Structure-based mutation analysis Gaucher Disease
Cystral structure
<figtable id="tab:mutations">
PDB | Res [Å] | R value | Coverage | pH |
---|---|---|---|---|
2nt0 | 1.80 | 0.18 | 96% (40-536) | 4.5 |
3gxi | 1.84 | 0.19 | 96% (40-536) | 5.5 |
2v3f | 1.95 | 0.15 | 96% (40-536) | 6.5 |
2v3d | 1.96 | 0.16 | 96% (40-536) | 6.5 |
1ogs | 2.00 | 0.18 | 96% (40-536) | 4.6 |
The 5 crystral structures of glycosylceramidase with the highest resolution. The physiological lysosomal pH value is 4.5. 2nt0 was selected for the analysis. </figtable>
Mutations
<figtable id="tab:mutations">
Nr | Pos P04062 |
Pos 2nt0_A |
From | To | Disease causing |
---|---|---|---|---|---|
1 | 99 | 60 | H | R | No |
2 | 211 | 172 | V | I | No |
3 | 150 | 111 | E | K | Yes |
4 | 236 | 197 | L | P | Yes |
5 | 248 | 209 | W | R | Yes |
6 | 509 | 470 | L | P | No |
7 | 351 | 312 | W | C | Yes |
8 | 423 | 384 | A | D | Yes |
9 | 482 | 443 | D | N | No |
10 | 83 | 44 | R | S | No |
Mutations used for the structure-based mutation analysis. </figtable>
<figure id="fig:mutations">
</figure>
SCWRL
We employed SCWRL <ref name="scwrl">Qiang Wang, Adrian A. Canutescu, and Roland L. Dunbrack, Jr.(2008). SCWRL and MolIDE: Computer programs for side-chain conformation prediction and homology modeling. Nat Protoc.</ref> for substituting the wildtype residues listed in <xr id="tab:mutations"/> by the corresponding mutatant residue which is chosen from a rotamer library. <xr id="fig:scwrl"/> denotes the results.
<figure id="fig:scwrl">
SNPs of <xr id="tab:mutations"/> introduced by SCWRL. Blue: wildtype residue; Red: mutant residue. </figure>
None of rotamers chosen by SCWRL clashed with another side-chain or the backbone. We further could not observer changes in the secondary structure or the formation cavities. The hydrogen bonding network changed in case of mutation number 1, 5, 7, and 8 (cf. <xr id="tab:scwrl"/>). W209R introduces a hydrophilic arginine which forms a hydrogen bond to T180. Although not predicted by SCWRL, the arginine might impact the protein structure. W312C is located next to the active site (cf. <xr id="fig:mutations"/>) and there exists a hydrogen bond to E340. Substitution the hydrophobic tryptohphane by a hydrophlic cysteine in the vicinity of the active site might account for the disease-causing effect of this mutation.
<figtable id="tab:scwrl">
Nr | Mutation | Wildtype | Mutatant | Clashes | Structural change | ||
---|---|---|---|---|---|---|---|
H-bonds | Hydrophobicity | H-bonds | Hydrophobicity | ||||
1 | H60R | T471 | Hydrophilic | G62 | Hydrophilic | No | No |
2 | V172I | Hydrophobic | Hydrophobic | No | No | ||
3 | E111K | Hydrophilic | Hydrophilic | No | No | ||
4 | L197P | Hydrophobic | Hydrophobic | No | No | ||
5 | W209R | Hydrophobic | T180 | Hydrophilic | No | No | |
6 | L470P | T482 | Hydrophobic | T482 | Hydrophobic | No | No |
7 | W312C | E340, C342, P316 | Hydrophobic | E340, C342 | Hydrophilic | No | No |
8 | A384D | Hydrophobic | V404 | Hydrophilic | No | No | |
9 | D443N | Hydrophilic | Hydrophilic | No | No | ||
10 | R44S | S13, Y487 | Hydrophilic | S13, Y487 | Hydrophilic | No | No |
Structure-based analysis of SNPs from <xr id="tab:mutations"/>. H-bonds: residues involved in forming hydrogen bonds (cut-off: 3.2 Å). </figtable>
References
<references/>