Difference between revisions of "Task 8: Molecular Dynamics Simulations"

From Bioinformatikpedia
(Created page with "== Task description == A detailed task description can be found here.")
 
Line 2: Line 2:
   
 
A detailed task description can be found [[Task_7_-_Structure-based_mutation_analysis| here]].
 
A detailed task description can be found [[Task_7_-_Structure-based_mutation_analysis| here]].
  +
  +
== Intro and selection of two mutants ==
  +
  +
The description given here was applied for our wild type (1J8U). However, the steps done for our two mutants R408W and P281L are the same.
  +
  +
We selected R408 we because it is the most abundant mutation of PAH which is associated with phenylketonuria. It has a total frequency of 6.67% (see [http://www.pahdb.mcgill.ca/cgi-bin/pahdb/mutation_statistics-1.cgi]).
  +
  +
The second mutation, P281L, was selected because it is the closed mutation to the binding site (HIS 285) and we hope that we are able to see some interesting things here which give us an explanation why this mutation is disease causing.
  +
  +
  +
== Preperation ==
  +
  +
Before we can start to generate all necessary files for our MD simulation we have to prepare our structure first. We employed the following steps:
  +
  +
1. Extracting the crystal water below 15 Å
  +
  +
<code>
  +
repairPDB 1J8U.pdb -ssw 15 > water_below_15.out
  +
</code>
  +
  +
We received the following output:
  +
  +
<code>
  +
HETATM 2559 O HOH A1008 2.996 9.738 16.094 1.00 14.91 O
  +
HETATM 2561 O HOH A1010 -3.667 12.788 8.538 1.00 14.80 O
  +
HETATM 2572 O HOH A1021 3.557 27.911 10.913 1.00 14.69 O
  +
HETATM 2879 O HOH A1328 -5.335 24.271 14.490 1.00 14.88 O
  +
TER
  +
</code>

Revision as of 14:58, 9 July 2011

Task description

A detailed task description can be found here.

Intro and selection of two mutants

The description given here was applied for our wild type (1J8U). However, the steps done for our two mutants R408W and P281L are the same.

We selected R408 we because it is the most abundant mutation of PAH which is associated with phenylketonuria. It has a total frequency of 6.67% (see [1]).

The second mutation, P281L, was selected because it is the closed mutation to the binding site (HIS 285) and we hope that we are able to see some interesting things here which give us an explanation why this mutation is disease causing.


Preperation

Before we can start to generate all necessary files for our MD simulation we have to prepare our structure first. We employed the following steps:

1. Extracting the crystal water below 15 Å

repairPDB 1J8U.pdb -ssw 15 > water_below_15.out

We received the following output:

HETATM 2559  O   HOH A1008       2.996   9.738  16.094  1.00 14.91           O  
HETATM 2561  O   HOH A1010      -3.667  12.788   8.538  1.00 14.80           O  
HETATM 2572  O   HOH A1021       3.557  27.911  10.913  1.00 14.69           O  
HETATM 2879  O   HOH A1328      -5.335  24.271  14.490  1.00 14.88           O  
TER