Table 5.
Change in RMSD [Å] after refinement for different protein parts.
| PDB code | Helical | Extended | Coil | Membrane | Water | Ligand binding pocket |
|---|---|---|---|---|---|---|
| Initial models – RMSD [Å] | ||||||
| 1j4n | 1.33 | - | 4.26 | 1.32 | 4.64 | - |
| 1py6 | 1.07 | 3.52 | 2.20 | 0.92 | 2.18 | 0.78 |
| 1qj8 | - | 2.16 | 4.82 | 1.59 | 4.04 | - |
| 3odu | 2.57 | 2.65 | 5.97 | 1.97 | 4.76 | 3.30 |
| 3vg9 | 2.41 | - | 5.43 | 1.91 | 4.60 | 3.31 |
| 4hyj | 2.20 | - | 5.47 | 1.64 | 4.67 | 1.58 |
| 4kr8 | 0.80 | 0.72 | 2.22 | 0.83 | 2.29 | - |
| 4n6h | 1.21 | 1.27 | 2.59 | 0.79 | 2.08 | 1.05 |
| Ave. | 1.66±0.72 | 2.06±1.11 | 4.12±1.56 | 1.37±0.17 | 3.66±0.44 | 2.00+1.22 |
| DPPC bilayer simulations – ΔRMSD [Å] | ||||||
| 1j4n | −0.08 | - | −0.13 | −0.08 | −0.14 | - |
| 1py6 | −0.10 | −0.03 | −0.17 | −0.09 | −0.14 | −0.05 |
| 1qj8 | - | −0.30 | −0.56 | −0.17 | −0.57 | - |
| 3odu | −0.08 | −0.26 | −0.20 | −0.13 | −0.09 | −0.12 |
| 3vg9 | 0.06 | - | −0.02 | −0.06 | 0.13 | −0.02 |
| 4hyj | 0.08 | - | −0.23 | 0.09 | −0.09 | 0.23 |
| 4kr8 | −0.22 | 0.05 | −0.03 | 0.06 | −0.08 | - |
| 4n6h | −0.18 | −0.14 | −0.18 | −0.11 | −0.24 | −0.08 |
| Ave. | −0.07±0.04 | −0.14±0.07 | −0.19±0.06 | −0.06±0.03 | −0.15±0.07 | −0.01±0.06 |
| Water simulations – ΔRMSD [Å] | ||||||
| 1j4n | −0.10 | - | −0.10 | −0.09 | −0.14 | - |
| 1py6 | −0.10 | −0.01 | −0.17 | −0.11 | −0.10 | 0.02 |
| 1qj8 | - | −0.23 | −0.40 | −0.11 | −0.46 | - |
| 3odu | 0.00 | −0.07 | −0.26 | −0.05 | −0.06 | 0.27 |
| 3vg9 | −0.01 | - | −0.03 | −0.06 | 0.03 | −0.05 |
| 4hyj | 0.00 | - | −0.28 | 0.02 | −0.17 | 0.20 |
| 4kr8 | −0.23 | 0.00 | −0.17 | −0.01 | −0.20 | - |
| 4n6h | −0.07 | −0.20 | −0.16 | −0.04 | −0.14 | −0.04 |
| Ave. | −0.07±0.03 | −0.10±0.05 | −0.20±0.04 | −0.05±0.02 | −0.15±0.05 | 0.08±0.07 |
Residue-based RMSD and ΔRMSD values are shown for the initial homology models and final models after refinement. The rows labeled “Ave.” report the average values over proteins for each part of the structures for the initial models and for the refined models in DPPC and in water separately. Homology and final models were superimposed onto the experimental structure using Cα atoms for the calculation of residue based RMSD values. ΔRMSD values for each residue were then calculated by subtracting residue-based RMSD of homology models from that of the final models. Secondary structures were determined using DSSP for the experimental structures and residue-based RMSD values for helical, extended and coil regions were averaged over residues for each region. Residues for the membrane and water regions were determined with respect to the z-positions of the center of mass of each residue. Taking 28.5 Å as the membrane width of DPPC bilayer, the z-positions locate between +14.25 and −14.25 Å were assigned to the membrane region and residues outside of that range were assigned to the water region. The last column shows the change in RMSD for residues with the center of mass within 10 Å distance from the ligand center of mass. The coordinates of ligands were taken from the corresponding target crystal structures.