Table 3.
Biochemical and physical change prediction between wild-type and mutated PRPH2. Analyses of biochemical and physical parameters by Protean 3D showed an increased global instability from wild-type to mutated PRPH2 protein. Bold text highlights parameters with differences.
| Feature | Wild-Type | Rs390659 | Wild-Type | Rs425876 | Wild-Type | Rs434102 |
|---|---|---|---|---|---|---|
| AA change | E304Q—GLUTAMINE (GLN) | GLUTAMIC ACID (GLU) | K310R—ARGININE (ARG) | LYSINE (LYS) | G338D—ASPARTIC ACID (ASP) | GLYCINE (GLY) |
| Position | 304 | 304 | 310 | 310 | 338 | 338 |
| Type | L-PEPTIDE LINKING | L-PEPTIDE LINKING | L-PEPTIDE LINKING | L-PEPTIDE LINKING | PEPTIDE LINKING | L-PEPTIDE LINKING |
| MW [g/mol] | 147.129 | 146.144 | 147.195 | 175.209 | 75.067 | 133.103 |
| Net charge [pH = 7] | −1 | −0.01 | 0.99 | 0.99 | 0 | −1 |
| pI | 4 | 5.52 | 8.75 | 9.75 | 5.52 | 3.8 |
| Average hydropathy | −3.5 | −3.5 | −3.9 | −4.5 | −0.4 | −3.5 |
| Aliphatic index | 0 | 0 | 0 | 0 | 0 | 0 |
| A₂₈₀ (ox.) | 0 | 0 | 0 | 0 | 0 | 0 |
| A₂₈₀ (red.) | 0 | 0 | 0 | 0 | 0 | 0 |
| ε₂₈₀ [M⁻1 cm⁻1] | 0 | 0 | 0 | 0 | 0 | 0 |
| φ | −62.5° | −62.5° | −66.3° | −66.3° | −162.2° | −162.2° |
| ψ | 15.4° | 15.4° | 32.9° | 32.9° | −2.7° | −2.7° |
| ω | 111.0° | 111.0° | 123.8° | 123.8° | 161.5° | 161.5° |
| Median B-factor | 10.18 | 25 | 12.28 | 25 | 10.9 | 17.95 |
| Effect on protein structure | stabilizing | stabilizing | destabilizing | |||
| Delta_energy | −0.554 | −0.143 | 1664 | |||
| Potential | DFIRE-A | DFIRE-A | DFIRE-A |