Table 1.
Comparison of Hydration-free Energies ΔGhyd of Amino Acid (AA) Analogs
| |
|
ΔGhyd,calc |
|||||
|---|---|---|---|---|---|---|---|
| AA analog | ΔGhyd,exp | ffG53A6 | ATB | k = 5 | |||
| Asn | −40.6 | −42.7 | (2.1) | −40.5 | (0.1) | −47.0 | (6.4) |
| Asp | −28.0 | −30.1 | (2.1) | −29.1 | (1.1) | −28.6 | (0.6) |
| Cys | −5.2 | −4.9 | (0.3) | −7.0 | (1.8) | −7.1 | (1.9) |
| Gln | −39.4 | −40.4 | (1.0) | −35.9 | (3.5) | −35.9 | (3.5) |
| Glu | −27.0 | −27.0 | (0.0) | −28.2 | (1.2) | −32.1 | (5.1) |
| His | −42.9 | −44.8 | (1.9) | −43.7 | (0.8) | −40.9 | (2.0) |
| Ile | 8.7; 8.8 | 9.1 | (0.3) | 6.3 | (2.5) | 6.7 | (2.1) |
| Leu | 9.4; 9.7 | 10.8 | (1.2) | 7.4 | (2.2) | 7.1 | (2.5) |
| Lys | −18.3 | −18.1 | (0.2) | −7.2 | (11.1) | −7.2 | (11.1) |
| Met | −6.2 | −7.4 | (1.2) | 2.5 | (8.7) | 2.6 | (8.8) |
| Phe | −3.1 | −1.3 | (1.8) | 1.8 | (4.9) | 0.6 | (3.7) |
| Trp | −24.7 | −25.9 | (1.2) | −20.9 | (3.8) | −19.7 | (5.0) |
| Tyr | −26.6 | −26.9 | (0.3) | −30.1 | (3.5) | −39.5 | (12.9) |
| Val | 8.2 | 8.5 | (0.3) | 8.0 | (0.2) | 8.0 | (0.2) |
| Average | (1.1) | (3.2) | (4.7) | ||||
All free-energy values are given in kJ/mol. When two values separated by a semicolon are given, two experimental values were found. The absolute free-energy differences between simulation outcomes and the experimental values are given in parentheses. The average values of these differences are given in the bottom line. “ffG53A6” denotes results using the default gromos force field parameters for the analog, “ATB” denotes those using the atb charge group assignment, “k = 5” denotes those using our method. We performed a two-tailed paired Student's t-test between the distributions given in column 6 (ATB) and column 8 (k = 5) resulting in a p-value of 0.2867. The difference in hydration-free energy differences is thus not statistically significant.