Folding and Insertion of Transmembrane Helices at the ER

In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches ‘know’ to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices?

[1]  J. Mondal,et al.  Spontaneous Transmembrane Pore Formation by Short-chain Synthetic Peptide. , 2021, Biophysical journal.

[2]  Ákos Farkas,et al.  Capture and delivery of tail-anchored proteins to the endoplasmic reticulum , 2021, The Journal of cell biology.

[3]  J. Ruysschaert,et al.  Interhelical H-Bonds Modulate the Activity of a Polytopic Transmembrane Kinase , 2021, Biomolecules.

[4]  M. Rodnina,et al.  Lateral gate dynamics of the bacterial translocon during cotranslational membrane protein insertion , 2021, Proceedings of the National Academy of Sciences.

[5]  S. Sanyal,et al.  Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis , 2021, iScience.

[6]  Thomas F. Miller,et al.  Residue-by-residue analysis of cotranslational membrane protein integration in vivo , 2020, bioRxiv.

[7]  G. von Heijne,et al.  The ribosome modulates folding inside the ribosomal exit tunnel , 2020, Communications Biology.

[8]  R. M. Voorhees,et al.  Structural basis for membrane insertion by the human ER membrane protein complex , 2020, Science.

[9]  N. Pfanner,et al.  The Mitochondrial Import Complex MIM Functions as Main Translocase for α-Helical Outer Membrane Proteins. , 2020, Cell reports.

[10]  Thomas F. Miller,et al.  Dynamics of co-translational membrane protein integration and translocation via the Sec translocon. , 2020, Journal of the American Chemical Society.

[11]  F. Förster,et al.  A clearer picture of the ER translocon complex , 2020, Journal of Cell Science.

[12]  Koreaki Ito,et al.  Sec translocon has an insertase-like function in addition to polypeptide conduction through the channel , 2019, F1000Research.

[13]  M. Bogdanov,et al.  Lipid-Assisted Membrane Protein Folding and Topogenesis , 2019, The Protein Journal.

[14]  R. Hegde,et al.  The Role of EMC during Membrane Protein Biogenesis. , 2019, Trends in cell biology.

[15]  T. Ueda,et al.  Artificial photosynthetic cell producing energy for protein synthesis , 2019, Nature Communications.

[16]  G. von Heijne,et al.  Dynamic membrane topology in an unassembled membrane protein , 2019, bioRxiv.

[17]  G. von Heijne,et al.  Transmembrane but not soluble helices fold inside the ribosome tunnel , 2018, Nature Communications.

[18]  R. Hegde,et al.  EMC Is Required to Initiate Accurate Membrane Protein Topogenesis , 2018, Cell.

[19]  R. Keenan,et al.  A structural perspective on tail-anchored protein biogenesis by the GET pathway. , 2018, Current opinion in structural biology.

[20]  Jeffrey A. Hussmann,et al.  The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins , 2018, eLife.

[21]  F. Förster,et al.  Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum , 2018, Science.

[22]  I. Vattulainen,et al.  The role of hydrophobic matching on transmembrane helix packing in cells , 2017, Cell stress.

[23]  T. Rapoport,et al.  Structural and Mechanistic Insights into Protein Translocation. , 2017, Annual review of cell and developmental biology.

[24]  I. Mingarro,et al.  Membrane insertion and topology of the translocon-associated protein (TRAP) gamma subunit. , 2017, Biochimica et biophysica acta. Biomembranes.

[25]  Friedrich Förster,et al.  Dissecting the molecular organization of the translocon-associated protein complex , 2017, Nature Communications.

[26]  R. Hegde,et al.  Toward a structural understanding of co-translational protein translocation. , 2016, Current opinion in cell biology.

[27]  C. Chipot,et al.  Decrypting protein insertion through the translocon with free-energy calculations. , 2016, Biochimica et biophysica acta.

[28]  G. von Heijne,et al.  Biological insertion of computationally designed short transmembrane segments , 2016, Scientific Reports.

[29]  R. Hegde,et al.  Structure of the Sec61 channel opened by a signal sequence , 2016, Science.

[30]  F. Förster,et al.  Structure of the native Sec61 protein-conducting channel , 2015, Nature Communications.

[31]  Thomas F. Miller,et al.  Regulation of multispanning membrane protein topology via post-translational annealing , 2015, eLife.

[32]  G. von Heijne,et al.  Cotranslational Protein Folding inside the Ribosome Exit Tunnel , 2015, Cell reports.

[33]  Jeremy G. Wideman The ubiquitous and ancient ER membrane protein complex (EMC): tether or not? , 2015, F1000Research.

[34]  Gunnar von Heijne,et al.  Mechanisms of integral membrane protein insertion and folding. , 2015, Journal of molecular biology.

[35]  P. Whitley,et al.  Stitching proteins into membranes, not sew simple , 2014, Biological chemistry.

[36]  M. Rodnina,et al.  Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion , 2014, Nature Communications.

[37]  Gunnar von Heijne,et al.  SPONTANEOUS TRANSMEMBRANE HELIX INSERTION THERMODYNAMICALLY MIMICS TRANSLOCON-GUIDED INSERTION , 2014, Nature Communications.

[38]  Yutetsu Kuruma,et al.  In vitro synthesis of the E. coli Sec translocon from DNA. , 2014, Angewandte Chemie.

[39]  Thomas Becker,et al.  Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion , 2014, Nature.

[40]  J. Taunton,et al.  An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate , 2014, eLife.

[41]  C. Deutsch,et al.  Transmembrane segments form tertiary hairpins in the folding vestibule of the ribosome. , 2014, Journal of molecular biology.

[42]  E. Hartmann,et al.  TRAP assists membrane protein topogenesis at the mammalian ER membrane. , 2013, Biochimica et biophysica acta.

[43]  T. Rapoport,et al.  Structure of the SecY channel during initiation of protein translocation , 2013, Nature.

[44]  Marc A. Marti-Renom,et al.  Structure-based statistical analysis of transmembrane helices , 2013, European Biophysics Journal.

[45]  A. Elofsson,et al.  Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. , 2013, Journal of molecular biology.

[46]  G. von Heijne,et al.  Positional editing of transmembrane domains during ion channel assembly , 2013, Journal of Cell Science.

[47]  K. Schulten,et al.  Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane–Protein Insertion , 2013, Journal of the American Chemical Society.

[48]  A. Johnson,et al.  Membrane protein TM segments are retained at the translocon during integration until the nascent chain cues FRET-detected release into bulk lipid. , 2012, Molecular cell.

[49]  M. Martí-Renom,et al.  Polar/Ionizable Residues in Transmembrane Segments: Effects on Helix-Helix Packing , 2012, PloS one.

[50]  T. Rapoport,et al.  Mechanisms of Sec61/SecY-mediated protein translocation across membranes. , 2012, Annual review of biophysics.

[51]  R. Hegde,et al.  Membrane protein insertion at the endoplasmic reticulum. , 2011, Annual review of cell and developmental biology.

[52]  M. Martí-Renom,et al.  Membrane protein integration into the endoplasmic reticulum , 2011, The FEBS journal.

[53]  R. Gilmore,et al.  Translocation channel gating kinetics balances protein translocation efficiency with signal sequence recognition fidelity , 2011, Molecular biology of the cell.

[54]  W. Skach,et al.  Stepwise Insertion and Inversion of a Type II Signal Anchor Sequence in the Ribosome-Sec61 Translocon Complex , 2011, Cell.

[55]  K. Schulten,et al.  Free energy of nascent-chain folding in the translocon. , 2011, Journal of the American Chemical Society.

[56]  Klaus Schulten,et al.  Cryo–EM structure of the ribosome–SecYE complex in the membrane environment , 2011, Nature Structural &Molecular Biology.

[57]  T. Rapoport,et al.  Preserving the membrane barrier for small molecules during bacterial protein translocation , 2011, Nature.

[58]  I. Mingarro,et al.  Membrane insertion and topology of the translocating chain-associating membrane protein (TRAM). , 2011, Journal of molecular biology.

[59]  R. Stroud,et al.  Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes , 2010, Proceedings of the National Academy of Sciences.

[60]  Gunnar von Heijne,et al.  Control of Membrane Protein Topology by a Single C-Terminal Residue , 2010, Science.

[61]  T. Junne,et al.  The Hydrophobic Core of the Sec61 Translocon Defines the Hydrophobicity Threshold for Membrane Integration , 2010, Molecular biology of the cell.

[62]  T. F. Miller,et al.  Hydrophobically stabilized open state for the lateral gate of the Sec translocon , 2010, Proceedings of the National Academy of Sciences.

[63]  Marco Gartmann,et al.  α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel , 2010, Nature Structural &Molecular Biology.

[64]  Klaus Schulten,et al.  Regulation of the protein-conducting channel by a bound ribosome. , 2009, Structure.

[65]  G. von Heijne,et al.  Insertion of short transmembrane helices by the Sec61 translocon , 2009, Proceedings of the National Academy of Sciences.

[66]  W. Skach Cellular mechanisms of membrane protein folding , 2009, Nature Structural &Molecular Biology.

[67]  S. High,et al.  Dissecting the physiological role of selective transmembrane-segment retention at the ER translocon , 2009, Journal of Cell Science.

[68]  Michael Y. Galperin,et al.  Co-evolution of primordial membranes and membrane proteins. , 2009, Trends in biochemical sciences.

[69]  I. Mingarro,et al.  Viral membrane protein topology is dictated by multiple determinants in its sequence. , 2009, Journal of molecular biology.

[70]  K. Schulten,et al.  The Roles of Pore Ring and Plug in the SecY Protein-conducting Channel , 2008, The Journal of general physiology.

[71]  I. Mingarro,et al.  The surfactant peptide KL4 sequence is inserted with a transmembrane orientation into the endoplasmic reticulum membrane. , 2008, Biophysical journal.

[72]  W F Drew Bennett,et al.  Distribution of amino acids in a lipid bilayer from computer simulations. , 2008, Biophysical journal.

[73]  K. V. van Wijk,et al.  Coli Escherichia Outer Membrane Proteomes of Effects of Sece Depletion on the Inner and Supplemental Material , 2007 .

[74]  G. Heijne,et al.  Molecular code for transmembrane-helix recognition by the Sec61 translocon , 2007, Nature.

[75]  E. London,et al.  Effect of sequence hydrophobicity and bilayer width upon the minimum length required for the formation of transmembrane helices in membranes. , 2007, Journal of molecular biology.

[76]  G. von Heijne,et al.  Contribution of hydrophobic and electrostatic interactions to the membrane integration of the Shaker K+ channel voltage sensor domain , 2007, Proceedings of the National Academy of Sciences.

[77]  Olaf S Andersen,et al.  Bilayer thickness and membrane protein function: an energetic perspective. , 2007, Annual review of biophysics and biomolecular structure.

[78]  I. Mingarro,et al.  Sec61alpha and TRAM are sequentially adjacent to a nascent viral membrane protein during its ER integration. , 2007, Journal of molecular biology.

[79]  M Gerstein,et al.  The geometry of the ribosomal polypeptide exit tunnel. , 2006, Journal of molecular biology.

[80]  I. Mingarro,et al.  Peptides corresponding to helices 5 and 6 of Bax can independently form large lipid pores , 2006, The FEBS journal.

[81]  Gunnar von Heijne,et al.  Identification and evolution of dual-topology membrane proteins , 2006, Nature Structural &Molecular Biology.

[82]  J. Bowie Solving the membrane protein folding problem , 2005, Nature.

[83]  Jianli Lu,et al.  Folding zones inside the ribosomal exit tunnel , 2005, Nature Structural &Molecular Biology.

[84]  M. Lemmon Faculty Opinions recommendation of Sequential triage of transmembrane segments by Sec61alpha during biogenesis of a native multispanning membrane protein. , 2005 .

[85]  T. Rapoport,et al.  Protein translocation by the Sec61/SecY channel. , 2005, Annual review of cell and developmental biology.

[86]  W. Skach,et al.  Sequential triage of transmembrane segments by Sec61α during biogenesis of a native multispanning membrane protein , 2005, Nature Structural &Molecular Biology.

[87]  I. Mingarro,et al.  Double-spanning Plant Viral Movement Protein Integration into the Endoplasmic Reticulum Membrane Is Signal Recognition Particle-dependent, Translocon-mediated, and Concerted* , 2005, Journal of Biological Chemistry.

[88]  I. Mingarro,et al.  Peptides derived from apoptotic Bax and Bid reproduce the poration activity of the parent full-length proteins. , 2005, Biophysical journal.

[89]  C. Deutsch,et al.  Secondary structure formation of a transmembrane segment in Kv channels. , 2005, Biochemistry.

[90]  G. Heijne,et al.  Recognition of transmembrane helices by the endoplasmic reticulum translocon , 2005, Nature.

[91]  T. Junne,et al.  Topogenesis of membrane proteins at the endoplasmic reticulum. , 2004, Biochemistry.

[92]  Graham Warren,et al.  Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[93]  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.

[94]  R. Stuart,et al.  Yeast Oxa1 interacts with mitochondrial ribosomes: the importance of the C‐terminal region of Oxa1 , 2003, The EMBO journal.

[95]  Renhao Li,et al.  Activation of Integrin αIIbß3 by Modulation of Transmembrane Helix Associations , 2003, Science.

[96]  S. White,et al.  How Membranes Shape Protein Structure* , 2001, The Journal of Biological Chemistry.

[97]  D. Engelman,et al.  Polar residues drive association of polyleucine transmembrane helices , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[98]  G. von Heijne,et al.  Different conformations of nascent polypeptides during translocation across the ER membrane , 2000, BMC Cell Biology.

[99]  A. Verkman,et al.  Reorientation of aquaporin-1 topology during maturation in the endoplasmic reticulum. , 2000, Molecular biology of the cell.

[100]  E. Evans,et al.  Effect of chain length and unsaturation on elasticity of lipid bilayers. , 2000, Biophysical journal.

[101]  V. Moy,et al.  Cross-linking of cell surface receptors enhances cooperativity of molecular adhesion. , 2000, Biophysical journal.

[102]  Stephen H. White,et al.  Designing Transmembrane α-Helices That Insert Spontaneously† , 2000 .

[103]  D. Engelman,et al.  The GxxxG motif: a framework for transmembrane helix-helix association. , 2000, Journal of molecular biology.

[104]  William F. DeGrado,et al.  Asparagine-mediated self-association of a model transmembrane helix , 2000, Nature Structural Biology.

[105]  D. Engelman,et al.  Interhelical hydrogen bonding drives strong interactions in membrane proteins , 2000, Nature Structural Biology.

[106]  G von Heijne,et al.  A turn propensity scale for transmembrane helices. , 1999, Journal of molecular biology.

[107]  J. Killian,et al.  Hydrophobic mismatch between proteins and lipids in membranes. , 1998, Biochimica et biophysica acta.

[108]  G von Heijne,et al.  Forced transmembrane orientation of hydrophilic polypeptide segments in multispanning membrane proteins. , 1998, Molecular cell.

[109]  W. Wickner,et al.  Sec‐dependent membrane protein biogenesis: SecYEG, preprotein hydrophobicity and translocation kinetics control the stop‐transfer function , 1998, The EMBO journal.

[110]  G. Heijne,et al.  Saccharomyces cerevisiae mitochondria lack a bacterial‐type Sec machinery , 1996, Protein science : a publication of the Protein Society.

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

[112]  G. von Heijne,et al.  A Nascent Secretory Protein 5 Traverse the Ribosome/Endoplasmic Reticulum Translocase Complex as an Extended Chain (*) , 1996, The Journal of Biological Chemistry.

[113]  M. Bloom,et al.  Mattress model of lipid-protein interactions in membranes. , 1984, Biophysical journal.

[114]  Jeremy G. Wideman The ubiquitous and ancient ER membrane protein complex (EMC): tether or not? , 2015, F1000Research.

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

[116]  Renhao Li,et al.  Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations. , 2003, Science.

[117]  R. Stroud,et al.  The signal recognition particle. , 2001, Annual review of biochemistry.

[118]  S H White,et al.  Designing transmembrane alpha-helices that insert spontaneously. , 2000, Biochemistry.

[119]  A. Johnson,et al.  The translocon: a dynamic gateway at the ER membrane. , 1999, Annual review of cell and developmental biology.