Journal of Protein Chemistry

, Volume 15, Issue 1, pp 63–76 | Cite as

Hydrophobic organization of α-helix membrane bundle in bacteriorhodopsin

  • Roman G. Efremov
  • Gérard Vergoten
Article
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Abstract

The hydrophobic organization of the intramembraneα-helical bundle in bacteriorhodopsin (BRh) was assessed based on a new approach to characterization of spatial hydrophobic properties of transmembrane (TM)α-helical peptides. The method employs two independent techniques: Monte Carlo simulations of nonpolar solvent around TM peptides and analysis of molecular hydrophobicity potential on their surfaces. The results obtained by the two methods agree with each other and permit precise hydrophobicity mapping of TM peptides. Superimposition of such data on the experimentally derived spatial model of the membrane moiety together with 2D maps of hydrophobic hydrophilic contacts provide considerable insight into the hydrophobic organization of BRh. The helix bundle is stabilized to a large extent by hydrophobic interactions between helices—neighbors in the sequence of BRh, by long-range interactions in helix pairs C-E, C-F, and C-G, and by nonpolar contracts between retinal and helices C, D, E, F. Unlike globular proteins, no polar contacts between residues distantly separated in the sequence of BRh were found in the bundle. One of the most striking results of this study is the finding that the hydrophobic organization of BRh is significantly different from those in bacterial photoreaction centers. Thus, TMα-helices in BRh expose their most nonpolar sides to the bilayer as well as to the neighboring helices and to the interior of the bundle. Some of them contact lipids with their relatively hydrophilic surfaces. No correlation was found between disposition of the most hydrophobic and the most variable sides of the TM helices.

Key words

Molecular modeling integral membrane proteins hydrophobic organization transmembrane helices Monte Carlo simulations 3D molecular hydrophobicity potential bacteriorhodopsin 

Abbreviations

BRh

bacteriorhodopsin

TM

transmembrane segment

MHP

molecular hydrophobicity potential

ESS

energy of solute-solvent interaction

2D, 3D

two- and three-dimensional, respectively

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Copyright information

© Plenum Publishing Corporation 1996

Authors and Affiliations

  • Roman G. Efremov
    • 1
    • 2
  • Gérard Vergoten
    • 2
  1. 1.Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscow V-437Russia
  2. 2.Centre de Recherches et d'Etudes en Simulations et Modélisation Molécularies, UFR de ChimieUniversité des Sciences et Technologies de LilleVilleneuve d'Ascq, CedexFrance

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