Table 2.
Comparison of hydrophobicity scales for free energies of insertion
| Scale | Free energy of insertion for 21-mer (kJ/mol) | Reference |
|---|---|---|
| Translocon-mediated insertion | −2 | (7) |
| All atom side-chain PMFs | −124 | (10) |
| Continuum electrostatics | −153 | (40) |
| Side-chain partition coefficients | −163 | (41) |
| CG side-chain PMFs (modified MARTINI) | −192 | (16) |
| CG side-chain PMFs (MARTINI) | −209 | (25) |
These estimates are based upon an insertion model in which we simply sum the individual free energies of insertion into the hydrophobic core of a bilayer for M219 (i.e., SIAIYLGIGLCLLFIVRTL) to calculate an overall free energy of insertion. The individual free energies of insertion are taken from various residue-based scales, as listed. It should be noted that: the all-atom side-chain scale does not include values for Pro, Gly, or His; the continuum electrostatics and side-chain partition coefficients scales do not include a value for Pro; the MARTINI scale does not include values for Gly or Ala; and the modified MARTINI scale does not include values for Pro or Gly.