Table 1: Results from free energy calculations that summarize values obtained for at 298 K.
Data for the temperature dependence of were fit to equation (1), setting T0 = 298 K, to extract values for and .
Residue / unit | Model compound |
kcal/mol |
kcal/mol |
cal / mol-K |
---|---|---|---|---|
Ala | methane | 1.63 | −2.57 | 48.93 |
Val / Pro | propane | 1.85 | −6.33 | 105.80 |
Leu | 2-methalpropane | 2.22 | −5.92 | 109.38 |
Ile | -butane | 2.00 | −6.34 | 105.23 |
Met | ethyl methyl thioether | −1.92 | −10.11 | 71.10 |
Phe | toluene | −0.17 | −8.68 | 102.24 |
Cys | methanethiol | −1.04 | −5.84 | 43.61 |
Tyr | p-Cresol | −5.85 | −15.62 | 71.09 |
Trp | 3-Methylindole | −4.46 | −12.67 | 108.10 |
Ser | methanol | −5.08 | −10.41 | 10.43 |
Thr | ethanol | −4.98 | −12.55 | 50.06 |
Asn | acetamide | −8.61 | −14.37 | 6.18 |
Gln | propionamide | −8.39 | −16.06 | 51.47 |
His | 4-methylimidazole | −10.04 | −17.60 | 38.01 |
backbone / Gly | N-methylacetamide | −8.33 | −16.10 | 44.73 |
Arg | -propylguanidine | −47.62* | −57.24* | 69.39 |
Lys | 1-butylamine | −60.49* | −70.37* | 29.98 |
Asp | acetic acid | −89.91* | −98.65* | −44.97 |
Glu | propionic acid | −86.16* | −96.62* | −8.75 |
As with the default ABSINTH model, in ABSINTH-T, the rFoS values, and therefore the values we used for ionizable residues are offset from the calculated by a fixed constant of −30 kcal/mol. This, as was shown in the original work, is required to avoid the chelation of solution ions around ionizable residues. This “feature” remains a continuing weakness of the ABSINTH paradigm and one that we hope to remedy through suitable generalization of the model used in ABSINTH to interpolate between fully solvated and fully desolvated states.