Skip to main content
SpringerLink
Log in

Design of Transmembrane Peptides: Coping with Sticky Situations

  • Protocol
  • First Online:
Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1063))

Abstract

Membrane proteins have central roles in cellular processes ranging from nutrient uptake to cell–cell communication, and are key drug targets. However, research on α-helical integral membrane proteins is in its relative infancy vs. water-soluble proteins, largely because of their water insolubility when extracted from their native membrane environment. Peptides with sequences that correspond to the membrane-spanning segments of α-helical integral membrane proteins, termed transmembrane (TM) peptides, provide valuable tools for the characterization of these molecules. Here we describe in detail protocols for the design of TM peptides from the sequences of natural α-helical integral membrane proteins and outline strategies for their synthesis and for improving their solubility properties.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev 5(12):993–996

    Article  CAS  Google Scholar 

  2. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25(10):1119–1126

    Article  PubMed  CAS  Google Scholar 

  3. Bordag N, Keller S (2010) Alpha-helical transmembrane peptides: a “divide and conquer” approach to membrane proteins. Chem Phys Lipids 163(1):1–26

    Article  PubMed  CAS  Google Scholar 

  4. Ulmschneider MB, Sansom MS, Di Nola A (2005) Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 59(2):252–265

    Article  PubMed  CAS  Google Scholar 

  5. Melnyk RA, Partridge AW, Deber CM (2001) Retention of native-like oligomerization states in transmembrane segment peptides: application to the Escherichia coli aspartate receptor. Biochemistry 40(37):11106–11113

    Article  PubMed  CAS  Google Scholar 

  6. Rath A, Melnyk RA, Deber CM (2006) Evidence for assembly of small multidrug resistance proteins by a “two-faced” transmembrane helix. J Biol Chem 281(22):15546–15553

    Article  PubMed  CAS  Google Scholar 

  7. Oates J, Hicks M, Dafforn TR, DiMaio D, Dixon AM (2008) In vitro dimerization of the bovine papillomavirus E5 protein transmembrane domain. Biochemistry 47(34):8985–8992

    Article  PubMed  CAS  Google Scholar 

  8. Gan SW, Xin L, Torres J (2007) The transmembrane homotrimer of ADAM 1 in model lipid bilayers. Protein Sci 16(2):285–292

    Article  PubMed  CAS  Google Scholar 

  9. Torres J, Wang J, Parthasarathy K, Liu DX (2005) The transmembrane oligomers of coronavirus protein E. Biophys J 88(2):1283–1290

    Article  PubMed  CAS  Google Scholar 

  10. Tulumello DV, Deber CM (2012) Efficiency of detergents at maintaining membrane protein structures in their biologically relevant forms. Biochim Biophys Acta 1818(5):1351–1358

    Article  PubMed  CAS  Google Scholar 

  11. Amblard M, Fehrentz JA, Martinez J, Subra G (2005) Fundamentals of modern peptide synthesis. Methods Mol Biol 298:3–24

    PubMed  CAS  Google Scholar 

  12. Duarte AM, Wolfs CJ, van Nuland NA, Harrison MA, Findlay JB, van Mierlo CP, Hemminga MA (2007) Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H+−V-ATPase. Biochim Biophys Acta 1768(2):218–227

    Article  PubMed  CAS  Google Scholar 

  13. Tusnady GE, Simon I (2010) Topology prediction of helical transmembrane proteins: how far have we reached? Curr Protein Pept Sci 11(7):550–561

    Article  PubMed  CAS  Google Scholar 

  14. Cuthbertson JM, Doyle DA, Sansom MS (2005) Transmembrane helix prediction: a comparative evaluation and analysis. Protein Eng Des Sel 18(6):295–308

    Article  PubMed  CAS  Google Scholar 

  15. Ng DP, Deber CM (2010) Deletion of a terminal residue disrupts oligomerization of a transmembrane alpha-helix. Biochem Cell Biol 88(2):339–345

    Article  PubMed  CAS  Google Scholar 

  16. von Heijne G, Gavel Y (1988) Topogenic signals in integral membrane proteins. Eur J Biochem 174(4):671–678

    Article  Google Scholar 

  17. Melnyk RA, Partridge AW, Yip J, Wu Y, Goto NK, Deber CM (2003) Polar residue tagging of transmembrane peptides. Biopolymers 71(6):675–685

    Article  PubMed  CAS  Google Scholar 

  18. Parthasarathy K, Ng L, Lin X, Liu DX, Pervushin K, Gong X, Torres J (2008) Structural flexibility of the pentameric SARS coronavirus envelope protein ion channel. Biophys J 95(6):L39–L41

    Article  PubMed  CAS  Google Scholar 

  19. Lew S, Caputo GA, London E (2003) The effect of interactions involving ionizable residues flanking membrane-inserted hydrophobic helices upon helix-helix interaction. Biochemistry 42(36):10833–10842

    Article  PubMed  CAS  Google Scholar 

  20. Iwamoto T, You M, Li E, Spangler J, Tomich JM, Hristova K (2005) Synthesis and initial characterization of FGFR3 transmembrane domain: consequences of sequence modifications. Biochim Biophys Acta 1668(2): 240–247

    Article  PubMed  CAS  Google Scholar 

  21. van Iwaarden PR, Pastore JC, Konings WN, Kaback HR (1991) Construction of a functional lactose permease devoid of cysteine residues. Biochemistry 30(40):9595–9600

    Article  PubMed  Google Scholar 

  22. Karim CB, Paterlini MG, Reddy LG, Hunter GW, Barany G, Thomas DD (2001) Role of cysteine residues in structural stability and function of a transmembrane helix bundle. J Biol Chem 276(42):38814–38819

    Article  PubMed  CAS  Google Scholar 

  23. Afara MR, Trieber CA, Glaves JP, Young HS (2006) Rational design of peptide inhibitors of the sarcoplasmic reticulum calcium pump. Biochemistry 45(28):8617–8627

    Article  PubMed  CAS  Google Scholar 

  24. Cui L, Aleksandrov L, Hou YX, Gentzsch M, Chen JH, Riordan JR, Aleksandrov AA (2006) The role of cystic fibrosis transmembrane conductance regulator phenylalanine 508 side chain in ion channel gating. J Physiol 572(Pt 2): 347–358

    Article  PubMed  CAS  Google Scholar 

  25. Mordoch SS, Granot D, Lebendiker M, Schuldiner S (1999) Scanning cysteine accessibility of EmrE, an H+−coupled multidrug transporter from Escherichia coli, reveals a hydrophobic pathway for solutes. J Biol Chem 274(27):19480–19486

    Article  PubMed  CAS  Google Scholar 

  26. Loo TW, Clarke DM (1995) Membrane topology of a cysteine-less mutant of human P-glycoprotein. J Biol Chem 270(2):843–848

    Article  PubMed  CAS  Google Scholar 

  27. Greer JM, Lees MB (2002) Myelin proteolipid protein–the first 50 years. Int J Biochem Cell Biol 34(3):211–215

    Article  PubMed  CAS  Google Scholar 

  28. Chen CP, Rost B (2002) State-of-the-art in membrane protein prediction. Appl Bioinformatics 1(1):21–35

    PubMed  CAS  Google Scholar 

  29. Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B (2007) Membrane protein prediction methods. Methods 41(4):460–474

    Article  PubMed  CAS  Google Scholar 

  30. Hennerdal A, Elofsson A (2011) Rapid membrane protein topology prediction. Bioinformatics 27(9):1322–1323

    Article  PubMed  CAS  Google Scholar 

  31. Liu LP, Deber CM (1998) Guidelines for membrane protein engineering derived from de novo designed model peptides. Biopolymers 47(1):41–62

    Article  PubMed  CAS  Google Scholar 

  32. Cserzo M, Eisenhaber F, Eisenhaber B, Simon I (2002) On filtering false positive transmembrane protein predictions. Protein Eng 15(9):745–752

    Article  PubMed  CAS  Google Scholar 

  33. Tusnady GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17(9):849–850

    Article  PubMed  CAS  Google Scholar 

  34. Shen H, Chou JJ (2008) MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One 3(6):e2399

    Article  PubMed  Google Scholar 

  35. Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R (2011) MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res 39(Web Server issue):W375–W380

    Article  PubMed  CAS  Google Scholar 

  36. Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23(5):538–544

    Article  PubMed  CAS  Google Scholar 

  37. Nugent T, Jones DT (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinforma 10:159

    Article  Google Scholar 

  38. Snider C, Jayasinghe S, Hristova K, White SH (2009) MPEx: a tool for exploring membrane proteins. Protein Sci 18(12):2624–2628

    Article  PubMed  CAS  Google Scholar 

  39. Viklund H, Elofsson A (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 24(15): 1662–1668

    Article  PubMed  CAS  Google Scholar 

  40. Liakopoulos TD, Pasquier C, Hamodrakas SJ (2001) A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng 14(6):387–390

    Article  PubMed  CAS  Google Scholar 

  41. Rost B, Casadio R, Fariselli P, Sander C (1995) Transmembrane helices predicted at 95% accuracy. Protein Sci 4(3):521–533

    Article  PubMed  CAS  Google Scholar 

  42. Reynolds SM, Kall L, Riffle ME, Bilmes JA, Noble WS (2008) Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol 4(11):e1000213

    Article  PubMed  Google Scholar 

  43. Kall L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338(5):1027–1036

    Article  PubMed  CAS  Google Scholar 

  44. Viklund H, Elofsson A (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 13(7):1908–1917

    Article  PubMed  CAS  Google Scholar 

  45. Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci USA 105(20): 7177–7181

    Article  PubMed  CAS  Google Scholar 

  46. Hirokawa T, Boon-Chieng S, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14(4):378–379

    Article  PubMed  CAS  Google Scholar 

  47. Juretic D, Zoranic L, Zucic D (2002) Basic charge clusters and predictions of membrane protein topology. J Chem Inf Comput Sci 42(3):620–632

    Article  PubMed  CAS  Google Scholar 

  48. Viklund H, Bernsel A, Skwark M, Elofsson A (2008) SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24(24):2928–2929

    Article  PubMed  CAS  Google Scholar 

  49. Lo A, Chiu HS, Sung TY, Lyu PC, Hsu WL (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J Proteome Res 7(2):487–496

    Article  PubMed  CAS  Google Scholar 

  50. Deber CM, Wang C, Liu LP, Prior AS, Agrawal S, Muskat BL, Cuticchia AJ (2001) TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales. Protein Sci 10(1):212–219

    Article  PubMed  CAS  Google Scholar 

  51. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580

    Article  PubMed  CAS  Google Scholar 

  52. Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J (2008) Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinforma 9(Suppl 1):S4

    Article  Google Scholar 

  53. von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225(2): 487–494

    Article  Google Scholar 

Download references

Acknowledgements

We wish to thank Derek P. Ng for assistance in preparation of Fig. 1. This work was supported, in part, by grants to C.M.D. from the Canadian Institutes of Health Research (CIHR FRN-5810) and the Natural Science and Engineering Research Council of Canada (NSERC I2I Grant). A.R. was the recipient of a Research Training Centre (RESTRACOMP) award from the Hospital for Sick Children and held a postdoctoral award from the CIHR Strategic Training Program in Protein Folding: Principles and Diseases.

Author information

Authors and Affiliations

  1. Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, ON, Canada

    Arianna Rath & Charles M. Deber

Authors
  1. Arianna Rath
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Charles M. Deber
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dept. of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA

    Giovanna Ghirlanda

  2. Department of Biochemistry, University of Wisconsin, Madison, Madison, Wisconsin, USA

    Alessandro Senes

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Rath, A., Deber, C.M. (2013). Design of Transmembrane Peptides: Coping with Sticky Situations. In: Ghirlanda, G., Senes, A. (eds) Membrane Proteins. Methods in Molecular Biology, vol 1063. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-583-5_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-583-5_11

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-582-8

  • Online ISBN: 978-1-62703-583-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation