Table 4. Conformational Free Energies from MMPB/SA Analysis for the Drew-Dickerson Dodecamera.
| Ab | Bc | canonical Ad | (B – A) | (B – Can.A) | |
|---|---|---|---|---|---|
| ⟨E(gas)⟩e | 2742.6 (5.8) | 2812.8 (7.3) | 2944.2 (5.3) | 70.2 | –131.4 |
| ⟨E(nonpolar)⟩f | 26.9 (0.0) | 26.7 (0.0) | 26.2 (0.0) | –0.2 | 0.5 |
| ⟨E(PB), ε = 80⟩g | –5818.1 (3.9) | –5931.7 (6.1) | –6090.8 (4.6) | –113.6 | 159.1 |
| ⟨E(total), ε = 80⟩ | –3048.6 (5.5) | –3092.3 (3.5) | –3120.4 (2.0) | –43.7 | 28.1 |
| ⟨ΔE(total), salt: 0.1 M⟩ | –40.5 (0.0) | –41.1 (0.1) | –43.1 (0.0) | –0.6 | 2.0 |
| ⟨ΔE(total), salt: 1.0 M⟩ | –53.1 (0.1) | –54.2 (0.1) | –59.1 (0.1) | –1.1 | 4.9 |
| ⟨ΔE(total), ε = 20⟩ | 239.2(0.2) | 245.0 (0.3) | 260.4 (0.3) | 5.8 | –15.4 |
a
Standard errors are given in the parentheses.
b
100 snapshots selected from DD1 and DD1 clusters as in Table 3.
c
100 snapshots selected from DD3 cluster as in Table 3.
d
Snapshots from 1 ns restrained implicit solvent simulation of canonical A-DNA structure taken at 5 ps intervals starting from 0.5 ns.
e
CHARMM force field energy in vacuum.
f
Solvent-accessible surface area term: γ*SASA+β with γ = 0.00542 kcal/mol/Å2 and β = 0.92 kcal/mol.63,64
g
Solution of Poisson–Boltzmann equation using PBEQ module65 in CHARMM program with a grid spacing of 0.25 Å.