Table 1. Summary of computed residence times and experimental kinetic/thermodynamic data for HSP90, Grp78, and A2A.
HSP90 | BS2 | BSM | BS1 | BS3 |
---|---|---|---|---|
Exp. tr [s] | 163.9 | 144.9 | 90.9 | 45.5 |
ΔH [kcal mol−1]13 | −2.7 | −3.7 | −3.8 | −1.5 |
TΔS [kcal mol−1]13 | −7.6 | −6.7 | −6.4 | −7.5 |
Comp. Avg. tr ± σ [ns] | 32.8 ± 17.5 | 30.7 ± 24.7 | 21.5 ± 13.8 | 19.1 ± 11.4 |
Comp. Avg. tr ± σe [ns] | 32.8 ± 1.8 | 30.7 ± 2.5 | 21.5 ± 1.4 | 19.1 ± 1.1 |
Comp. Avg. tr ± σBS [ns] | 32.3 ± 3.5 | 30.7 ± 4.5 | 21.5 ± 2.6 | 18.9 ± 2.2 |
Estimated koff [s−1] | 6.6 × 10−3 | reference | 9.9 × 10−3 | 1.1 × 10−2 |
Grp78 | L01 | L14 | L10 | L02 |
Exp. tr [s] | 200.0 | 25.0 | 2.5 | 1.0 |
ΔH [kcal mol−1]14 | −1.3 | −17.5 | n.a. | −13.2 |
TΔS [kcal mol-1]14 | 0.5 | −0.6 | n.a. | −0.7 |
Comp. Avg. tr ± σ [ns] | 11.3 ± 9.0 | 8.4 ± 6.7 | 5.9 ± 3.8 | 2.8 ± 1.6 |
Comp. Avg. tr ± σe [ns] | 11.3 ± 1.0 | 8.4 ± 0.8 | 5.9 ± 0.4 | 2.8 ± 0.2 |
Comp. Avg. tr ± σBS [ns] | 12.0 ± 2.2 | 8.4 ± 1.4 | 5.8 ± 0.8 | 2.8 ± 0.4 |
Estimated koff [s−1] | reference | 7.1 × 10−3 | 1.0 × 10−2 | 2.1 × 10−2 |
A2A | 4e | 4g | 4h | 4a |
Exp. tr [s] | 990.1 | 90.0 | 8.7 | ~ 1 |
Comp. Avg. tr ± σ [ns] | 37.8 ± 25.5 | 31.8 ± 20.2 | 26.5 ± 22.6 | 25.3 ± 18.9 |
Comp. Avg. tr ± σe [ns] | 37.8 ± 5.7 | 31.8 ± 4.5 | 26.5 ± 5.1 | 25.3 ± 4.1 |
Comp. Avg. tr ± σBS [ns] | 37.2 ± 5.1 | 30.4 ± 4.4 | 26.6 ± 4.2 | 25.2 ± 4.1 |
Estimated koff [s−1] | reference | 1.2 × 10−3 | 1.4 × 10−3 | 1.4 × 10−2 |
Experimental residence times (Exp. tr) were obtained by inversion of the reported koff values and are reported in seconds, whereas computational residence times (Comp. Avg. tr) averaged over replicas are reported in nanoseconds; ΔH and TΔS are expressed in kcal mol−1. Residence times are reported together with standard deviation, σ, and standard error of the mean over n samples27, . Moreover, data statistics analyzed by means of the bootstrapping (BS) method is also reported.