The structure of a membrane-spanning polypeptide studied by molecular dynamics.

We have performed a molecular dynamics simulation of a 46-residue segment of glycophorin which includes the hydrophobic membrane-spanning region of this protein. The presence of a membrane and of water is taken into account in a continuum approximation which makes use of phenomenological hydrophobic energies. The initial alpha-helical conformation and the membrane incorporation of the hydrophobic segment remain stable for the length of the simulation which is 100 ps. Moreover, when the hydrophobic segment is partially shifted out of the membrane, it moves back into the membrane. Superimposed on these deterministic effects one also observes thermal fluctuations in the form of bending and tilting of the membrane-spanning helix.