TABLE 1.
I-domain ion-pairs and pKa values
| Residue | pKaa | Ion-pair partner | Salt bridgeb | d(O … HN)c | Structure context | Energeticsd |
|---|---|---|---|---|---|---|
| % | Å | |||||
| Asp-244e | NAf | None | 0 | NA | D-loop | NA |
| Asp-246 | 4.2 ± 0.1 | None | 0 | NA | D-loop | Null |
| Asp-253 | <2.8 | Lys-311 | 60 | 1.7 | Links β2-β5 | Stabilizing |
| Asp-271 | <2.8 | Lys-268 | 53 | 1.7 | Turn before β3 | Stabilizing |
| Asp-292 | <2.8 | Lys-279 | 37 | 3.4 | Links β4-βi | Stabilizing |
| Asp-302 | <2.8 | His-305 | 43 | 2.2 | β4-β5 hairpin | Stabilizing |
| His-305 | 9.05 ± 0.04 | Asp-302 | See Asp-302 | See Asp-302 | see Asp-302 | Stabilizing |
| Glu-307 | 3.9 ± 0.3 | Arg-299 | 10 | 5.3 | Links β5-β4 | Slight stabilizing |
| Asp-316 | 3.0 ± 0.3 | Arg-325 | 0 | 6.0 | Links βii-αi | Slight stabilizing |
| Asp-317 | < 2.8 | Lys-237 | 97 | 1.7 | Links βii-β1 | Stabilizing |
| Glu-323 | 3.6 ± 0.1 | Unknown | 0 | NA | Unknown | Slight stabilizing |
| Asp-336 | 4.3 ± 0.3 | None | 0 | NA | Surface β6 | Null |
a Uncertainties in pKa values are given as the S.E. of non-linear least square fits of the chemical shift data as a function of pH (e.g. Fig. 1, B and C). The minimum error in the pKa, however, is likely to be limited by the accuracy of the pH meter, which is 0.1 pH units.
b We use the terminology “salt bridge” for a hydrogen-bonded ion pair that has the closest approach distance between the side-chain NH hydrogen-bond donor and O carbonyl acceptor atoms shorter than 2.5 Å in the NMR structure closest to the ensemble mean (structure 1 in the ensemble of PDB code 2M5S). The column gives the fraction of structures in the NMR ensemble of 30 structures (32) in which the side chains of the ion-pair are hydrogen-bonded.
c Nearest approach NH to O side-chain distance in the NMR structure of the I-domain closest to the ensemble average.
d Based on differences of pKa values in the I-domain from the following random-coil values (43): histidine = 6.5, aspartate = 4.0; glutamate = 4.4. An interaction is considered stabilizing if the pKa shift is greater than 1 pH unit, slightly stabilizing if the shift is between 0.5 and 1 pH unit and negligible if it is <0.5 pH.
e Resonances for Asp-244 were not observed in the NMR spectrum due to conformational exchange line-broadening (19).
f NA, not applicable.