The optimisation of the helix/helix interaction of a transmembrane dimer is improved by the IMPALA restraint field

Abstract

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 105 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.