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Membrane Proteins pp 95–116Cite as

Analyzing the Effects of Hydrophobic Mismatch on Transmembrane α-Helices Using Tryptophan Fluorescence Spectroscopy

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

Abstract

Hydrophobic matching between transmembrane protein segments and the lipid bilayer in which they are embedded is a significant factor in the behavior and orientation of such transmembrane segments. The condition of hydrophobic mismatch occurs when the hydrophobic thickness of a lipid bilayer is significantly different than the length of the membrane spanning segment of a protein, resulting in a mismatch. This mismatch can result in altered function of proteins as well as nonnative structural arrangements including effects on transmembrane α-helix tilt angles, oligomerization state, and/or the formation of non-transmembrane topographies. Here, a fluorescence-based protocol is described for testing model transmembrane α-helices and their sensitivity to hydrophobic mismatch by measuring the propensity of these helices to form non-transmembrane structures. Overall, good hydrophobic matching between the bilayer and transmembrane segments is an important factor that must be considered when designing membrane proteins or peptides.

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References

  1. Fagerberg L, Jonasson K, von Heijne G, Uhlen M, Berglund L (2010) Prediction of the human membrane proteome. Proteomics 10(6):1141–1149. doi:10.1002/pmic.200900258

    Article  PubMed  CAS  Google Scholar 

  2. Grigoryan G, Moore DT, DeGrado WF (2011) Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K(+) channels, and integrin receptors. Annu Rev Biochem 80:211–237. doi:10.1146/annurev-biochem-091008-152423

    Article  PubMed  CAS  Google Scholar 

  3. Perez-Aguilar JM, Saven JG (2012) Computational design of membrane proteins. Structure 20(1):5–14. doi:10.1016/j.str.2011.12.003

    Article  PubMed  CAS  Google Scholar 

  4. Senes A, Engel DE, DeGrado WF (2004) Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 14(4):465–479. doi:10.1016/j.sbi.2004.07.007

    Article  PubMed  CAS  Google Scholar 

  5. Slivka PF, Wong J, Caputo GA, Yin H (2008) Peptide probes for protein transmembrane domains. ACS Chem Biol 3(7):402–411. doi:10.1021/cb800049w

    Article  PubMed  CAS  Google Scholar 

  6. Caffrey M, Feigenson GW (1981) Fluorescence quenching in model membranes. 3. Relationship between calcium adenosinetriphosphatase enzyme activity and the affinity of the protein for phosphatidylcholines with different acyl chain characteristics. Biochemistry 20(7):1949–1961

    Article  PubMed  CAS  Google Scholar 

  7. Deshmukh SS, Akhavein H, Williams JC, Allen JP, Kalman L (2011) Light-induced conformational changes in photosynthetic reaction centers: impact of detergents and lipids on the electronic structure of the primary electron donor. Biochemistry 50(23):5249–5262. doi:10.1021/bi200595z

    Article  PubMed  CAS  Google Scholar 

  8. In’t Veld G, Driessen AJ, Op den Kamp JA, Konings WN (1991) Hydrophobic membrane thickness and lipid-protein interactions of the leucine transport system of Lactococcus lactis. Biochim Biophys Acta 1065(2):203–212

    Article  Google Scholar 

  9. Montecucco C, Smith GA, Dabbeni-sala F, Johannsson A, Galante YM, Bisson R (1982) Bilayer thickness and enzymatic activity in the mitochondrial cytochrome c oxidase and ATPase complex. FEBS Lett 144(1):145–148

    Article  PubMed  CAS  Google Scholar 

  10. Pilot JD, East JM, Lee AG (2001) Effects of bilayer thickness on the activity of diacylglycerol kinase of Escherichia coli. Biochemistry 40(28):8188–8195

    Article  PubMed  CAS  Google Scholar 

  11. Andersen OS, Koeppe RE II (2007) Bilayer thickness and membrane protein function: an energetic perspective. Annu Rev Biophys Biomol Struct 36:107–130. doi:10.1146/annurev.biophys.36.040306.132643

    Article  PubMed  CAS  Google Scholar 

  12. Hessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH, von Heijne G (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450(7172):1026–1030. doi:10.1038/nature06387

    Article  PubMed  CAS  Google Scholar 

  13. Sharpe HJ, Stevens TJ, Munro S (2010) A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142(1):158–169. doi:10.1016/j.cell.2010.05.037

    Article  PubMed  CAS  Google Scholar 

  14. Killian JA (1998) Hydrophobic mismatch between proteins and lipids in membranes. Biochim Biophys Acta 1376(3):401–415

    Article  PubMed  CAS  Google Scholar 

  15. Killian JA, von Heijne G (2000) How proteins adapt to a membrane-water interface. Trends Biochem Sci 25(9):429–434

    Article  PubMed  CAS  Google Scholar 

  16. Caputo GA, London E (2003) Cumulative effects of amino acid substitutions and hydrophobic mismatch upon the transmembrane stability and conformation of hydrophobic alpha-helices. Biochemistry 42(11):3275–3285. doi:10.1021/bi026697d

    Article  PubMed  CAS  Google Scholar 

  17. Bretscher MS, Munro S (1993) Cholesterol and the Golgi apparatus. Science 261(5126):1280–1281

    Article  PubMed  CAS  Google Scholar 

  18. Perozo E, Kloda A, Cortes DM, Martinac B (2002) Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating. Nat Struct Biol 9(9):696–703. doi:10.1038/nsb827

    Article  PubMed  CAS  Google Scholar 

  19. Kloda A, Petrov E, Meyer GR, Nguyen T, Hurst AC, Hool L, Martinac B (2008) Mechanosensitive channel of large conductance. Int J Biochem Cell Biol 40(2):164–169. doi:10.1016/j.biocel.2007.02.003

    Article  PubMed  CAS  Google Scholar 

  20. de Planque MR, Greathouse DV, Koeppe RE II, Schafer H, Marsh D, Killian JA (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(26):9333–9345. doi:10.1021/bi980233r

    Article  PubMed  Google Scholar 

  21. Ramadurai S, Holt A, Schafer LV, Krasnikov VV, Rijkers DT, Marrink SJ, Killian JA, Poolman B (2010) Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys J 99(5):1447–1454. doi:10.1016/j.bpj.2010.05.042

    Article  PubMed  CAS  Google Scholar 

  22. van der Wel PC, Pott T, Morein S, Greathouse DV, Koeppe RE II, Killian JA (2000) Tryptophan-anchored transmembrane peptides promote formation of nonlamellar phases in phosphatidylethanolamine model membranes in a mismatch-dependent manner. Biochemistry 39(11):3124–3133

    Article  PubMed  CAS  Google Scholar 

  23. Zhang YP, Lewis RN, Hodges RS, McElhaney RN (1992) Interaction of a peptide model of a hydrophobic transmembrane alpha-helical segment of a membrane protein with phosphatidylcholine bilayers: differential scanning calorimetric and FTIR spectroscopic studies. Biochemistry 31(46):11579–11588

    Article  PubMed  CAS  Google Scholar 

  24. Krishnakumar SS, London E (2007) Effect of sequence hydrophobicity and bilayer width upon the minimum length required for the formation of transmembrane helices in membranes. J Mol Biol 374(3):671–687

    Article  PubMed  CAS  Google Scholar 

  25. Kim T, Im W (2010) Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophys J 99(1):175–183. doi:10.1016/j.bpj.2010.04.015

    Article  PubMed  CAS  Google Scholar 

  26. Webb RJ, East JM, Sharma RP, Lee AG (1998) Hydrophobic mismatch and the incorporation of peptides into lipid bilayers: a possible mechanism for retention in the Golgi. Biochemistry 37(2):673–679. doi:10.1021/bi972441+

    Article  PubMed  CAS  Google Scholar 

  27. Weiss TM, van der Wel PC, Killian JA, Koeppe RE II, Huang HW (2003) Hydrophobic mismatch between helices and lipid bilayers. Biophys J 84(1):379–385. doi:10.1016/S0006-3495(03)74858-9

    Article  PubMed  CAS  Google Scholar 

  28. Morein S, Killian JA, Sperotto MM (2002) Characterization of the thermotropic behavior and lateral organization of lipid-peptide mixtures by a combined experimental and theoretical approach: effects of hydrophobic mismatch and role of flanking residues. Biophys J 82(3):1405–1417. doi:10.1016/S0006-3495(02)75495-7

    Article  PubMed  CAS  Google Scholar 

  29. Morein S, Koeppe IR, Lindblom G, de Kruijff B, Killian JA (2000) The effect of peptide/lipid hydrophobic mismatch on the phase behavior of model membranes mimicking the lipid composition in Escherichia coli membranes. Biophys J 78(5):2475–2485

    Article  PubMed  CAS  Google Scholar 

  30. Kandasamy SK, Larson RG (2006) Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch. Biophys J 90(7):2326–2343. doi:10.1529/biophysj.105.073395

    Article  PubMed  CAS  Google Scholar 

  31. Holt A, Rougier L, Reat V, Jolibois F, Saurel O, Czaplicki J, Killian JA, Milon A (2010) Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide. Biophys J 98(9):1864–1872. doi:10.1016/j.bpj.2010.01.016

    Article  PubMed  CAS  Google Scholar 

  32. Strandberg E, Morein S, Rijkers DT, Liskamp RM, van der Wel PC, Killian JA (2002) Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides. Biochemistry 41(23):7190–7198

    Article  PubMed  CAS  Google Scholar 

  33. Liu F, Lewis RN, Hodges RS, McElhaney RN (2002) Effect of variations in the structure of a polyleucine-based alpha-helical transmembrane peptide on its interaction with phosphatidylcholine bilayers. Biochemistry 41(29):9197–9207

    Article  PubMed  CAS  Google Scholar 

  34. Liu F, Lewis RN, Hodges RS, McElhaney RN (2004) Effect of variations in the structure of a polyleucine-based alpha-helical transmembrane peptide on its interaction with phosphatidylethanolamine Bilayers. Biophys J 87(4):2470–2482. doi:10.1529/biophysj.104.046342

    Article  PubMed  CAS  Google Scholar 

  35. Liu F, Lewis RN, Hodges RS, McElhaney RN (2004) Effect of variations in the structure of a polyleucine-based alpha-helical transmembrane peptide on its interaction with phosphatidylglycerol bilayers. Biochemistry 43(12):3679–3687. doi:10.1021/bi036214l

    Article  PubMed  CAS  Google Scholar 

  36. Zhang YP, Lewis RN, Hodges RS, McElhaney RN (1995) Interaction of a peptide model of a hydrophobic transmembrane alpha-helical segment of a membrane protein with phosphatidylethanolamine bilayers: differential scanning calorimetric and Fourier transform infrared spectroscopic studies. Biophys J 68(3):847–857. doi:10.1016/S0006-3495(95)80261-4

    Article  PubMed  CAS  Google Scholar 

  37. Zhang YP, Lewis RN, Hodges RS, McElhaney RN (2001) Peptide models of the helical hydrophobic transmembrane segments of membrane proteins: interactions of acetyl-K2-(LA)12-K2-amide with phosphatidylethanolamine bilayer membranes. Biochemistry 40(2):474–482

    Article  PubMed  CAS  Google Scholar 

  38. Caputo GA, London E (2004) Position and ionization state of Asp in the core of membrane-inserted alpha helices control both the equilibrium between transmembrane and nontransmembrane helix topography and transmembrane helix positioning. Biochemistry 43(27):8794–8806

    Article  PubMed  CAS  Google Scholar 

  39. Ren J, Lew S, Wang J, London E (1999) Control of the transmembrane orientation and interhelical interactions within membranes by hydrophobic helix length. Biochemistry 38(18):5905–5912

    Article  PubMed  CAS  Google Scholar 

  40. Ren J, Lew S, Wang Z, London E (1997) Transmembrane orientation of hydrophobic alpha-helices is regulated both by the relationship of helix length to bilayer thickness and by the cholesterol concentration. Biochemistry 36(33):10213–10220

    Article  PubMed  CAS  Google Scholar 

  41. Krishnakumar SS, London E (2007) The control of transmembrane helix transverse position in membranes by hydrophilic residues. J Mol Biol 374(5):1251–1269. doi:10.1016/j.jmb.2007.10.032

    Article  PubMed  CAS  Google Scholar 

  42. Ipsen JH, Mouritsen OG, Bloom M (1990) Relationships between lipid membrane area, hydrophobic thickness, and acyl-chain orientational order. The effects of cholesterol. Biophys J 57(3):405–412. doi:10.1016/S0006-3495(90)82557-1

    Article  PubMed  CAS  Google Scholar 

  43. King GI, White SH (1986) Determining bilayer hydrocarbon thickness from neutron diffraction measurements using strip-function models. Biophys J 49(5):1047–1054. doi:10.1016/S0006-3495(86)83733-X

    Article  PubMed  CAS  Google Scholar 

  44. Lewis BA, Engelman DM (1983) Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J Mol Biol 166(2):211–217

    Article  PubMed  CAS  Google Scholar 

  45. Rawicz W, Olbrich KC, McIntosh T, Needham D, Evans E (2000) Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys J 79(1):328–339. doi:10.1016/S0006-3495(00)76295-3

    Article  PubMed  CAS  Google Scholar 

  46. Caputo GA, London E (2003) Using a novel dual fluorescence quenching assay for measurement of tryptophan depth within lipid bilayers to determine hydrophobic alpha-helix locations within membranes. Biochemistry 42(11):3265–3274

    Article  PubMed  CAS  Google Scholar 

  47. Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G (2010) Repositioning of transmembrane alpha-helices during membrane protein folding. J Mol Biol 397(1):190–201. doi:10.1016/j.jmb.2010.01.042

    Article  PubMed  CAS  Google Scholar 

  48. Hessa T, Monne M, von Heijne G (2003) Stop-transfer efficiency of marginally hydrophobic segments depends on the length of the carboxy-terminal tail. EMBO Rep 4(2):178–183. doi:10.1038/sj.embor.embor728

    Article  PubMed  CAS  Google Scholar 

  49. Monne M, Nilsson I, Elofsson A, von Heijne G (1999) Turns in transmembrane helices: determination of the minimal length of a “helical hairpin” and derivation of a fine-grained turn propensity scale. J Mol Biol 293(4):807–814. doi:10.1006/jmbi.1999.3183

    Article  PubMed  CAS  Google Scholar 

  50. Monne M, Nilsson I, Johansson M, Elmhed N, von Heijne G (1998) Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. J Mol Biol 284(4):1177–1183. doi:10.1006/jmbi.1998.2218

    Article  PubMed  CAS  Google Scholar 

  51. Nilsson I, Saaf A, Whitley P, Gafvelin G, Waller C, von Heijne G (1998) Proline-induced disruption of a transmembrane alpha-helix in its natural environment. J Mol Biol 284(4):1165–1175. doi:10.1006/jmbi.1998.2217

    Article  PubMed  CAS  Google Scholar 

  52. Sperotto MM, Mouritsen OG (1991) Monte Carlo simulation studies of lipid order parameter profiles near integral membrane proteins. Biophys J 59(2):261–270. doi:10.1016/S0006-3495(91)82219-6

    Article  PubMed  CAS  Google Scholar 

  53. Harroun TA, Heller WT, Weiss TM, Yang L, Huang HW (1999) Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys J 76(6):3176–3185. doi:10.1016/S0006-3495(99)77469-2

    Article  PubMed  CAS  Google Scholar 

  54. Harroun TA, Heller WT, Weiss TM, Yang L, Huang HW (1999) Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys J 76(2):937–945. doi:10.1016/S0006-3495(99)77257-7

    Article  PubMed  CAS  Google Scholar 

  55. Liu F, Lewis RN, Hodges RS, McElhaney RN (2001) A differential scanning calorimetric and 31P NMR spectroscopic study of the effect of transmembrane alpha-helical peptides on the lamellar-reversed hexagonal phase transition of phosphatidylethanolamine model membranes. Biochemistry 40(3):760–768

    Article  PubMed  CAS  Google Scholar 

  56. Harzer U, Bechinger B (2000) Alignment of lysine-anchored membrane peptides under conditions of hydrophobic mismatch: a CD, 15N and 31P solid-state NMR spectroscopy investigation. Biochemistry 39(43):13106–13114

    Article  PubMed  CAS  Google Scholar 

  57. Duong-Ly KC, Nanda V, Degrado WF, Howard KP (2005) The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci 14(4):856–861. doi:10.1110/ps.041185805

    Article  PubMed  CAS  Google Scholar 

  58. Nguyen PA, Soto CS, Polishchuk A, Caputo GA, Tatko CD, Ma C, Ohigashi Y, Pinto LH, DeGrado WF, Howard KP (2008) pH-induced conformational change of the influenza M2 protein C-terminal domain. Biochemistry 47(38):9934–9936. doi:10.1021/bi801315m

    Article  PubMed  CAS  Google Scholar 

  59. Strandberg E, Ozdirekcan S, Rijkers DT, van der Wel PC, Koeppe RE II, Liskamp RM, Killian JA (2004) Tilt angles of transmembrane model peptides in oriented and non-oriented lipid bilayers as determined by 2H solid-state NMR. Biophys J 86(6):3709–3721. doi:10.1529/biophysj.103.035402

    Article  PubMed  CAS  Google Scholar 

  60. van der Wel PC, Strandberg E, Killian JA, Koeppe RE II (2002) Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by (2)H NMR. Biophys J 83(3):1479–1488. doi:10.1016/S0006-3495(02)73918-0

    Article  PubMed  Google Scholar 

  61. de Planque MR, Goormaghtigh E, Greathouse DV, Koeppe RE II, Kruijtzer JA, Liskamp RM, de Kruijff B, Killian JA (2001) Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: effects on backbone structure, orientation, and extent of membrane incorporation. Biochemistry 40(16):5000–5010

    Article  PubMed  CAS  Google Scholar 

  62. Burck J, Roth S, Wadhwani P, Afonin S, Kanithasen N, Strandberg E, Ulrich AS (2008) Conformation and membrane orientation of amphiphilic helical peptides by oriented circular dichroism. Biophys J 95(8):3872–3881. doi:10.1529/biophysj.108.136085

    Article  PubMed  CAS  Google Scholar 

  63. Clayton AH, Sawyer WH (2000) Oriented circular dichroism of a class A amphipathic helix in aligned phospholipid multilayers. Biochim Biophys Acta 1467(1):124–130

    Article  PubMed  CAS  Google Scholar 

  64. Kuball HG, Hofer T (2000) Chirality and circular dichroism of oriented molecules and anisotropic phases. Chirality 12(4):278–286. doi:10.1002/(SICI)1520-636X(2000)12:4<278::AID-CHIR14>3.0.CO;2-O

    Article  PubMed  CAS  Google Scholar 

  65. de Jongh HH, Goormaghtigh E, Killian JA (1994) Analysis of circular dichroism spectra of oriented protein-lipid complexes: toward a general application. Biochemistry 33(48): 14521–14528

    Article  PubMed  Google Scholar 

  66. Wu Y, Huang HW, Olah GA (1990) Method of oriented circular dichroism. Biophys J 57(4):797–806. doi:10.1016/S0006-3495(90)82599-6

    Article  PubMed  CAS  Google Scholar 

  67. Vigano C, Manciu L, Buyse F, Goormaghtigh E, Ruysschaert JM (2000) Attenuated total reflection IR spectroscopy as a tool to investigate the structure, orientation and tertiary structure changes in peptides and membrane proteins. Biopolymers 55(5):373–380. doi:10.1002/1097-0282(2000)55:5<373::AID-BIP1011>3.0.CO;2-U

    Article  PubMed  CAS  Google Scholar 

  68. Reinl HM, Bayerl TM (1993) Interaction of myelin basic protein with single bilayers on a solid support: an NMR, DSC and polarized infrared ATR study. Biochim Biophys Acta 1151(2):127–136

    Article  PubMed  CAS  Google Scholar 

  69. Frey S, Tamm LK (1991) Orientation of melittin in phospholipid bilayers. A polarized attenuated total reflection infrared study. Biophys J 60(4):922–930. doi:10.1016/S0006-3495(91)82126-9

    Article  PubMed  CAS  Google Scholar 

  70. Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, Degrado WF, Bennett JS (2006) Activation of platelet alphaIIbbeta3 by an exogenous peptide corresponding to the transmembrane domain of alphaIIb. J Biol Chem 281(48):36732–36741. doi:10.1074/jbc.M605877200

    Article  PubMed  CAS  Google Scholar 

  71. Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF (2007) Computational design of peptides that target transmembrane helices. Science 315(5820):1817–1822. doi:10.1126/science.1136782

    Article  PubMed  CAS  Google Scholar 

  72. Axelsen PH, Kaufman BK, McElhaney RN, Lewis RN (1995) The infrared dichroism of transmembrane helical polypeptides. Biophys J 69(6):2770–2781. doi:10.1016/S0006-3495(95)80150-5

    Article  PubMed  CAS  Google Scholar 

  73. Ausili A, Corbalan-Garcia S, Gomez-Fernandez JC, Marsh D (2011) Membrane docking of the C2 domain from protein kinase Calpha as seen by polarized ATR-IR. The role of PIP(2). Biochim Biophys Acta 1808(3):684–695. doi:10.1016/j.bbamem.2010.11.035

    Article  PubMed  CAS  Google Scholar 

  74. Lorenz-Fonfria VA, Granell M, Leon X, Leblanc G, Padros E (2009) In-plane and out-of-plane infrared difference spectroscopy unravels tilting of helices and structural changes in a membrane protein upon substrate binding. J Am Chem Soc 131(42):15094–15095. doi:10.1021/ja906324z

    Article  PubMed  CAS  Google Scholar 

  75. DeGrado WF, Gratkowski H, Lear JD (2003) How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci 12(4):647–665

    Article  PubMed  CAS  Google Scholar 

  76. Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF (2004) Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J 87(5):3421–3429. doi:10.1529/biophysj.103.032839

    Article  PubMed  CAS  Google Scholar 

  77. Runnels LW, Scarlata SF (1995) Theory and application of fluorescence homotransfer to melittin oligomerization. Biophys J 69(4): 1569–1583. doi:10.1016/S0006-3495(95)80030-5

    Article  PubMed  CAS  Google Scholar 

  78. You M, Li E, Wimley WC, Hristova K (2005) Forster resonance energy transfer in liposomes: measurements of transmembrane helix dimerization in the native bilayer environment. Anal Biochem 340(1):154–164. doi:10.1016/j.ab.2005.01.035

    Article  PubMed  CAS  Google Scholar 

  79. 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 

  80. Lew S, London E (1997) Simple procedure for reversed-phase high-performance liquid chromatographic purification of long hydrophobic peptides that form transmembrane helices. Anal Biochem 251(1):113–116

    Article  PubMed  CAS  Google Scholar 

  81. Ladokhin AS (1997) Distribution analysis of depth-dependent fluorescence quenching in membranes: a practical guide. Methods Enzymol 278:462–473

    Article  PubMed  CAS  Google Scholar 

  82. Abrams FS, London E (1992) Calibration of the parallax fluorescence quenching method for determination of membrane penetration depth: refinement and comparison of quenching by spin-labeled and brominated lipids. Biochemistry 31(23):5312–5322

    Article  PubMed  CAS  Google Scholar 

  83. Chattopadhyay A, London E (1987) Parallax method for direct measurement of membrane penetration depth utilizing fluorescence quenching by spin-labeled phospholipids. Biochemistry 26(1):39–45

    Article  PubMed  CAS  Google Scholar 

  84. Bolen EJ, Holloway PW (1990) Quenching of tryptophan fluorescence by brominated phospholipid. Biochemistry 29(41):9638–9643

    Article  PubMed  CAS  Google Scholar 

  85. Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF (2007) E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. J Mol Biol 366(2):436–448

    Article  PubMed  CAS  Google Scholar 

  86. Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I (2012) Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure 20(5):924–935. doi:10.1016/j.str.2012.03.016

    Article  PubMed  CAS  Google Scholar 

  87. Landolt-Marticorena C, Williams KA, Deber CM, Reithmeier RA (1993) Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J Mol Biol 229(3):602–608. doi:10.1006/jmbi.1993.1066

    Article  PubMed  CAS  Google Scholar 

  88. Strandberg E, Esteban-Martin S, Ulrich AS, Salgado J (2012) Hydrophobic mismatch of mobile transmembrane helices: merging theory and experiments. Biochim Biophys Acta 1818(5):1242–1249. doi:10.1016/j.bbamem.2012.01.023

    Article  PubMed  CAS  Google Scholar 

  89. Holt A, Killian JA (2010) Orientation and dynamics of transmembrane peptides: the power of simple models. Eur Biophys J 39(4):609–621. doi:10.1007/s00249-009-0567-1

    Article  PubMed  CAS  Google Scholar 

  90. Ozdirekcan S, Etchebest C, Killian JA, Fuchs PF (2007) On the orientation of a designed transmembrane peptide: toward the right tilt angle? J Am Chem Soc 129(49):15174–15181. doi:10.1021/ja073784q

    Article  PubMed  CAS  Google Scholar 

  91. Pan J, Tristram-Nagle S, Nagle JF (2009) Alamethicin aggregation in lipid membranes. J Membr Biol 231(1):11–27. doi:10.1007/s00232-009-9199-8

    Article  PubMed  CAS  Google Scholar 

  92. Killian JA (2003) Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett 555(1):134–138

    Article  PubMed  CAS  Google Scholar 

  93. de Planque MR, Killian JA (2003) Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr Biol 20(4):271–284. doi:10.1080/09687680310001605352

    Article  PubMed  CAS  Google Scholar 

  94. Rankenberg JM, Vostrikov VV, DuVall CD, Greathouse DV, Koeppe RE II, Grant CV, Opella SJ (2012) Proline kink angle distributions for GWALP23 in lipid bilayers of different thicknesses. Biochemistry 51(17):3554–3564. doi:10.1021/bi300281k

    Article  PubMed  CAS  Google Scholar 

  95. Shahidullah K, London E (2008) Effect of lipid composition on the topography of membrane-associated hydrophobic helices: stabilization of transmembrane topography by anionic lipids. J Mol Biol 379(4):704–718. doi:10.1016/j.jmb.2008.04.026

    Article  PubMed  CAS  Google Scholar 

  96. Kremer JM, Esker MW, Pathmamanoharan C, Wiersema PH (1977) Vesicles of variable diameter prepared by a modified injection method. Biochemistry 16(17):3932–3935

    Article  PubMed  CAS  Google Scholar 

  97. Aarts PA, Gijeman OL, Kremer JM, Wiersema PH (1977) Dynamics of phospholipid aggregation in ethanol–water solutions. Chem Phys Lipids 19(3):267–274

    Article  PubMed  CAS  Google Scholar 

  98. London E (2007) Using model membrane-inserted hydrophobic helices to study the equilibrium between transmembrane and nontransmembrane states. J Gen Physiol 130(2):229–232

    Article  PubMed  CAS  Google Scholar 

  99. Shahidullah K, Krishnakumar SS, London E (2010) The effect of hydrophilic substitutions and anionic lipids upon the transverse positioning of the transmembrane helix of the ErbB2 (neu) protein incorporated into model membrane vesicles. J Mol Biol 396(1):209–220. doi:10.1016/j.jmb.2009.11.037

    Article  PubMed  CAS  Google Scholar 

  100. Jones JD, Gierasch LM (1994) Effect of charged residue substitutions on the membrane-interactive properties of signal sequences of the Escherichia coli LamB protein. Biophys J 67(4):1534–1545. doi:10.1016/S0006-3495(94)80627-7

    Article  PubMed  CAS  Google Scholar 

  101. McIntosh TJ, Simon SA, MacDonald RC (1980) The organization of n-alkanes in lipid bilayers. Biochim Biophys Acta 597(3):445–463

    Article  PubMed  CAS  Google Scholar 

  102. Uhrikova D, Balgavy P, Kucerka N, Islamov A, Gordeliy V, Kuklin A (2000) Small-angle neutron scattering study of the n-decane effect on the bilayer thickness in extruded unilamellar dioleoylphosphatidylcholine liposomes. Biophys Chem 88(1–3):165–170

    Article  PubMed  CAS  Google Scholar 

  103. Nezil FA, Bloom M (1992) Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes. Biophys J 61(5):1176–1183. doi:10.1016/S0006-3495(92)81926-4

    Article  PubMed  CAS  Google Scholar 

  104. Sanchez SA, Gunther G, Tricerri MA, Gratton E (2011) Methyl-beta-cyclodextrins preferentially remove cholesterol from the liquid disordered phase in giant unilamellar vesicles. J Membr Biol 241(1):1–10. doi:10.1007/s00232-011-9348-8

    Article  PubMed  CAS  Google Scholar 

  105. Veatch SL, Keller SL (2003) Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol. Biophys J 85(5):3074–3083. doi:10.1016/S0006-3495(03)74726-2

    Article  PubMed  CAS  Google Scholar 

  106. Caputo GA, Litvinov RI, Li W, Bennett JS, Degrado WF, Yin H (2008) Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry 47(33):8600–8606. doi:10.1021/bi800687h

    Article  PubMed  CAS  Google Scholar 

  107. Hayashibara M, London E (2005) Topography of diphtheria toxin A chain inserted into lipid vesicles. Biochemistry 44(6): 2183–2196

    Article  PubMed  CAS  Google Scholar 

  108. Follenius-Wund A, Piemont E, Freyssinet JM, Gerard D, Pigault C (1997) Conformational adaptation of annexin V upon binding to liposomes: a time-resolved fluorescence study. Biochem Biophys Res Commun 234(1):111–116. doi:10.1006/bbrc.1997.6596

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA

    Gregory A. Caputo

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  1. Gregory A. Caputo
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  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

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Caputo, G.A. (2013). Analyzing the Effects of Hydrophobic Mismatch on Transmembrane α-Helices Using Tryptophan Fluorescence Spectroscopy. 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_5

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  • DOI: https://doi.org/10.1007/978-1-62703-583-5_5

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