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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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36

METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS

Marialuisa Pellegrini-Calace and Janet M. Thornton

GLOSSARY

  • Cell membrane: lipid bilayer common to all living cells that separates the cell from the external environment
  • Cell wall: rigid layer external to the cell membrane that provides the cell with structural support, protection, and a filtering mechanism
  • Outer membrane: the outside membrane (external to the cell membrane) of Gram-negative bacteria, choroplasts, and mytochondria
  • Membrane core: very hydrophobic slab in the middle of the membrane made of the alkyl chain of phospholipids
  • Membrane interfaces: polar areas that separate the membrane core from aqueous solutions and are made of phospholipid polar heads
  • Membrane plane: any plane running parallel to the bilayer slab
  • Membrane axis: any direction perpendicular to the membrane plane
  • Membrane protein topology: number of transmembrane secondary structure elements (helices or strands) + location of the protein N-terminus at the cytoplasmic side of the membrane (“IN”) or at the opposite side (“OUT”)
  • Positive-inside rule: basic residues Arg and Lys are about four times more frequent in cytosolic than in periplasmic loops
  • Lily-pad effect: the stretch of hydrophobic amino acids interacting with the membrane core is flanked by aromatic belts made of Tyr and Trp
  • Re-entrant loops: loops that penetrate the membrane but do not cross it

Membrane proteins represent about 20-30% of the expressed genes as predicted ...

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