Molecular Dynamics Simulations (PKU)

Oh, good. For a moment there I thought we were in trouble.

Short task description

This week, we will start the molecular dynamics simulation of our protein with the wildtype and two mutations. The simulation will be analyzed at a later time, see the complete task description for details. A journal will probably not be neccessary...

Selected Models

Besides the wildtype, we chose the hyperphenylalaninemia causing ALA322GLY mutation, since this mutation only reduces the enzyme activity and should have a visible but not severe effect on the protein, and the PKU causing ARG408TRP mutation, since this mutation should have a large impact on energy and flexibility of the protein, that has already been visible in the previous minimization simulations.

• Wildtype 1J8U --> could not commence production runs, prepared manually, final run pending
• Mutation ALA322GLY --> run finished in 04:28:48, simulation successfull
• Mutation ARG408TRP --> run finished in 04:34:08, simulation successfull

The Molecular Dynamics Simulation

We simulated the movement of the three selected structure with AGRoS, an automated Gromacs simulation pipeline.

One AGRoS run consists first of basic checks of the input structure for breaks and gaps. Then water in close distance to to the protein is saved as structural water, that might interact with the protein and be neccessary for protein stability, the other crystal water molecules are remoced. scwrl is used to complete sidechains and the complete structure is minimized for the first time in vacuum. Then, a surrounding box is defined and filled with water and ions to simulate solvent. First, the whole protein is fixed in place and the solvent minimized, then the backbone is fixed in place and the sidechains are minimized in solvent, finally the whole system is minimized.

After this preparations, two short MD runs try to relax the system from the crystalized to a more native state. The final simulation spans 10 nanoseconds in 2 million steps of 5 femtoseconds.

Job submission

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34faw/logs/1J8U_wildtype_MD.out
#SBATCH -D /home/hpc/pr58ni/di34faw/MD/
#SBATCH -J 1J8U_wildtype
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=boidolj@in.tum.de
#SBATCH --export=NONE
#SBATCH --time=10:00:00
source /etc/profile.d/modules.sh
module load gromacs

cd $HOME/
$HOME/AGroS/AGroS /home/hpc/pr58ni/di34faw/Gromacs/Models/1J8U.pdb -dir $HOME/MD/ -threads 32 --scwrlPATH $HOME/SCWRL

Intermediate Structures

During the simulation, a lot of intermediate PDB files are created. Most of them only have minimal differences (explained in the list below) but we show the differences after sidechain completion and the three minimizations in the next subsections.

e.g. for the ARG408TRP mutant (model file mut408.pdb)

• mut408.pdb: input structure with clashing water removed.
• mut408_br.pdb: just the protein, no DNA, crystal water, etc..
• mut408_br_0.pdb: 1 file for every chain, if several are present
• mut408.pdb2: structure with hydrogens removed
• mut408_repair.pdb: correctly numbered
• mut408_repair_0.pdb
• mut408_dna.pdb: extracted DNA, empty in our case
• mut408_water.pdb: contains structural water <15A from the protein, empty in our case
• mut408_sc.pdb: sidechains completed/adjusted with scwrl
• mut408_nh.pdb: removed hydrogens, added structural water (and DNA)
• mut408_solv_tmp.pdb: added ions
• mut408_solv.pdb: duplicate water removed (none in our case)
• mut408_solv.pdb2: just protein and added DNA, input to create individual files for each chain (see next step)
• mut408_solv_0.pdb: used to create restriction files for every chain (only 1 here)
• mut408_solv_min.pdb: structure with minimized solvent (protein fixed)
• mut408_solv_min.pdb2: just protein of previous structure, input to create individual files for each chain (see next step)
• mut408_solv_min_0.pdb: used to create restriction files for every chain (only 1 here)
• mut408_solv_min2.pdb: minimization with only backbone restrained
• mut408_solv_min3.pdb: final minimization before MD runs

ALA322GLY

<xr id="fig:ALA322GLY_solvation"> shows the In <xr id="fig:ALA322GLY_solvation_min1"> showing the first minimization in solvation the first differences are noticable: The beta sheet around 410 to 422 is bent and some of the loops shifted slightly. <xr id="fig:ALA322GLY_solvation_min1"> shows the second minimization with loosened sidechains