Structure-based mutation analysis BCKDHA

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

We could not use any of the PDB structures for BCKDHA because all of them had gaps in the secondary structure which means that some residues were missing. So we took the structure which has the less gaps: 1U5B

• resultion: 1.83
  
• R-factor: 0.156
  
• ph-value: 5.8

This structure has to be modified with some programms to close the gaps. Additionally the first residues which are in BCKDHA misses in 1U5B thats why the startposition corresponds to position 6 of the BCKDHA sequence.

As we can see non of the values correspond to the demand because it was ask for an structure which has a very small R-factor, a pH of 7.4 and a high resolution.

Mapping of the mutations on the crystal structure

M82L

Hydrogen Bonds for methionine on pos 82 in the wild type structure

Hydrogen Bonds for leucine on pos 82 in the mutated type structure

Q125E

Hydrogen Bonds for glutamine on pos 125 in the wild type structure

Hydrogen Bonds for glutamic acid on pos 125 in the mutated type structure

Y166N

Hydrogen Bonds for tyrosine on pos 166 in the wild type structure

Hydrogen Bonds for asparagine on pos 166 in the mutated type structure

G249S

Hydrogen Bonds for glycine 249 in the wild type structure

Hydrogen Bonds for serine on pos 249 in the mutated type structure

C264W

Hydrogen Bonds for cystein on pos 264 in the wild type structure

Hydrogen Bonds for tryptophan on pos 264 in the mutated type structure

R265W

Hydrogen Bonds for arginine on pos 265 in the wild type structure

Hydrogen Bonds for tryptophane on pos 265 in the mutated type structure

I326T

Hydrogen Bonds for isoleucine on pos 326 in the wild type structure

Hydrogen Bonds for threonine on pos 326 in the mutated type structure

F409C

Hydrogen Bonds for phenylalanine on pos 409 in the wild type structure

Hydrogen Bonds for cysteine on pos 409 in the mutated type structure

Y438N

Hydrogen Bonds for tyrosine on pos 438 in the wild type structure

Hydrogen Bonds for asparagine on pos 438 in the mutated type structure

Comparison energies

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. It is important to change values of <Temperature> and <pH> to the values of the used protein. These values can be found on the pdb side . Additionally we had to create one file with all PDB Ids each in a new line (list.txt). We used the command Foldx -runfile run.txt > Stout.txt to run the programm.

	total energy	difference
wildtype	401.00	0
M82L	437.88	-36.88
Q125E	431.77	-30.77
Y166N	432.24	-31.24
G249S	432.22	-31.22
C264W	488.43	-87.43
R265W	460.43	-59.43
I326T	432.94	-31.94
F409C	433.33	-32.33
Y438N	431.56	-30.56

After using foldx we have the total energy for the wiltype protein and for each mutation. The value of the wildtype protein is 401.00 which is already a high value. This means that the protein is quite instabile. To find out which mutation has a high influence on the protein we look at the energies and especially on the difference between the energy of the mutated protein and the wildtype protein. All of the mutated proteins have a much higher energy than the unmutated protein which means that these proteins are less stable. We can see in the table that the proteins can be divided into two groups. The first group has an energy difference of about 31 and the other group has a much higher difference.

Minimise

It is important to remove the hydrogens and water before using the programm. For this we used the new version of repairPDB of the virtualbox. The programm can be started with the command: repairPDB bckdha.pdb -nosol out.pdb > Stout.txt
It is also possible to use the old version but then the command is: repairPDB bckdha.pdb -nosol -noh out.pdb > Stout.txt
It is useful to save the output in a file because it includes the energy.

	total energy	difference
wildtype	-2485.452755	0
M82L	-4253.174790	1767.722015
Q125E	-4080.989512	1595.536757
Y166N	-4354.495238	1869.042483
G249S	-4280.043000	1794.590245
C264W	-3745.313620	1259.860865
R265W	-3989.790625	1504.33787
I326T	-4317.105618	1831.652863
F409C	-4358.528143	1873.075388
Y438N	-4339.778964	1854.326209

Minimise calculates the energy for a mutation by building a new model for each mutation. And then it calculates the energy for the whole mutated model. To find out if there is a difference between the wildtype and the model that is calculated by Minimise. The aim by comparing the mutated models with the wildtype is to find out if there is a structural change caused by a mutation. We superposed each mutated protein with the wildtype and focused on the mutated position. In the pictures there are always the superposed structures. In the wildtype pictures the structure of the unmutated residue is bold and in the mutated pictures the structure of the mutated residue is bold. So we can compare the two pictures to see if there is a change in the structure caused by the mutation on this residue.

mutation	wildtype structure	mutated structure
M82L	wildtype	mutation M82L
Q125E	wildtype	mutation Q125E
Y166N	wildtype	mutation Y166N
G249S	wildtype	mutation G249S
C264W	wildtype	mutation C264W
R265W	wildtype	mutation R265W
I326T	wildtype	mutation I326T
F409C	wildtype	mutation F409C
Y438N	wildtype	mutation Y438N

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

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

Wildtype analysis: nsteps vs time

steps	time (real) [s]
50	8.074
100	10.362
500	6.156
1000	15.240
5000	4.231

Wildtype analysis: force fields

The different force fields chosen for this task were:

• AMBER03

GROMACS Energy for the AMBER03 forcefield using the wildtype bckdha structure.

• CHARMM27

GROMACS Energy for the CHARMM27 forcefield using the wildtype bckdha structure.

• OPLS-AA

GROMACS Energy for the OPLS-AA forcefield using the wildtype bckdha structure.

Bond Analysis

Force Field	Average	Err. Est.	RMSD	Tot-Drift (kJ/mol)
AMBER03	3072.83	2200	-nan	-13100.2
CHARMM25	3180.46	1700	7382.72	-9958.05
OPLS	2780.55	2100	-nan	-11542.6

Angle Analysis

Force Field	Average	Err. Est.	RMSD	Tot-Drift (kJ/mol)
AMBER03	3616.97	230	-nan	-1295.57
CHARMM25	5018.38	490	1646.81	-2783.35
OPLS	3271.23	340	-nan	-1889.98

Potential Analysis

Force Field	Average	Err. Est.	RMSD	Tot-Drift (kJ/mol)
AMBER03	2.67001e+07	2.6e+07	-nan	-1.60382e+08
CHARMM25	487.479	97199.742	673.043
OPLS	2.38353e+07	2.4e+07	-nan	-1.39932e+08

Mutation analysis

M82L

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2518.71	1700	6337.97	-10023.3
Angle	3642.41	270	638.624	-1479.34
Potential	5.16e+06	5.1e+06	7.47e+07	-3.13e+07

Q125E

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2519.85	1700	6351.32	-10027.5
Angle	3626.21	260	618.433	-1418.24
Potential	5.23e+06	5.2e+06	7.5e+07	-3.17e+07

Y166N

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	3029.19	2200	-nan	-12529.5
Angle	3654.58	280	-nan	-1486.71
Potential	7.95e+06	7.8e+06	-nan	-4.67e+07

G249S

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2775.97	2000	6761.45	-11375.2
Angle	3682.24	300	670.885	-1625.24
Potential	5.96e+06	5.0e+06	8.02e+07	-3.61e+07

C264W

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	3186.75	2300	-nan	-13603.2
Angle	3831.06	370	-nan	-2070.89
Potential	3.41e+07	3.3e+07	-nan	-2.03e+08

R265W

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2473.43	1700	6385.14	-9741.04
Angle	3726.4	330	827.187	1803.54
Potential	5.36e+06	5.3e+06	7.68e+07	-3.26e+07

I326T

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	3214.03	2300	7364.47	-13490.1
Angle	3738.44	310	698.943	-1792.01
Potential	7.29e+06	6.9e+06	8.86e+07	-4.38e+07

F409C

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2341.69	1600	6048.14	-9087.07
Angle	3597.89	240	594.267	-1309.54
Potential	4.68e+06	4.7e+06	7.12e+07	-2.85e+07

Y438N

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	3141.2	2300	-nan	-13216.1
Angle	3672.66	290	-nan	-1550.04
Potential	8.33e+06	8.1e+06	-nan	-4.94e+07

Links

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go back to Task 6 Sequence based mutation analysis

go to Reference Sequence BCKDHA