title: Internally bridging water molecule in transmembrane alpha-helical kink.
abstract: There are hundreds of membrane protein atomic coordinates in the Protein Data Bank (PDB), and high-resolution structures of better than 2.5 A enable the visualization of a sizable number of amphiphiles (lipid and/or detergent) and bound water molecules as essential parts of the structure. Upon scrutinizing these high-resolution structures, water molecules were found to 'wedge' and stabilize large kink angle (30-40 degrees) in a simple cylindrical model at the transmembrane helical kinks so as to form an inter-helical cavity to accommodate a ligand binding or active site as a crucial structural feature in alpha-helical integral membrane proteins. Furthermore, some of these water molecules are proposed to play a pivotal role of their conformational change to exert their functional regulation.
authors.affiliation: Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. miyano@spring8.or.jp
authors.forename: Masashi
authors.initials: M
authors.lastname: Miyano
authors.forename: Hideo
authors.initials: H
authors.lastname: Ago
authors.forename: Hiromichi
authors.initials: H
authors.lastname: Saino
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Hori
authors.forename: Koh
authors.initials: K
authors.lastname: Ida
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D002462:Cell Membrane; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D014867:Water / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D014867:Water