Difference between revisions of "Structure-based mutation analysis"

From Bioinformatikpedia
m (→‎Mapping)
m (→‎Mapping)
Line 59: Line 59:
 
{|border="1" style="text-align:center; border-spacing:0" cellpadding="2" cellspacing="3" align = "center"
  
{|border="1" style="text-align:center; border-spacing:0" cellpadding="2" cellspacing="3" align = "center"
 
|-
  
|-
−
! colspan=4 | Mutation 2 [M35T] || colspan=4 | Mutation 3 [S65C] || colspan=4 | Mutation 4 [I105T] || colspan=4 | Mutation 5 [Q127H] || colspan=4 | Mutation 6 [A176V] || colspan=4 | Mutation 7 [T217I] || colspan=4 | Mutation 8a [C282Y] || colspan=4 | Mutation 8b [C282S]
 +
! colspan=2 | Mutation 2 [M35T] || colspan=2 | Mutation 3 [S65C] || colspan=2 | Mutation 4 [I105T] || colspan=2 | Mutation 5 [Q127H] || colspan=2 | Mutation 6 [A176V] || colspan=2 | Mutation 7 [T217I] || colspan=2 | Mutation 8a [C282Y] || colspan=2 | Mutation 8b [C282S]
 
|-
  
|-
−
! colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition || colspan=2 | Mutation || colspan=2 | Superposition
 +
! Mutation || Superposition || Mutation || Superposition || Mutation || Superposition || Mutation || Superposition || Mutation || Superposition || Mutation || Superposition || Mutation || Superposition || Mutation || Superposition
 
|-
  
|-
  +
! SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL || SCWRL
−
!
  
−
| Reference || -- || 247.944 || 1
  
 
|-
  
|-
  +
| [[File:UProt(35)_1a6z_35_35_mutant.png|100px]] || [[File:UProt(35)_1a6z_35_35_superpos.png|100px]] || [[File:UProt(65)_1a6z_65_65_mutant.png|100px]] || [[File:UProt(65)_1a6z_65_superpos.png|100px]] || [[File:UProt(105)_1a6z_105_mutant.png|100px]] || [[File:UProt(105)_1a6z_105_superpos.png|100px]] || [[File:UProt(127)_1a6z_127_mutant.png|100px]] || [[File:UProt(127)_1a6z_127_superpos.png|100px]] || [[File:UProt(176)_1a6z_176_mutant.png|100px]] || [[File:UProt(176)_1a6z_176_superpos.png|100px]] || [[File:UProt(217)_1a6z_217_mutant.png|100px]] || [[File:UProt(217)_1a6z_217_superpos.png|100px]] || [[File:UProt(282)_1a6z_282a_mutant.png|100px]] || [[File:UProt(282)_1a6z_282a_superpos.png|100px]] || [[File:UProt(282)_1a6z_282b_mutant.png|100px]] || [[File:UProt(282)_1a6z_282b_superpos.png|100px]]
−
| Mutation 2 [M35T] || 35 || 252.324 || 1,017665279
  
 
|-
  
|-
  +
| [[File:UProt(35)_pdb(13)_mutant.png|100px]] || [[File:UProt(35)_pdb(13)_superpos.png|100px]] || [[File:UProt(65)_pdb(43)_mutant.png|100px]] || [[File:UProt(65)_pdb(43)_superpos.png|100px]] || [[File:UProt(105)_pdb(83)_mutant.png|100px]] || [[File:UProt(105)_pdb(83)_superpos.png|100px]] || [[File:UProt(127)_pdb(105)_mutant.png|100px]] || [[File:UProt(127)_pdb(105)_superpos.png|100px]] || [[File:UProt(176)_pdb(154)_mutant.png|100px]] || [[File:UProt(176)_pdb(154)_superpos.png|100px]] || [[File:UProt(217)_pdb(195)_mutant.png|100px]] || [[File:UProt(217)_pdb(195)_superpos.png|100px]] || [[File:UProt(282a)_pdb(260)_mutant.png|100px]] || [[File:UProt(282a)_pdb(260)_superpos.png|100px]] || [[File:UProt(282b)_pdb(260)_mutant.png|100px]] || [[File:UProt(282b)_pdb(260)_superpos.png|100px]]
−
| Mutation 3 [S65C] || 65 || 246.695 || 0,994962572
  
 
|-
  
|-
  +
! PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL || PyMOL
−
| Mutation 4 [I105T] || 105 || 250.833 || 1,011651825
  
−
|-
  
−
| Mutation 5 [Q127H] || 127 || 252.368 || 1,017842739
  
−
|-
  
−
| Mutation 6 [A176V] || 176 || 280.381 || 1,130823896
  
−
|-
  
−
| Mutation 7 [T217I] || 217 || 260.189 || 1,049386152
  
−
|-
  
−
| Mutation 8a [C282Y] || 282 || 389.539 ||1,571076533
  
−
|-
  
−
| Mutation 8b [C282S] || 282 || 255.859 || 1,031922531
  
 
|-
  
|-
 
|}
  
|}

Revision as of 22:09, 4 July 2011

General

According to the UniProt entry about HFE_HUMAN are three 3D-structures of the HFE_HUMAN available, which are listed below. We have chosen the '1A6Z' because it has the best resolution, a very good R-Value (it measures the quality of the model obtained from the crystallographic data), a pH near the physiological optimum and is as good as complete. '1DE4' has a slightly better R-Value and pH, but this PDB also includes the transferrin receptor, which we do not need and do not want in our structure. Also the missing residues of chain A are the same as in the structure '1A6Z' which are only the first three positions. '1C42' is only a hypothetical model, so we exclude it from further research.

stereochemistrical properties of 1a6z

All stereochemistrical properties of the structure are shown in the figure to the right<ref>Lebrón JA, Bennett MJ, Vaughn DE, Chirino AJ, Snow PM, Mintier GA, Feder JN, Bjorkman PJ.: Crystal structure of the hemochromatosis protein HFE and characterization of its interaction with transferrin receptor.</ref>.

PDB Method Resolution (Å) Chain R-Value R-Free pH Temperature Completeness Missing residues (Chain:pos)
1A6Z X-ray 2.60 A/C 0.233 0.277 6.5 -150.15°C (123 k) 98.0 A:1-3 C:1-3 - - - -
1C42 model - A - - - - - - - - - - -
1DE4 X-ray 2.80 A/D/G 0.231 0.265 8.0 -173.15°C (100 k) 94.3 A:1-3 C:121,757-760 D:1-3 F:121,757-760 G:1-3 I:121,757-760

We used the following 7 mutations, because we were not able to map 3 of them to the 1A6ZA chain mostly because of position errors. We are using the same names as given in Task 6. Mutation 8 had to be split into two parts because of possible mutation into to different amino acids.

Mutation
Mutation 2 [M35T]
Mutation 3 [S65C]
Mutation 4 [I105T]
Mutation 5 [Q127H]
Mutation 6 [A176V]
Mutation 7 [T217I]
Mutation 8a [C282Y]
Mutation 8b [C282S]

Mapping

Because we have no annotation about the active site so we just visualized the mutations at the '1A6Z' structure. Secondly we are using the same mutations as in Task 6 and have therefore the same problemes with their visualization (only 7 of 10 visualizeable).

All mutations are scattered accross the protein with no affinity to some special region or secondary structure element. Mutations shown in red are near glycosylation positions and mutations in yellow are near disulfidbonds.

1A6ZA with 7 of 10 visualized mutations taken from task 6
Mutation 2 [M35T] Mutation 3 [S65C] Mutation 4 [I105T] Mutation 5 [Q127H] Mutation 6 [A176V] Mutation 7 [T217I] Mutation 8a [C282Y] Mutation 8b [C282S]
Mutation Superposition Mutation Superposition Mutation Superposition Mutation Superposition Mutation Superposition Mutation Superposition Mutation Superposition Mutation Superposition
SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL SCWRL
100px 100px 100px UProt(65) 1a6z 65 superpos.png UProt(105) 1a6z 105 mutant.png UProt(105) 1a6z 105 superpos.png UProt(127) 1a6z 127 mutant.png UProt(127) 1a6z 127 superpos.png UProt(176) 1a6z 176 mutant.png UProt(176) 1a6z 176 superpos.png UProt(217) 1a6z 217 mutant.png UProt(217) 1a6z 217 superpos.png UProt(282) 1a6z 282a mutant.png UProt(282) 1a6z 282a superpos.png UProt(282) 1a6z 282b mutant.png UProt(282) 1a6z 282b superpos.png
UProt(35) pdb(13) mutant.png UProt(35) pdb(13) superpos.png UProt(65) pdb(43) mutant.png UProt(65) pdb(43) superpos.png UProt(105) pdb(83) mutant.png UProt(105) pdb(83) superpos.png UProt(127) pdb(105) mutant.png UProt(127) pdb(105) superpos.png UProt(176) pdb(154) mutant.png UProt(176) pdb(154) superpos.png UProt(217) pdb(195) mutant.png UProt(217) pdb(195) superpos.png UProt(282a) pdb(260) mutant.png UProt(282a) pdb(260) superpos.png UProt(282b) pdb(260) mutant.png UProt(282b) pdb(260) superpos.png
PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL PyMOL

Energy comparison

SCWRL

SCWRL predicts protein side-chain confirmations given a fixed backbone. We are using SCWRL version 4 released in 2009.

Usage:

  • use only chain A of backbone pdb: 1A6ZA.pdb
  • extract amino acid sequence and change it to lowercase: aa.txt
  • introduce each mutation into on seperated aa_x.txt file as capital
    • cmd: scwrl -i 1A6ZA.pdb -s aa_x.txt -o ./mutant_pdbs/1A6ZA_mutant_x.pdb > 1A6ZA_mutant_x.txt

Results:

Robert: currently working.

Mutation Position Energy Energy normalized
Reference -- 247.944 1
Mutation 2 [M35T] 35 252.324 1,017665279
Mutation 3 [S65C] 65 246.695 0,994962572
Mutation 4 [I105T] 105 250.833 1,011651825
Mutation 5 [Q127H] 127 252.368 1,017842739
Mutation 6 [A176V] 176 280.381 1,130823896
Mutation 7 [T217I] 217 260.189 1,049386152
Mutation 8a [C282Y] 282 389.539 1,571076533
Mutation 8b [C282S] 282 255.859 1,031922531
  • The energy is normalized by the wild-type structure. A value larger then 1 means that the energy is increased compared to the wild-type. A value smaller 1 shows a decreased energy.

Minimise

Minimise is able to minimise the energy of an model.

Usage:

  • remove all hydrogen and water atoms from the pdb files with repairPDB: 1A6ZA_mutant_x_clean.pdb
    • cmd: repairPDB 1A6ZA_mutant_x.pdb -nosol > ./repair_pdb/1A6ZA_mutant_x_clean.pdb
  • minimise the energy of the models:
    • cmd: minimise 1A6ZA_mutant_x_clean.pdb ./minimised_pdb/1A6ZA_mutant_x_clean_minimised.pdb > 1A6ZA_mutant_x_clean_minimised.txt

Results:

Robert: currently working.

Mutation Position Energy Energy normalized
Reference -- -3724.153777 1
Mutation 2 [M35T] 35 -5020.465319 1,348082174
Mutation 3 [S65C] 65 -5040.815685 1,353546601
Mutation 4 [I105T] 105 -5028.869826 1,35033893
Mutation 5 [Q127H] 127 -5031.137220 1,350947765
Mutation 6 [A176V] 176 -4957.946411 1,331294761
Mutation 7 [T217I] 217 -5037.718631 1,352714988
Mutation 8a [C282Y] 282 -2596.778899 0,697280256
Mutation 8b [C282S] 282 -5017.057355 1,347167076
  • The energy is normalized by the wild-type structure. A value larger then 1 means that the energy is increased compared to the wild-type. A value smaller 1 shows a decreased energy.

FoldX

FoldX scores the importance of amino acid interactions according to the overall stability of the protein and calculates the energy.

Usage:

  • create a runfile tutorial and adjust all default parameters to known (if possible): runfile.txt
  • create a listfile of all pdb files that should be included in energy calculation: listfile.txt
  • run foldx with runlist
    • cmd: Foldx -runfile runfile.txt > output.txt

Results:

Mutation Position Energy Energy normalized
Reference -- 169.51 1
Mutation 2 [M35T] 35 208.08 1,227538198
Mutation 3 [S65C] 65 206.66 1,219161111
Mutation 4 [I105T] 105 210.39 1,241165713
Mutation 5 [Q127H] 127 205.04 1,209604153
Mutation 6 [A176V] 176 214.31 1,264291192
Mutation 7 [T217I] 217 208.15 1,227951153
Mutation 8a [C282Y] 282 242.23 1,429001239
Mutation 8b [C282S] 282 215.50 1,271311427
  • The energy is normalized by the wild-type structure. A value larger then 1 means that the energy is increased compared to the wild-type. A value smaller 1 shows a decreased energy.

Gromacs

  • We used the -ignh mode to ignore all hydroxen atom.
  • As forcefield, we chosed the AMBER03, CHARMM27 and AMBERGS model.

Energy table for the AMBER03 forcefield.

Mutation Total Energy Bond Difference Bond Total Energy Angle Difference Angle Total Energy Potential Difference Potential
Wild-Type 848,392 1 2707,42 1 -32380,6 1
[M35T] 774,332 0,912705447 2707,35 0,999974145 -32738 1,011037473
[S65C] 695,044 0,819248649 2699,65 0,997130109 -32872,2 1,01518193
[I105T] 0 0 0 0 0 0
[Q127H] 835,05 0,984273779 2782,21 1,027624085 -32213,2 0,994830238
[A176V] 760,573 0,896487709 2734,66 1,010061239 -33030,1 1,020058307
[T217I] 727,061 0,8569871 2712,54 1,001891099 -32609,5 1,007069048
[C282Y] 851,692 1,003889711 2754,62 1,017433571 -31431,1 0,970676887
[C282S] 852,244 1,004540354 2706,07 0,99950137 -32036,4 0,989370178
Energy curve of the AMBER03 forcefield with nstep = 500
Energy curve of the CHARMM27 forcefield with nstep = 500
Energy curve of the AMBERGS forcefield with nstep = 500
time versus nstep plot of the three different forcefields


Wild-Type force field comparisson

Forcefield Bond Angle Potetial
AMBER03 848,392 2707,42 -32380,6
CHARMM27 1064,95 --- -37356,1
AMBERGS 724.545 2785.47 -40390.8

Energy for the Wild-Type

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 848.392 380 -nan -2320.49
Angle 2707.42 22 -nan -96.9545
Potential -32380.6 1200 -nan -7696.01

Energy for the Mutation [M35T]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 774.332 300 2156.92 -1864.67
Angle 2707.35 16 130.232 -51.7455
Potential -32738 1100 3905.23 -7119.34

Energy for the Mutation [S65C]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 695.044 230 1873.95 -1383.66
Angle 2699.65 9.8 113.651 -42.4234
Potential -32872.2 890 3424.15 -5775.47

Energy for the Mutation [I105T]
For this mutation, gromacs faild to calculate energies.

Energy for the Mutation [Q127H]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 835.05 370 -nan -2189.82
Angle 2782.21 20 -nan -94.6097
Potential -32213.2 1100 -nan -7254.92


Energy for the Mutation [A176V]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 760.573 290 -nan -1676.2
Angle 2734.66 20 -nan -125.203
Potential -33030.1 1000 -nan -6485.15

Energy for the Mutation [T217I]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 727.061 260 1980.17 -1567.84
Angle 2712.54 12 119.206 -50.0057
Potential -32609.5 980 3633.19 -6435.18


Energy for the Mutation [C282Y]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 851.692 370 2500.48 -2249.54
Angle 2754.62 25 158.776 -152.741
Potential -31431.1 2100 16296.8 -13588.8


Energy for the Mutation [C282S]

Energy Average Err.Est. RMSD Tot-Drift (kJ/mol)
Bond 852.244 380 2424.32 -2374.34
Angle 2706.07 24 145.766 -110.811
Potential -32036.4 1200 4277.91 -7896.74

References

<references />

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Structure-based_mutation_analysis&oldid=9048"