Difference between revisions of "Structure-based mutation analysis BCKDHA"

From Bioinformatikpedia
(2. repairPDB)
(Gromacs)
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== Gromacs ==
 
== Gromacs ==
   
  +
The first part describes general background information for gromacs as well as how to run those programs.
===1. fetchpdb===
 
  +
The second part contains the result description and analysis.
  +
=== General ===
  +
  +
====1. fetchpdb====
   
 
The fetch-pdb script first checks, if it was called with an valid PDB-id. If the entered PDB code has 4letters, the script tries to download the pdb-file from the server. The successfully downloaded folder gets unzipped and everything except the actual pdb file is removed.
 
The fetch-pdb script first checks, if it was called with an valid PDB-id. If the entered PDB code has 4letters, the script tries to download the pdb-file from the server. The successfully downloaded folder gets unzipped and everything except the actual pdb file is removed.
   
===2. repairPDB===
+
====2. repairPDB====
   
 
repairPDB bckdha_mod.pdb -noh -nosol > bckdha_clean.pdb
 
repairPDB bckdha_mod.pdb -noh -nosol > bckdha_clean.pdb
   
===3. SCWRL ===
+
====3. SCWRL ====
   
 
scwrl -i bckdha_mod.pdb -s extractedPDB.seq -o bckdha_scwrl.pdb
 
scwrl -i bckdha_mod.pdb -s extractedPDB.seq -o bckdha_scwrl.pdb
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pdb including HEATOMS
 
pdb including HEATOMS
   
===4.pdb2gmx===
+
====4.pdb2gmx====
   
 
use clean pdb without HEATOMS
 
use clean pdb without HEATOMS
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pdb2gmx -f bckdha_clean.pdb -o bckdha.gro -p bckdha.top -water tip3p -ff amber03
 
pdb2gmx -f bckdha_clean.pdb -o bckdha.gro -p bckdha.top -water tip3p -ff amber03
   
===5. MDP===
+
====5. MDP====
 
<!--
 
<!--
 
<code>
 
<code>
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-->
 
-->
   
===6.grompp===
+
====6. grompp====
 
grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p bckdha.top -o bckdha.tpr
 
grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p bckdha.top -o bckdha.tpr
   
===7.System Minimization ===
+
====7. System Minimization ====
   
   
 
mdrun -v -deffnm bckdha 2> mdrun_out.txt
 
mdrun -v -deffnm bckdha 2> mdrun_out.txt
   
===8.Analyzation===
+
====8. Analyzation====
   
 
g_energy -f bckdha.edr -o energy_1.xvg
 
g_energy -f bckdha.edr -o energy_1.xvg
  +
  +
=== Analysis ===
   
 
== Links ==
 
== Links ==

Revision as of 13:23, 30 June 2011

Structure selection

The following table presents the PDB structures for BCKDHA to date:

PDB id resolution [Å] R-factor coverage ph-value
1DTW 2.70 0.224 7.5*
1OLS 1.85 0.172 5.5
1OLU 1.90 0.161 5.5
1OLX 2.25 0.161 5.5
1U5B 1.83 0.156 5.8
1V11 1.95 0.139* 5.5
1V16 1.90 0.132* 5.5
1V1M 2.00 0.130* 5.5
1V1R 1.80 0.158 5.5
1WCI 1.84 0.149 5.5
1X7W 1.73 0.148 5.8
1X7X 2.10 0.149 5.8
1X7Y 1.57 0.150 5.8
1X7Z 1.72 0.154 5.8
1X80 2.00 0.161 5.8
2BEU 1.89 0.171 5.5
2BEV 1.80 0.139 5.5
2BEW 1.79 0.147 5.5
2BFB 1.77 0.145 5.5
2BFC 1.64 0.144 5.5
2BFD 1.39* 0.150 5.5
2BFE 1.69 0.150 5.5
2BFF 1.46 0.150 5.5
2J9F 1.88 0.171 5.5

The following PDB Structure was chosen because of its good experimental resolution: <bold></bold>

  • resultion:
  • R-factor
  • ph-value

Comparison energies

Mapping of the mutations on the crystal structure

SCWRL

Before we could use SCWRL we first had to get the sequence of our model: repairPDB bckdha.pdb -seq >> bckdha.seq

When we have the sequence we have to make one file for each mutation. In these files we copied the bckdha.seq and changed the sequence to lower case letters. Then we add the mutation in an upper case letter.

To run SCWRL we used the command: scwrl -i bckdha.pdb -s mutation1.seq -o mutation1Model.pdb


Total minimal energy of the graph

Position Energy
M82L 642.213
Q125E 616.85
Y166N 616.293
G249S 633.378
C264W 805.257
R265W 710.647
I326T 619.424
F409C 617.305
Y438N 615.951

foldX

To use foldX we first build a runscript. Additionally we had to create one file with all PDB Ids each in a new line (list.txt).


<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>foldx_protein.txt;
<COMMANDS>FOLDX_commandfile;
<Stability>list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
//<Temperature>298;
<R>#;
<pH>5.5;
<IonStrength>0.050;
<water>-CRYSTAL;
<metal>-CRYSTAL;
<VdWDesign>2;
<OutPDB>false;
<pdb_hydrogens>false;
<END>#;
<JOBEND>#;
<ENDFILE>#;


total energy difference
wildtype 401.00 0
mutant1 437.88 -36.88
mutant2 431.77 -30.77
mutant3 432.24 -31.24
mutant4 432.22 -31.22
mutant5 488.43 -87.43
mutant6 460.43 -59.43
mutant7 432.94 -31.94
mutant8 433.33 -32.33
mutant9 431.56 -30.56


Minimise

gromacs

Gromacs

The first part describes general background information for gromacs as well as how to run those programs. The second part contains the result description and analysis.

General

1. fetchpdb

The fetch-pdb script first checks, if it was called with an valid PDB-id. If the entered PDB code has 4letters, the script tries to download the pdb-file from the server. The successfully downloaded folder gets unzipped and everything except the actual pdb file is removed.

2. repairPDB

repairPDB bckdha_mod.pdb -noh -nosol > bckdha_clean.pdb

3. SCWRL

scwrl -i bckdha_mod.pdb -s extractedPDB.seq -o bckdha_scwrl.pdb

pdb including HEATOMS

4.pdb2gmx

use clean pdb without HEATOMS

pdb2gmx -f bckdha_clean.pdb -o bckdha.gro -p bckdha.top -water tip3p -ff amber03

5. MDP

6. grompp

grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p bckdha.top -o bckdha.tpr

7. System Minimization

mdrun -v -deffnm bckdha 2> mdrun_out.txt

8. Analyzation

g_energy -f bckdha.edr -o energy_1.xvg

Analysis

Links

go back to Maple syrup urine disease main page

go back to Task 6 Sequence based mutation analysis

go to Reference Sequence BCKDHA