TABLE 1.
Various average properties from the melittin simulations
| Energy, kcal/mol‡
|
|||||||
|---|---|---|---|---|---|---|---|
| Zcom,* Å | Kink angle,† degree | 𝒲 | Uint | Uext | ΔGelec | ΔGnp | |
| S1 | 12.4 ± 1.2 | 154.9 ± 10.4 | −377.7 ± 15.2 | 445.6 ± 15.8 | −306.1 ± 36.7 | −565.3 ± 41.3 | 48.0 ± 6.7 |
| S2 | 13.4 ± 0.8 | 155.3 ± 10.7 | −395.3 ± 15.3 | 449.0 ± 15.8 | −373.6 ± 38.6 | −522.4 ± 38.2 | 51.6 ± 4.0 |
| S3 | 12.9 ± 0.9 | 154.2 ± 10.3 | −385.4 ± 15.9 | 443.1 ± 15.6 | −282.4 ± 35.8 | −596.3 ± 40.4 | 50.2 ± 5.0 |
| S4 | 15.3 ± 1.3 | 47.4 ± 19.8 | −381.5 ± 16.1 | 445.4 ± 16.0 | −288.7 ± 35.9 | −602.7 ± 42.7 | 64.3 ± 6.6 |
| S5 | 12.6 ± 1.1 | 162.1 ± 9.2 | −380.6 ± 15.2 | 445.9 ± 15.6 | −292.5 ± 28.0 | −581.2 ± 27.4 | 47.2 ± 5.9 |
| S6 | 5.8 ± 0.5 | 122.0 ± 11.4 | −380.1 ± 14.7 | 441.3 ± 15.3 | −311.1 ± 41.4 | −548.2 ± 40.6 | 37.9 ± 2.6 |
The average and fluctuations of the melittin simulations were taken from 2500 snapshots after 1.0 ns.
*
Zcom is the center of mass of melittin along the z axis.
†
Kink angle represents an angle between the two helical segments, defined by the two vectors connecting Val5 Cα to Gly12 Cα and Leu16 Cα to Lys23 Cα (Bernèche et al., 1998).
‡
The free energy, 𝒲, in solvent/membrane environment is defined as the sum of the internal (bond, angle, dihedral, etc.) molecular mechanics energy, Uint; the external (van der Waals, UvdW, and Coulomb, UCoul) molecular mechanics, energy Uext; the electrostatic solvation energy, ΔGelec; and the nonpolar solvation energy, ΔGnp.