Molecular Dynamics Simulations Analysis Hemochromatosis

Hemochromatosis>>Task 10: Molecular dynamics simulations analysis

Short task description

Detailed description: Molecular dynamics simulations analysis

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

Dummy

Calculation statistics

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

Input	Calc. time	Calc. speed	time to reach 1 s
Wildtype	13h31:15	17.750 ns/day	154350,8 years
C282S	13h35:05	17.667 ns/day	155075,9 years
R224W	13h35:02	17.668 ns/day	155067,1 years

</figtable>

GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.

Energies

Pressure

<figtable id="comparison">

Table 1: different pressures of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutatuin at position 282 (C282S)

</figtable>

Temperature

<figtable id="comparison">

Table 2: different temperature energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Potential

<figtable id="comparison">

Table 3: different potential energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Total energy

<figtable id="comparison">

Table 1: different total energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Minimum distance between periodic boundary cells

<figtable id="comparison">

Table 1: different total energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

RMSF for protein and C-alpha

Protein based

<figtable id="comparison">

Table 1: different RMS fluctuations (based on the whole protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

C-Alpha based

<figtable id="comparison">

Table 1: different tRMS fluctuations (based on the the C-alpha of the backbone of the protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Statistical values

Table 1:

	Average	StdDeviation	Ratio	significance
Wildtype	0.183621323529412	0.0605331780782099	50.0281092824371
R224W	0.232876838235294	0.0895836329605749	42.87282263833
C282S	0.268558823529412	0.0982244780281883	45.0924827835932

Pymol analysis of average and bfactor

<figtable id="comparison">

Table 1: different t gyrations (based on the the C-alphas of the backbone of the protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Radius of gyration

<figtable id="comparison">

Table 1: different t gyrations (based on the the C-alphas of the backbone of the protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

<figtable id="comparison">

Table 1: different t gyrations (based on the the whole protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

solvent accessible surface area

<figtable id="comparison">

Table 1: display of the different solvent accessible surface values of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

<figtable id="comparison">

Table 1: display of the different solvent accessible surface values (normalized to per residue values) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

hydrogen-bonds between protein and protein / protein and water

Protein-Protein

<figtable id="comparison">

Table 1: the number of hydrogen bonds inside the protein of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Protein-Water

<figtable id="comparison">

Table 1: the number of hydrogen bonds of the protein with water of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Ramachandran plots

<figtable id="comparison">

Table 1: tramachandran Plots of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

RMSD matrix

<figtable id="comparison">

Table 1: rmsd matrices of the three calculated models over time (based on the whole protein). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

<figtable id="comparison">

Table 1: rmsd matrices of the three calculated models over time (based on the mainchain and C-betas). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

cluster analysis

whole protein based

<figtable id="comparison">

Table 1: rmsd matrices of the three calculated models over time (based on the whole protein). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

C-alpha based

<figtable id="comparison">

Table 1: rmsd matrices of the three calculated models over time (based on the whole protein). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

internal RMSD

against starting structure

<figtable id="comparison">

Table 1: tramachandran Plots of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

against average structure

<figtable id="comparison">

Table 1: tramachandran Plots of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

References

<references/>