Recognition of transmembrane helices by the endoplasmic reticulum translocon

Membrane proteins depend on complex translocation machineries for insertion into target membranes. Although it has long been known that an abundance of nonpolar residues in transmembrane helices is the principal criterion for membrane insertion, the specific sequence-coding for transmembrane helices has not been identified. By challenging the endoplasmic reticulum Sec61 translocon with an extensive set of designed polypeptide segments, we have determined the basic features of this code, including a ‘biological’ hydrophobicity scale. We find that membrane insertion depends strongly on the position of polar residues within transmembrane segments, adding a new dimension to the problem of predicting transmembrane helices from amino acid sequences. Our results indicate that direct protein–lipid interactions are critical during translocon-mediated membrane insertion.

[1]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[2]  C. DeLisi,et al.  Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. , 1987, Journal of molecular biology.

[3]  G. Rose,et al.  Helix signals in proteins. , 1988, Science.

[4]  J. Richardson,et al.  Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.

[5]  M. Degli Esposti,et al.  A critical evaluation of the hydropathy profile of membrane proteins. , 1990, European journal of biochemistry.

[6]  D. Huylebroeck,et al.  In vitro mutagenesis of a full-length cDNA clone of Semliki Forest virus: the small 6,000-molecular-weight membrane protein modulates virus release , 1991, Journal of virology.

[7]  K. Mihara,et al.  Systematic analysis of stop-transfer sequence for microsomal membrane. , 1991, The Journal of biological chemistry.

[8]  P. Liljeström,et al.  A New Generation of Animal Cell Expression Vectors Based on the Semliki Forest Virus Replicon , 1991, Bio/Technology.

[9]  T. Creamer,et al.  Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. , 1996, Biochemistry.

[10]  Stephen H. White,et al.  Experimentally determined hydrophobicity scale for proteins at membrane interfaces , 1996, Nature Structural Biology.

[11]  Arne Elofsson,et al.  Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria , 1997, Protein science : a publication of the Protein Society.

[12]  S. White,et al.  The preference of tryptophan for membrane interfaces. , 1998, Biochemistry.

[13]  C. Deber,et al.  Guidelines for membrane protein engineering derived from de novo designed model peptides. , 1998, Biopolymers.

[14]  G. von Heijne,et al.  Stop-transfer function of pseudo-random amino acid segments during translocation across prokaryotic and eukaryotic membranes. , 1998, European journal of biochemistry.

[15]  B. Wilkinson,et al.  Signal Sequence Recognition in Posttranslational Protein Transport across the Yeast ER Membrane , 1998, Cell.

[16]  S. White,et al.  Membrane protein folding and stability: physical principles. , 1999, Annual review of biophysics and biomolecular structure.

[17]  M. Kozak.  Initiation of translation in prokaryotes and eukaryotes. , 1999, Gene.

[18]  Gunnar von Heijne,et al.  Recent advances in the understanding of membrane protein assembly and structure , 1999, Quarterly Reviews of Biophysics.

[19]  J. Killian,et al.  How proteins adapt to a membrane-water interface. , 2000, Trends in biochemical sciences.

[20]  T. Rapoport,et al.  The Sec61p Complex Mediates the Integration of a Membrane Protein by Allowing Lipid Partitioning of the Transmembrane Domain , 2000, Cell.

[21]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[22]  R. Hodges,et al.  A polyalanine-based peptide cannot form a stable transmembrane alpha-helix in fully hydrated phospholipid bilayers. , 2001, Biochemistry.

[23]  B. Bechinger.  Membrane insertion and orientation of polyalanine peptides: a (15)N solid-state NMR spectroscopy investigation. , 2001, Biophysical journal.

[24]  M. Sansom,et al.  Amino acid distributions in integral membrane protein structures. , 2001, Biochimica et biophysica acta.

[25]  S H White,et al.  Energetics, stability, and prediction of transmembrane helices. , 2001, Journal of molecular biology.

[26]  W. Skach,et al.  Molecular mechanism of P-glycoprotein assembly into cellular membranes. , 2002, Current protein & peptide science.

[27]  Jialing Lin,et al.  Cotranslational protein integration into the ER membrane is mediated by the binding of nascent chains to translocon proteins. , 2003, Molecular cell.

[28]  J. Killian,et al.  Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (Review) , 2003, Molecular membrane biology.

[29]  G. Heijne.  Membrane protein assembly in vivo. , 2003 .

[30]  J. Lippincott-Schwartz,et al.  The organization of engaged and quiescent translocons in the endoplasmic reticulum of mammalian cells , 2004, The Journal of cell biology.

[31]  T. Rapoport,et al.  Membrane-protein integration and the role of the translocation channel. , 2004, Trends in cell biology.

[32]  Peter J McCormick,et al.  Nascent Membrane and Secretory Proteins Differ in FRET-Detected Folding Far inside the Ribosome and in Their Exposure to Ribosomal Proteins , 2004, Cell.

[33]  Arthur E Johnson,et al.  Cotranslational Membrane Protein Biogenesis at the Endoplasmic Reticulum* , 2004, Journal of Biological Chemistry.

[34]  Bert van den Berg,et al.  X-ray structure of a protein-conducting channel , 2004, Nature.

[35]  Duan Yang,et al.  Proline substitutions are not easily accommodated in a membrane protein. , 2004, Journal of molecular biology.

[36]  Thijs Beuming,et al.  A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins , 2004, Bioinform..