Table 3 Influence of mutations as predicted by the solvation energy based approach compared with the literature. For each of the five protein structures in the first column, we listed the text mined protein point mutations and the manually extracted effect of this mutation as reported in the literature. We compared these effects with the stability change prediction by our model and evaluated if these were in compliance. In 71% of the cases a change in function or stability is correlated with interaction energy.
From: Improved mutation tagging with gene identifiers applied to membrane protein stability prediction
Protein name | Mutation in literature | Effect as reported in literature | Stability change | Compliance |
|---|---|---|---|---|
Bacteriorhodopsin PDB: 1brr UniProt: P02945 | G113Q | destabilized | slightly destabilizing | yes |
| Â | G113L | destabilized | destabilizing | yes |
| Â | G116Q | destabilized | slightly destabilizing | yes |
| Â | G116L | destabilized | destabilizing | yes |
| Â | I117F | destabilized | slightly destabilizing | yes |
| Â | I117A | destabilized | stabilizing | no |
| Â | M145F | still active | destabilizing | no |
Halorhodopsin PDB: 1e12 UniProt: P16102 | H95A | destabilized | slightly destabilizing | yes |
| Â | H95R | destabilized | slightly stabilizing | no |
| Â | R108Q | not functional | slightly destabilizing | yes |
| Â | T203V | less active | destabilizing | yes |
Rhodospin PDB: 1f88 UniProt: P02699 | T93P | misfolded | destabilizing | yes |
| Â | T94I | night blindness | destabilizing | yes |
| Â | C110F | r. pigmentosa | destabilizing | yes |
| Â | C110Y | r. pigmentosa | destabilizing | yes |
| Â | C110A | r. pigmentosa | slightly destabilizing | yes |
| Â | E122Q | still active | slightly destabilizing | no |
| Â | E122D | still active | slightly destabilizing | no |
| Â | E122A | Â | slightly destabilizing | Â |
| Â | E122R | no retinal binding | slightly destabilizing | yes |
| Â | C185A | wrong disulfide | slightly destabilizing | yes |
| Â | G188R | misfolding | slightly destabilizing | yes |
| Â | S186A | incr. activation energy | slightly destabilizing | yes |
| Â | C187Y | r. pigmentosa | destabilizing | yes |
| Â | C187A | r. pigmentosa | slightly destabilizing | yes |
| Â | N310C | less activity | slightly destabilizing | yes |
| Â | M317C | less activity | slightly destabilizing | yes |
Antiporter PDB: 1zcd UniProt: P13738 | A130C | Â | slightly stabilizing | Â |
| Â | D133A | not functional | slightly destabilizing | yes |
| Â | H225P | less activity | destabilizing | yes |
| Â | H225C | less activity | none | no |
| Â | G303C | not functional | slightly destabilizing | yes |
Aquaporin PDB: 1h6i UniProt: P29972 | N42A | still active | slightly destabilizing | no |
| Â | A73M | not functional | slightly stabilizing | no |
| Â | Y186F | conduct water | slightly destabilizing | Â |
| Â | Y186A | no water conductance | stabilizing | Â |
| Â | Y186N | no water conductance | stabilizing | Â |
| Â | C189M | less activity | slightly stabilizing | no |
| Â | C189S | still active | slightly stabilizing | yes |
| Â | H209A | still active | slightly destabilizing | no |