Table 4.
Effect of the pH on the State of Ionizable Residues for the Rhodopsins of the m-Seta
| modelb | chain | pH | neutral residuesd | ΔES1–S0e | e,f |
|---|---|---|---|---|---|
| m-Set | |||||
| ASRAT-1 | A | 5.6c | D(198,217), E(36), H(8,69) | 52.3 (2.27) | 0.3 (0.01) |
| ASRAT-1(c-pH) | A | 7.4 | E(36), H(8,69) | 58.9 (2.46) | 6.9 (0.29) |
| ASR13C-2 | A | 5.6c | D(198,217), E(36), H(8,69) | 54.2 (2.26) | 1.0 (0.04) |
| ASR13C-2(c-pH) | A | 7.4 | E(36), H(8–69) | 59.2 (2.47) | 6.0 (0.25) |
| bR13C | A | 5.2c | D(85,96,115), E(194) | 53.3 (2.22) | 1.1 (0.05) |
| A | 7.4 | D(96), E(194) | 63.2 (2.64) | 11.0 (0.48) | |
| bRAT | A | 5.6c | D(85,96,115), E(194) | 53.2 (2.30) | 2.9 (0.13) |
| A | 7.4 | D(96), E(194) | 64.2 (2.78) | 13.9 (0.60) | |
| bathoRh | A | 6.0c | D(83), E(122,181,249), H(211) | 56.2 (2.44) | 2.2 (0.09) |
| bathoRh(c-pH) | A | 7.4 | D(83), E(122,181), H(211) | 57.1 (2.48) | 3.1 (0.13) |
| bathoRhc | B | 6.0c | D(83), E(122,181), H(211) | 54.0 (2.34) | 0.0 (0.00) |
| bathoRh(c-pH-2) | B | 7.4 | D(83), E(122,181), H(211) | 54.0 (2.34) | 0.0 (0.00) |
| BPR | A | 4.5c | E(90,124) | 63.7 (2.76) | 5.4 (0.23) |
| BPR(c) | A | 7.4 | E(90) | 57.2 (2.48) | −1.1 (−0.05) |
| BPR(c-2) | B | 4.5c | E(90,124) | 63.7 (2.76) | 5.4 (0.23) |
| BPR(c-pH-2) | B | 7.4 | E(90) | 57.0 (2.47) | −1.3 (0.06) |
| Rh | A | 6.0c | D(83), E(122,181), H(211) | 57.7 (2.50) | 0.3 (0.01) |
| Rh(c-pH) | A | 7.4 | D(83), E(122,181), H(211) | 57.7 (2.50) | 0.3 (0.01) |
| Rhc | B | 6.0c | D(83), E(122,181), H(211) | 55.8 (2.42) | −1.6 (−0.07) |
| Rh(c-pH-2) | B | 7.4 | D(83), E(122), H(211) | 65.0 (2.82) | 7.6 (0.33) |
| SqRh | A | 6.4c | D(80), H(319) | 60.9 (2.64) | 2.4 (0.10) |
| SqRh(c-pH) | A | 7.4 | D(80), H(319) | 60.9 (2.64) | 2.4 (0.10) |
| SqRh(c) | B | 6.4c | D(80), H(319) | 59.4 (2.57) | 0.9 (0.04) |
| SqRh(c-pH-2) | B | 7.4 | D(80), H(319) | 59.4 (2.57) | 0.9 (0.04) |
| hMeOp | A | 6.4c | D(50), H(288,279) | 61.2 (2.65) | 0.8 (0.03) |
| hMeOp(c-pH) | A | 7.4 | D(50), H(288,279) | 61.2 (2.65) | 0.8 (0.03) |
a
Residues with neutral charge at physiological (7.4) and experimental crystallographic pH.
b
Customized models at physiological pH (c-pH).
c
Experimental crystallographic pH.
d
One letter code: Aspartic acid (D), Glutamic acid (E) and Histidine (H).
e
Values in kcal mol−1 and in eV in parentheses.
f
Experimental values are reported in Table 2.