Molecular Dynamics Simulations Analysis (PKU)

Short Introduction

We will analyze our completed molecular dynamics simulations, following the task description and the tutorial of the Utrecht University Molecular Modeling Practical. We have completed one run for the wildtype protein and for the mutations ALA322GLY and ARG408TRP, a second run of the wildtype is pending. The second run for the wildtype might be necessary as the trajectory of the wildtype differs significantly from both the mutants. The commands used to generate plots, images etc. can be found in our journal.

Initial Checks

All three simulations run for the desired 10 ns, the trajectories contain 2000 frames in 5 ps steps each. The wildtype simulation took significantly longer, since we used only 16 cores for the widtype, 32 for the mutants. Almost half of the calculation time, 44.2% in each run, is spent on calculating Coulomb interactions and the Lennard-Jones potential of the solvent molecules. A few key statistics can be found in <xr id="tab:simulation_stats"/>.

<figtable id="tab:simulation_stats"> Statistics of the MD simulations

Mutation	Sim. time	Sim. speed	time to reach 1 s
Wildtype	11:32 h	20.8 ns/day	131,621 years
ALA322GLY	4:20 h	55.3 ns/day	49,543 years
ARG408TRP	4:26 h	54.1 ns/day	50,685 years

</figtable>

Wildtype analysis

<figure id="fig:1J8U_overlay">

Overlay of all frames of the 10 ns simulation of the wildtype phenylalanine hydroxylase structure 1J8U.

</figure>

Gly322Ala analysis

<figure id="fig:mut322_overlay">

Overlay of all frames of the 10 ns simulation of the Gly322Ala mutation of phenylalanine hydroxylase structure 1J8U.

</figure>

Arg408Trp analysis

<figure id="fig:mut408_overlay">

Overlay of all frames of the 10 ns simulation of the Arg408Trp mutation of phenylalanine hydroxylase structure 1J8U.

</figure>