Internally bridging water molecule in transmembrane alpha-helical kink.
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.
Miyano
Masashi
M
Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. miyano@spring8.or.jp
Ago
Hideo
H
Saino
Hiromichi
H
Hori
Tetsuya
T
Ida
Koh
K
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*
D001426:Bacterial Proteins; D008565:Membrane Proteins; D014867:Water