The Optimisation Of The Helix/Helix Interaction Of A Transmembrane Dimer Is Improved By The Impala Restraint Field

A continuous membrane model (IMPALA) was previously developed to predict how
hydrophobic spans of proteins insert in membranes (Mol. Mod. 2 (1996) 27). Using
that membrane model, we looked for the interactions between several hydrophobic
spans. We used the glycophorin A dimer as an archetype of polytopic protein to
validate the approach. We find that the native complex do not dislocate when it
is submitted to a 10(5) steps optimisation whereas separated spans converge back
to a native-like complex in the same conditions. We also observe that IMPALA
restraints are not strictly mandatory but do increase the efficiency of the
procedure.