Difference between revisions of "Fabry:Structure-based mutation analysis"
Staniewski (talk | contribs) (→Preparation) |
Staniewski (talk | contribs) |
||
Line 15: | Line 15: | ||
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Chain |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Chain |
||
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Positions (up to 429) |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Positions (up to 429) |
||
− | ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-factor<ref>R value [http://www.proteopedia.org/wiki/index.php?title=R_value&oldid=569063], last checked on June 21, 2012</ref> |
+ | ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-factor<ref>R value [http://www.proteopedia.org/wiki/index.php?title=R_value&oldid=569063 http://www.proteopedia.org/wiki/index.php?title=R_value&oldid=569063], last checked on June 21, 2012</ref> |
− | ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-free<ref>Free R [http://www.proteopedia.org/wiki/index.php?title=Free_R&oldid=1390871], last checked on June 21, 2012</ref> |
+ | ! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-free<ref>Free R [http://www.proteopedia.org/wiki/index.php?title=Free_R&oldid=1390871 http://www.proteopedia.org/wiki/index.php?title=Free_R&oldid=1390871], last checked on June 21, 2012</ref> |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pH |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pH |
||
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDBsum |
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDBsum |
Revision as of 22:27, 21 June 2012
Fabry Disease » Structure-based mutation analysis
The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.
Contents
Preparation
<figtable id="tab:Prep">
All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.
Entry | Method | Resolution (Å) | Chain | Positions (up to 429) | R-factor<ref>R value http://www.proteopedia.org/wiki/index.php?title=R_value&oldid=569063, last checked on June 21, 2012</ref> | R-free<ref>Free R http://www.proteopedia.org/wiki/index.php?title=Free_R&oldid=1390871, last checked on June 21, 2012</ref> | pH | PDBsum | PDB |
---|---|---|---|---|---|---|---|---|---|
1R46 | X-ray | 3.25 | A/B | 32-422 | 0.262 | 0.301 | 8.0 | [»] | [»] |
1R47 | X-ray | 3.45 | A/B | 32-422 | 0.285 | 0.321 | 8.0 | [»] | [»] |
3GXN | X-ray | 3.01 | A/B | 32-421 | 0.239 | 0.301 | 4.5 | [»] | [»] |
3GXP | X-ray | 2.20 | A/B | 32-422 | 0.204 | 0.265 | 4.5 | [»] | [»] |
3GXT | X-ray | 2.70 | A/B | 32-422 | 0.245 | 0.306 | 4.5 | [»] | [»] |
3HG2 | X-ray | 2.30 | A/B | 32-422 | 0.178 | 0.202 | 4.6 | [»] | [»] |
3HG3 | X-ray | 1.90 | A/B | 32-426 | 0.167 | 0.197 | 6.5 | [»] | [»] |
3HG4 | X-ray | 2.30 | A/B | 32-423 | 0.166 | 0.221 | 4.6 | [»] | [»] |
3HG5 | X-ray | 2.30 | A/B | 32-422 | 0.192 | 0.227 | 4.6 | [»] | [»] |
3LX9 | X-ray | 2.04 | A/B | 32-422 | 0.178 | 0.218 | 6.5 | [»] | [»] |
3LXA | X-ray | 3.04 | A/B | 32-426 | 0.216 | 0.244 | 6.5 | [»] | [»] |
3LXB | X-ray | 2.85 | A/B | 32-427 | 0.227 | 0.264 | 6.5 | [»] | [»] |
3LXC | X-ray | 2.35 | A/B | 32-422 | 0.186 | 0.237 | 6.5 | [»] | [»] |
3S5Y | X-ray | 2.10 | A/B | 32-422 | 0.195 | 0.230 | 5.1 | [»] | [»] |
3S5Z | X-ray | 2.00 | A/B | 32-421 | 0.211 | 0.234 | 5.1 | [»] | [»] |
3TV8 | X-ray | 2.64 | A/B | 32-422 | 0.203 | 0.239 | 4.6 | [»] | [»] |
</figtable>
We did not choose the structure 3HG3, although it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>), which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, since it has an Alanin at position 170 (part of the active site) instead of an Aspartic acid. After excluding those structures, that had deviations in the sequence, we had to choose between ten sequences (1R46, 1R47, 3GXN, 3GXP, 3GXT, 3HG2, 3HG4, 3HG5, 3S5Y, 3S5Z) and decided to use 3S5Y. This structure has the advantage of a good pH, very good coverage and still reasonable resolution and R-factor.
Vizualisation
From the first glance, we would consider A143T as disease causing, because it is located right next to a Cysteine, that forms a disulfide bond (yellow) and might interfere with it. The same applies for S65T, which is in the structural neighborhood of this bond and also might cause atom clashes.
There is no mutation that can interfere with the active site(purple) or the substrate binding site (cyan).
The mutation N215S seems to play an important role in the binding of the ligand N-Acetyl-D-Glucosamine.
Both prolines Pro 323 and Pro 40 do not give the impression as if they would be very important. Also Arg 356 is on the surface of the protein and is not involved in any binding, although it might be influencing the nearby helix. This also is applicable for the SNP R118H.
It seems possible, that the mutation V316I does not have a big impact on the helix it is located in.
Neither Q279E nor I289V have an obvious reason to be considered as crucial in this structure.
Create mutation
SCWRL
Comparison energies
foldX
<figtable id="tab:energyStart"> ADD CAPTION HERE
Type | Energy |
---|---|
BackHbond | -528.41 |
SideHbond | -149.96 |
Energy_VdW | -1013.85 |
Electro | -25.51 |
Energy_SolvP | 1310.89 |
Energy_SolvH | -1318.53 |
Energy_vdwclash | 99.21 |
energy_torsion | 26.73 |
backbone_vdwclash | 478.11 |
Entropy_sidec | 482.20 |
Entropy_mainc | 1219.31 |
water bonds | -29.53 |
helix dipole | -12.51 |
loop_entropy | 0.00 |
cis_bond | 4.50 |
disulfide | -29.93 |
kn electrostatic | -0.98 |
partial covalent interactions | 0.00 |
Energy_Ionisation | 1.20 |
Entropy Complex | 0.00 |
Total | 34.82 |
</figtable>
Minimise
Gromacs
References
<references />