title: The alpha helix dipole: screened out?
abstract: Aligned alpha helix peptide dipoles sum to a "macroscopic" dipole parallel to the helix axis that has been implicated in protein folding and function. However, in aqueous solution the dipole is counteracted by an electrostatic reaction field generated by the solvent, and the strength of the helix dipole may reduce drastically from its value in vacuum. Here, using atomic-detail helix models and Poisson-Boltzmann continuum electrostatics calculations, the net effective dipole moment, mu(eff), is calculated. Some initially surprising results are found. Whereas in vacuum mu(eff) increases with helix length, the opposite is found to be the case for transmembrane helices. In soluble proteins, mu(eff) is found to vary strongly with the orientation and position of the helix relative to the aqueous medium. A set of rules is established to estimate of the strength of mu(eff) from graphical inspection of protein structures.
authors.affiliation: IWR-Computational Molecular Biophysics, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
authors.forename: Durba
authors.initials: D
authors.lastname: Sengupta
authors.forename: Raghu Nath
authors.initials: RN
authors.lastname: Behera
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.forename: G Matthias
authors.initials: GM
authors.lastname: Ullmann
mesh_terms: D000409:Alanine / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D008956:Models, Chemical; D008958:Models, Molecular; D008961:Models, Structural; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
chemical_list: D010455:Peptides; D011506:Proteins; D014867:Water; D000409:Alanine