Detailed description of an alpha helix->pi bulge transition detected by molecular dynamics simulations of the p185(c-erbB2) V659G transmembrane domain

Molecular dynamics simulations of a 29-residue peptide including the transmembrane domain of the V659G mutant of the c-erbB2 protein demonstrate important dynamical behavior. Although the alpha helix is the structure commonly assumed for transmembrane hydrophobic segments, we found that hydrogen bond rearrangements can occur, giving rise to a structural deformation termed pi bulge stabilized by successive hydrogen bonds of pi helix type. A series of simulations enables us to give a detailed description, at the atomic level, of the alpha helix-->pi bulge transition. The major consequence of this deformation covering one and a half rum of helix results in a noticeable shift around the helix axis of the C-terminal residues relatively to those of the N-terminus. Such a deformation closely related to structural motifs described in the litterature, induces a change in the distribution of the residues along the helix faces which could modulate the protein activity mediated by a dimerization process.