

Submission script for creating a membrane-only simulation system:

#!/bin/bash
#SBATCH -c1 --mem-per-cpu=2000 --time=3:0:0

module purge
module load StdEnv/2020 gcc cuda/11.4 ambertools/22
packmol-memgen \
    --lipids DOPE:DOPG \
    --ratio 3:1 \
    --distxy_fix 100 \
    --parametrize

• if the option –parametrize is given the solvated system is bilayer_only_lipid.pdb
• without –parametrize the solvated system is bilayer_only.pdb
• Multiple bilayers can be generated by repeating corresponding flags.
• Bilayers with different leaflet composition can be generated: –lipids CHL1:POPC:POPE:PSM//CHL1:POPC:POPE:PSM:POPS:POPI:POGL –ratio 4:4:2:1//6:2:3:2:2:2:2

This example illustrates the building of a bilayer where leaflets consist of different types of lipids:

#!/bin/bash
#SBATCH -c1 --mem-per-cpu=4000 --time=6:0:0

module purge
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 ambertools/23

rm -f bilayer* *.log
packmol-memgen \
    --lipids CHL1:POPC:POPE:PSM//CHL1:POPC:POPE:PSM \
    --salt --salt_c Na+ --salt_a Cl- --saltcon 0.15 \
    --dist_wat 15 \
    --ratio 4:3:1:2//4:3:1:2 \
    --distxy_fix 100 \
    --parametrize

Embedding a protein into a bilayer

We will use PDB file 6U9P (wild-type MthK pore in ~150 mM K+) for this exercise.

1. Use PPM server to orient a protein. PPM server will also take care of assembling the complete tetrameric pore.
2. Use vmd to remove ligands and conformers B.

module load StdEnv/2020 vmd
vmd

mol new 6u9pout.pdb
set sel [atomselect top "protein and not altloc B"]
$sel writepdb 6U9P-clean.pdb
quit

1. Submission script to embed a protein into a lipid bilayer

 #!/bin/bash
 #SBATCH -c1 --mem-per-cpu=2000 --time=1:0:0
 
 module purge
 module load StdEnv/2020 gcc cuda/11.4 ambertools/22
 packmol-memgen \
	--pdb 6U9P-clean.pdb \ 
	--lipids DOPE:DOPG \
	--ratio 3:1 \
    --preoriented 

• Use --parametrize to make simulation input files. The default protein force field is FF14SB, water model TIP3P.
• To use a different force field: --fprot ff19SB --ffwat opc --gaff2
• To add salt (default K+, 0.15M): --salt

Links to advanced AMBER tutorials

• Placing waters and ions using 3D-RISM and MOFT
• Building a Membrane System with PACKMOL-Memgen
• Minimizing and Equilibrating a packed membrane system
• Setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen.

Key Points