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.
Ducarme
P
P
Centre de Biophysique Móleculaire Numérique, Faculté Universitaire des Sciences Agronomiques de Gambloux, Belgium.
Thomas
A
A
Brasseur
R
R
D000465:Algorithms; D019281:Dimerization; D006021:Glycophorins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008565:Membrane Proteins / Q000737:chemistry*; D008566:Membranes / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012984:Software
D006021:Glycophorins; D008565:Membrane Proteins; D010455:Peptides