Modeling of peptides and proteins in a membrane environment: II. Structural and energetic aspects of glycophorin A in a lipid bilayer

The conformational space of a hydrophobic peptide fragment of glycophorin A in a lipid membrane was studied with the Monte Carlo method using the solvation model described in the first communication of this series. The simulation was performed for various starting orientations of the peptide relative the membrane bilayer: outside, inside, partially immersed, and transbilayer. We showed that the membrane substantially stabilizes the α-helical conformation of the central hydrophobic part of the glycophorin A molecule, which for the most part is immersed in the apolar core of the bilayer. For various conformational states, energy values were calculated and the orientations of the peptide relative to the membrane were characterized. Depending on the thickness of the bilayer, either an entirely α-helical conformation in transbilayer orientation or a conformation with a kink in the central part of the helix with theN- andC-termini exposed on one side of the membrane corresponds to the minimal-energy structure. The transmembrane orientation of glycophorin A is energetically advantageous when the membrane thickness is close to the length of its hydrophobic helical portion, which is consistent with the effect ofhydrophobic match observed experimentally. The prospects for further refinement of the model are discussed. For communication I, see [1].