Table 1.
Kinetic and equilibrium parameters for chromophore-tryptophan association
| Chromophore | kon/M−1 ns−1 | koff/ns−1 | Kd/mM | |
|---|---|---|---|---|
| Alexa488, experimenta | 1.2 (0.2) | 0.071 (0.014) | 59 (17) | |
| Alexa488 qHF, TIP4P/2005 | 2.7 (0.5) | 0.052 (0.012) | 20 (6) | |
| Alexa488 qHF, TIP4P/2005(1.10) | 1.4 (0.3) | 0.128 (0.036) | 91 (32) | |
| Alexa488 qHF, TIP3P | 14.3 (2.6) | 0.102 (0.019) | 7.1 (1.8) | |
| Alexa488 qDFT, TIP4P/2005 | 3.2 (0.9) | 0.075 (0.021) | 23 (9) | |
| Alexa488 qDFT, TIP4P/2005(1.10) | 1.8 (0.5) | 0.134 (0.042) | 75 (30) | |
| Alexa594, experiment | 1.1 (0.2) | 0.036 (0.007) | 33 (9) | |
| Alexa594 qHF, TIP4P/2005 | 3.1 (0.7) | 0.012 (0.008) | 3.9 (2.7) | |
| Alexa594 qHF, TIP4P/2005(1.10) | 1.3 (0.3) | 0.083 (0.020) | 63 (20) | |
| Alexa594 qHF, TIP3P | 11.9 (3.3) | 0.037 (0.011) | 3.1 (1.3) | |
| Alexa594 qDFT, TIP4P/2005 | 5.2 (1.0) | 0.006 (0.003) | 1.2 (0.6) | |
| Alexa594 qDFT, TIP4P/2005(1.10) | 1.8 (0.2) | 0.139 (0.059) | 76 (34) | |
The chromophores have charges determined from a Hartree-Fock electrostatic potential (qHF) or DFT electrostatic potential (qDFT), and are used together with the TIP3P, TIP4P/2005, or TIP4P/2005(1.10) water models (the last is TIP4P/2005 with solute-water interactions scaled by a factor λpw = 1.10). The tryptophan concentration was 29 mM in simulations and 40 mM in experiment (37).
Experimental data taken from Haenni et al. (37). Experimental errors are estimated as 20% of the reported rates. Note that these data were recorded for each dye together with C5 maleimide linker, reacted with β-mercaptoethanol. However, essentially identical results, considering experimental error, are obtained for the free dyes.