Tuning Chemoreceptor Signaling by Positioning Aromatic Residues at the Lipid–Aqueous Interface

  • Rahmi Yusuf
  • Robert J. Lawrence
  • Lucy V. Eke
  • Roger R. Draheim
Part of the Methods in Molecular Biology book series (MIMB, volume 1729)


Aromatic tuning facilitates stimulus-independent modulation of receptor output. The methodology is based upon the affinity of amphipathic aromatic residues, namely Trp and Tyr, for the polar–hydrophobic interfaces found within biological membranes. Here, we describe the application of aromatic tuning within the aspartate chemoreceptor of Escherichia coli (Tar). We have also employed the method within other related proteins, such as sensor histidine kinases (SHKs), and therefore hope that other research groups find it useful to modulate signal output from their receptor of interest.


Aromatic tuning Stimulus-independent signaling Signal output modulation Signal pathway mapping Polar–hydrophobic interfaces Membrane–protein interactions 



R.Y. was generously supported by the Indonesia Endowment Fund for Education, Ministry of Finance (S-4833/LPDP.3/2015). R.J.L. and L.V.E. received support from the University of Portsmouth. R.R.D. was supported with start-up funding from the Faculty of Science and from the Institute of Biological and Biomolecular Science (IBBS) at the University of Portsmouth.


  1. 1.
    Draheim RR, Bormans AF, Lai RZ, Manson MD (2006) Tuning a bacterial chemoreceptor with protein-membrane interactions. Biochemistry 45(49):14655–14664CrossRefPubMedGoogle Scholar
  2. 2.
    Norholm MH, von Heijne G, Draheim RR (2015) Forcing the issue: aromatic tuning facilitates stimulus-independent modulation of a two-component signaling circuit. ACS Synth Biol 4:474–481CrossRefPubMedGoogle Scholar
  3. 3.
    Yusuf R, Draheim RR (2015) Employing aromatic tuning to modulate output from two-component signaling circuits. J Biol Eng 9:7CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Lehning CE, Heidelberger JB, Reinhard J, Norholm MH et al (2017) A modular high-throughput in vivo screening platform based on chimeric bacterial receptors. ACS Synth Biol 6(7):1315–1326CrossRefPubMedGoogle Scholar
  5. 5.
    Killian JA, Salemink I, de Planque MR, Lindblom G, Koeppe RE II et al (1996) Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane alpha-helical peptides: importance of hydrophobic mismatch and proposed role of tryptophans. Biochemistry 35:1037–1045CrossRefPubMedGoogle Scholar
  6. 6.
    de Planque MR, Greathouse DV, Koeppe RE II, Schafer H, Marsh D et al (1998) Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A 2H NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A. Biochemistry 37:9333–9345CrossRefPubMedGoogle Scholar
  7. 7.
    de Planque MR, Boots JW, Rijkers DT, Liskamp RM, Greathouse DV et al (2002) The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane alpha-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry 41:8396–8404CrossRefPubMedGoogle Scholar
  8. 8.
    de Planque MR, Bonev BB, Demmers JA, Greathouse DV, Koeppe RE II et al (2003) Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry 42:5341–5348CrossRefPubMedGoogle Scholar
  9. 9.
    Nilsson I, Saaf A, Whitley P, Gafvelin G, Waller C et al (1998) Proline-induced disruption of a transmembrane alpha-helix in its natural environment. J Mol Biol 284:1165–1175CrossRefPubMedGoogle Scholar
  10. 10.
    Braun P, von Heijne G (1999) The aromatic residues Trp and Phe have different effects on the positioning of a transmembrane helix in the microsomal membrane. Biochemistry 38:9778–9782CrossRefPubMedGoogle Scholar
  11. 11.
    Hessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y et al (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450(7172):1026–1030CrossRefPubMedGoogle Scholar
  12. 12.
    Botelho SC, Enquist K, von Heijne G, Draheim RR (2015) Differential repositioning of the second transmembrane helices from E. coli Tar and EnvZ upon moving the flanking aromatic residues. Biochim Biophys Acta 1848:615–621CrossRefPubMedGoogle Scholar
  13. 13.
    Draheim RR, Bormans AF, Lai RZ, Manson MD (2005) Tryptophan residues flanking the second transmembrane helix (TM2) set the signaling state of the Tar chemoreceptor. Biochemistry 44:1268–1277CrossRefPubMedGoogle Scholar
  14. 14.
    Falke JJ, Hazelbauer GL (2001) Transmembrane signaling in bacterial chemoreceptors. Trends Biochem Sci 26:257–265CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Falke JJ, Erbse AH (2009) The piston rises again. Structure 17:1149–1151CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Miller AS, Falke JJ (2004) Side chains at the membrane-water interface modulate the signaling state of a transmembrane receptor. Biochemistry 43:1763–1770CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Isaac B, Gallagher GJ, Balazs YS, Thompson LK (2002) Site-directed rotational resonance solid-state NMR distance measurements probe structure and mechanism in the transmembrane domain of the serine bacterial chemoreceptor. Biochemistry 41:3025–3036CrossRefGoogle Scholar
  18. 18.
    Hall BA, Armitage JP, Sansom MS (2011) Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol 7:e1002204CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Wright GA, Crowder RL, Draheim RR, Manson MD (2011) Mutational analysis of the transmembrane helix 2-HAMP domain connection in the Escherichia coli aspartate chemoreceptor Tar. J Bacteriol 193:82–90CrossRefGoogle Scholar
  20. 20.
    Adase CA, Draheim RR, Manson MD (2012) The residue composition of the aromatic anchor of the second transmembrane helix determines the signaling properties of the aspartate/maltose chemoreceptor Tar of Escherichia coli. Biochemistry 51:1925–1932CrossRefPubMedGoogle Scholar
  21. 21.
    Adase CA, Draheim RR, Rueda G, Desai R, Manson MD (2013) Residues at the cytoplasmic end of transmembrane helix 2 determine the signal output of the TarEc chemoreceptor. Biochemistry 52:2729–2738CrossRefPubMedGoogle Scholar
  22. 22.
    Berg HC, Block SM (1984) A miniature flow cell designed for rapid exchange of media under high-power microscope objectives. J Gen Microbiol 130:2915–2920Google Scholar
  23. 23.
    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 305:567–580CrossRefPubMedGoogle Scholar
  24. 24.
    Ward SM, Delgado A, Gunsalus RP, Manson MD (2002) A NarX-Tar chimera mediates repellent chemotaxis to nitrate and nitrite. Mol Microbiol 44:709–719CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Heininger A, Yusuf R, Lawrence R, Draheim RR (2016) Identification of transmembrane helix 1 (TM1) surfaces important for EnvZ signalling and dimerisation. Biochim Biophys Acta 1858:1868–1875CrossRefPubMedGoogle Scholar
  26. 26.
    Lai RZ, Bormans AF, Draheim RR, Wright GA, Manson MD (2008) The region preceding the C-terminal NWETF pentapeptide modulates baseline activity and aspartate inhibition of Escherichia coli Tar. Biochemistry 47:13287–13295CrossRefPubMedGoogle Scholar
  27. 27.
    Cohen SN, Chang AC, Hsu L (1972) Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. Proc Natl Acad Sci U S A 69:2110–2114CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Kuwajima G (1988) Construction of a minimum-size functional flagellin of Escherichia coli. J Bacteriol 170:3305–3309CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Nyholm TK, Ozdirekcan S, Killian JA (2007) How protein transmembrane segments sense the lipid environment. Biochemistry 46:1457–1465CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Rahmi Yusuf
    • 1
  • Robert J. Lawrence
    • 1
  • Lucy V. Eke
    • 1
  • Roger R. Draheim
    • 1
  1. 1.School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical SciencesUniversity of PortsmouthPortsmouthUK

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