Interdigitation of Lipids Induced by Membrane–Active Proteins

  • T. Devanand
  • Sankaran Krishnaswamy
  • Satyavani VemparalaEmail author
Part of the following topical collections:
  1. Membrane and Receptor Dynamics


The membrane–active protein Nogo-66 is found to induce interdigitation in dimyristoylphosphocholine membranes. Extensive molecular dynamics simulations have been employed to probe the interactions of Nogo-66 with these model membranes. This phase change happens when the temperature is close to the main transition temperature of the membrane (Tm) and only in the presence of the protein. No similar interdigitation of the membrane lipids was observed temperatures well above Tm in the presence of the protein. In addition, in protein-free simulations, no interdigitation of the membrane lipids was found both at temperatures near or well above Tm indicating that the observed effect is caused by the interactions of Nogo-66 with the membrane. Analysis of the simulations suggest protein–membrane interactions, even if transient, alter the lifetimes of lipid head defects and can potentially alter the effective Tm and cause interdigitation. This study emphasize the importance of membrane–active proteins and their interactions with membranes leading to phase transitions which would affect other membrane-related processes such as domain formation.


Nogo-66 DMPC membrane Ripple phase Interdigitation Asymmetric ripples 



The simulations were carried out on the supercomputing machines Annapurna and Nandadevi at the Institute of Mathematical Sciences.

Supplementary material

232_2019_72_MOESM1_ESM.pdf (1.1 mb)
Electronic supplementary material 1 (PDF 1099 kb)


  1. Akabori K, Nagle JF (2015) Structure of the DMPC lipid bilayer ripple phase. Soft Matter 11(5):918–926Google Scholar
  2. Almeida C, Lamazière A, Filleau A, Corvis Y, Espeau P, Ayala-Sanmartin J (2016) Membrane re-arrangements and rippled phase stabilisation by the cell penetrating peptide penetratin. Biochim Biophys Acta 1858(11):2584–2591Google Scholar
  3. Aoun B, Pellegrini E, Trapp M, Natali F, Cantú L, Brocca P, Gerelli Y, Demé B, Koza MM, Johnson M et al (2016) Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of dmpc phase transitions. Eur Phys J E 39(4):48Google Scholar
  4. Baoukina S, Tielemanm DP (2015) Computer simulations of phase separation in lipid bilayers and monolayers. Methods in membrane lipids. Springer, New York, pp 307–322Google Scholar
  5. Baul U, Vemparala S (2015) Membrane-bound conformations of antimicrobial agents and their modes of action, vol 22. Advances in planar lipid bilayers and liposomes. Elsevier, Amsterdam, pp 97–128Google Scholar
  6. Baul U, Vemparala S (2017) Influence of lipid composition of model membranes on methacrylate antimicrobial polymer–membrane interactions. Soft Matter 13(41):7665–7676Google Scholar
  7. Best RB, Zhu X, Shim J, Lopes PEM, Mittal J, Feig M, MacKerell AD Jr (2012) Optimization of the additive charmm all-atom protein force field targeting improved sampling of the backbone \(\phi\), \(\psi\) and side-chain \(\chi\)1 and \(\chi\)2 dihedral angles. J Chem Theory Comput 8(9):3257–3273Google Scholar
  8. Bigay J, Casella J-F, Drin G, Mesmin B, Antonny B (2005) Arfgap1 responds to membrane curvature through the folding of a lipid packing sensor motif. EMBO J 24(13):2244–2253Google Scholar
  9. Cevc G, Marsh D (1987) Phospholipid bilayers: physical principles and models. Wiley, HobokenGoogle Scholar
  10. Chen C-M, Lubensky TC, MacKintosh FC (1995) Phase transitions and modulated phases in lipid bilayers. Phys Rev E 51(1):504Google Scholar
  11. Chen W, Duša F, Witos J, Ruokonen S-K, Wiedmer SK (2018) Determination of the main phase transition temperature of phospholipids by nanoplasmonic sensing. Sci Rep 8(1):14815Google Scholar
  12. Choubey A, Nomura K, Kalia RK, Nakano A, Vashishta P (2014) Small interfering ribonucleic acid induces liquid-to-ripple phase transformation in a phospholipid membrane. Appl Phys Lett 105(11):113702Google Scholar
  13. Cui H, Lyman E, Voth GA (2011) Mechanism of membrane curvature sensing by amphipathic helix containing proteins. Biophys J 100(5):1271–1279Google Scholar
  14. Darden T, York D, Pedersen L (1993) Particle mesh ewald: an n log (n) method for ewald sums in large systems. J Chem Phys 98(12):10089–10092Google Scholar
  15. de Vries AH, Serge Y, Mark AE, Marrink SJ (2005) Molecular structure of the lecithin ripple phase. Proc Natl Acad Sci 102(15):5392–5396Google Scholar
  16. Debnath A, Thakkar FM, Maiti PK, Kumaran V, Ayappa KG (2014) Laterally structured ripple and square phases with one and two dimensional thickness modulations in a model bilayer system. Soft Matter 10(38):7630–7637Google Scholar
  17. Destainville N, Schmidt TH, Lang T (2016) Where biology meets physics: a converging view on membrane microdomain dynamics, vol 77. Current topics in membranes. Elsevier, Amsterdam, pp 27–65Google Scholar
  18. Di Pisa M, Chassaing G, Swiecicki J-M (2014) Translocation mechanism (s) of cell-penetrating peptides: biophysical studies using artificial membrane bilayers. Biochemistry 54(2):194–207Google Scholar
  19. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) Pdb2pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations. Nucl Acids Res 32(suppl 2):W665–W667Google Scholar
  20. Drin G, Antonny B (2010) Amphipathic helices and membrane curvature. FEBS Lett 584(9):1840–1847Google Scholar
  21. Edidin M (2003) The state of lipid rafts: from model membranes to cells. Annu Rev Biophys Biomol Struct 32(1):257–283Google Scholar
  22. Epand RM, Walker C, Epand RF, Magarvey NA (2016) Molecular mechanisms of membrane targeting antibiotics. Biochim Biophys Acta 1858(5):980–987Google Scholar
  23. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh ewald method. J Chem Phys 103(19):8577–8593Google Scholar
  24. Feller FSE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the langevin piston method. J Chem Phys 103(11):4613–4621Google Scholar
  25. Feng ZV, Granick S, Gewirth AA (2004) Modification of a supported lipid bilayer by polyelectrolyte adsorption. Langmuir 20(20):8796–8804Google Scholar
  26. Fusco G, Sanz-Hernandez M, De Simone A (2018) Order and disorder in the physiological membrane binding of α-synuclein. Curr Opin Struct Biol 48:49–57Google Scholar
  27. Gautier R, Bacle A, Tiberti ML, Fuchs PF, Vanni S, Antonny B (2018) Packmem: a versatile tool to compute and visualize interfacial packing defects in lipid bilayers. Biophys J 115(3):436–444Google Scholar
  28. Giorgino T (2014) Computing 1-d atomic densities in macromolecular simulations: the density profile tool for vmd. Comput Phys Commun 185(1):317–322Google Scholar
  29. Gray E, Karslake J, Machta BB, Veatch SL (2013) Liquid general anesthetics lower critical temperatures in plasma membrane vesicles. Biophys J 105(12):2751–2759Google Scholar
  30. Griffn KL, Cheng C-Y, Smith EA, Dea PK (2010) Effects of pentanol isomers on the phase behavior of phospholipid bilayer membranes. Biophys Chem 152(1–3):178–183Google Scholar
  31. Guixa-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J (2014) Membplugin: studying membrane complexity in vmd. Bioinformatics 30(10):1478–1480Google Scholar
  32. Harrison PL, Heath GR, Johnson BRG, Abdel-Rahman MA, Strong PN, Evans SD, Miller K (2016) Phospholipid dependent mechanism of smp24, an α-helical antimicrobial peptide from scorpion venom. Biochim Biophys Acta 1858(11):2737–2744Google Scholar
  33. Heller WT, Waring AJ, Lehrer RI, Harroun TA, Weiss TM, Yang L, Huang HW (2000) Membrane thinning effect of the β-sheet antimicrobial protegrin. Biochemistry 39(1):139–145Google Scholar
  34. Humphrey W, Dalke A, Schulten K (1996) VMD—visual molecular dynamics. J Mol Graph 14:33–38Google Scholar
  35. Jain MK, White HB (1977) Long-range order in biomembranes, vol 15. Advances in lipid research. Elsevier, Amsterdam, pp 1–60Google Scholar
  36. Jain MK, Wu NM (1977) Effect of small molecules on the dipalmitoyl lecithin liposomal bilayer: III. Phase transition in lipid bilayer. J Membr Biol 34(1):157–201Google Scholar
  37. Jo S, Kim T, Iyer VG, Im W (2008) Charmm-gui: a web-based graphical user interface for charmm. J Comput Chem 29(11):1859–1865Google Scholar
  38. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein Michael L (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935Google Scholar
  39. Kaiser H-J, Lingwood D, Levental I, Sampaio JL, Kalvodova L, Rajendran L, Simons K (2009) Order of lipid phases in model and plasma membranes. Proc Natl Acad Sci 106(39):16645–16650Google Scholar
  40. Khakbaz P, Klauda JB (2018) Investigation of phase transitions of saturated phosphocholine lipid bilayers via molecular dynamics simulations. Biochim Biophys Acta 180(8):1489–1501Google Scholar
  41. Koukos PI, Glykos NM (2013) Grcarma: a fully automated task-oriented interface for the analysis of molecular dynamics trajectories. J Comput Chem 34(26):2310–2312Google Scholar
  42. Kranenburg M, Smit B (2005) Phase behavior of model lipid bilayers. J Phys Chem B 109(14):6553–6563Google Scholar
  43. Kranenburg M, Venturoli M, Smit B (2003) Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. J Phys Chem B 107(41):11491–11501Google Scholar
  44. Kranenburg M, Vlaar M, Smit B (2004) Simulating induced interdigitation in membranes. Biophys J 87(3):1596–1605Google Scholar
  45. Kučerka N, Nieh M-P, Katsaras J (2011) Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. Biochim Biophys Acta 1808(11):2761–2771Google Scholar
  46. Lamaziére A, Wolf C, Lambert O, Chassaing G, Trugnan G, Ayala-Sanmartin J (2008) The homeodomain derived peptide penetratin induces curvature of fluid membrane domains. PLoS ONE 3(4):e1938Google Scholar
  47. Lamaziére A, Chassaing G, Trugnan G, Ayala-Sanmartin J (2009) Tubular structures in heterogeneous membranes induced by the cell penetrating peptide penetratin. Commun Integr Biol 2(3):223–224Google Scholar
  48. Laner M, Hünenberger PH (2015) Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations in quest of the biphasic effect. J Mol Graph Model 55:85–104Google Scholar
  49. Lee AG (2003) Lipid–protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta 1612(1):1–40Google Scholar
  50. Lee M-T, Chen F-Y, Huang HW (2004) Energetics of pore formation induced by membrane active peptides. Biochemistry 43(12):3590–3599Google Scholar
  51. Lee M-T, Sun T-L, Hung W-C, Huang HW (2013) Process of inducing pores in membranes by melittin. Proc Natl Acad Sci 110(35):14243–14248Google Scholar
  52. Lenz O, Schmid F (2007) Structure of symmetric and asymmetric “ripple” phases in lipid bilayers. Phys Rev Lett 98(5):058104Google Scholar
  53. Lewis BA, Engelman DM (1983) Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J Mol Biol 166(2):211–217Google Scholar
  54. Lingwood D, Simons K (2010) Lipid rafts as a membrane-organizing principle. Science 327(5961):40–50Google Scholar
  55. Lubensky TC, MacKintosh FC (1993) Theory of “ripple” phases of lipid bilayers. Phys Rev Lett 71(10):1565Google Scholar
  56. Lyman E, Hsieh CL, Eggeling C (2018) From dynamics to membrane organization: experimental breakthroughs occasion a “modeling manifesto”. Biophys JGoogle Scholar
  57. Mabrey M, Sturtevant JM (1976) Investigation of phase transitions of lipids and lipid mixtures by sensitivity differential scanning calorimetry. Proc Natl Acad Sci 73(11):3862–3866Google Scholar
  58. MacKerell AD Jr, Bashford D, Bellott MLDR, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586–3616Google Scholar
  59. Marrink SJ, De Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks, and curves. Biochim Biophys Acta 1788(1):149–168Google Scholar
  60. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101(5):4177–4189Google Scholar
  61. Mavromoustakos T, Chatzigeorgiou P, Koukoulitsa C, Durdagi S (2011) Partial interdigitation of lipid bilayers. Int J Quantum Chem 111(6):1172–1183Google Scholar
  62. McIntosh TJ, McDaniel RV, Simon SA (1983) Induction of an interdigitated gel phase in fully hydrated phosphatidylcholine bilayers. Biochim Biophys Acta 731(1):109–114Google Scholar
  63. McIntosh TJ, Lin H, Li S, Huang C (2001) The effect of ethanol on the phase transition temperature and the phase structure of monounsaturated phosphatidylcholines. Biochim Biophys Acta 1510(1):219–230Google Scholar
  64. McMahon HT, Gallop JL (2005) Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature 438(7068):590Google Scholar
  65. Meck A, Lee D-K, Ramamoorthy A, Orr BG (2005) Membrane thinning due to antimicrobial peptide binding: an atomic force microscopy study of msi-78 in lipid bilayers. Biophys J 89(6):4043–4050Google Scholar
  66. Mizuno N, Varkey J, Kegulian NC, Hegde BG, Naiqian C, Ralf L, Steven Alasdair C (2012) Remodeling of lipid vesicles into cylindrical micelles by α-synuclein in an extended α-helical conformation. J Biol Chem 287(35):29301–29311Google Scholar
  67. Nagle JF, Wilkinson DA (1978) Lecithin bilayers density measurement and molecular interactions. Biophys J 23(2):159–175Google Scholar
  68. Nicovich PR, Kwiatek JM, Ma Y, Benda A, Gaus K (2018) Fscs reveals the complexity of lipid domain dynamics in the plasma membrane of live cells. Biophys J 114(12):2855–2864Google Scholar
  69. Ouberai MM, Wang J, Swann MJ, Galvagnion C, Guilliams T, Dobson CM, Welland ME (2013) α-Synuclein senses lipid packing defects and induces lateral expansion of lipids leading to membrane remodeling. J Biol Chem 288:20883–20895Google Scholar
  70. O’Leary EI, Jiang Z, Strub MP, Lee JC (2018) Effects of phosphatidylcholine membrane fluidity on the conformation and aggregation of n-terminally acetylated \(\alpha\)-synuclein. J Biol Chem 293(28):11195–11205Google Scholar
  71. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with namd. J Comput Chem 26(16):1781–1802Google Scholar
  72. Qian S, Heller WT (2011) Peptide-induced asymmetric distribution of charged lipids in a vesicle bilayer revealed by small-angle neutron scattering. J Phys Chem B 115(32):9831–9837Google Scholar
  73. Ramalho JPP, Gkeka P, Sarkisov L (2011) Structure and phase transformations of dppc lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations. Langmuir 27(7):3723–3730Google Scholar
  74. Reddy ST, Shrivastava S, Chattopadhyay A (2018) Local anesthetics induce interdigitation and thermotropic changes in dipalmitoylphosphatidylcholine bilayers. Chem Phys Lipids 210:22–27Google Scholar
  75. Reynolds NP, Soragni A, Rabe M, Verdes D, Liverani E, Handschin S, Riek R, Seeger S (2011) Mechanism of membrane interaction and disruption by α-synuclein. J Am Chem Soc 133(48):19366–19375Google Scholar
  76. Rowe ES, Campion JM (1994) Alcohol induction of interdigitation in distearoylphosphatidylcholine: fluorescence studies of alcohol chain length requirements. Biophys J 67(5):1888–1895Google Scholar
  77. Schmid F (2017) Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes. Biochim Biophys Acta 1859(4):509–528Google Scholar
  78. Sevcsik E, Pabst G, Jilek A, Lohner K (2007) How lipids influence the mode of action of membrane–active peptides. Biochim Biophys Acta 1768(10):2586–2595Google Scholar
  79. Sharma VK, Qian S (2019) Effect of an antimicrobial peptide on lateral segregation of lipids, a structure and dynamics study by neutron scattering. Langmuir 35:4152–4160Google Scholar
  80. Sharma VK, Mamontov E, Tyagi M, Qian S, Rai DK, Urban VS (2016) Dynamical and phase behavior of a phospholipid membrane altered by an antimicrobial peptide at low concentration. J Phys Chem Lett 7(13):2394–2401Google Scholar
  81. Shigematsu T, Koshiyama K, Wada S (2018) Stretch-induced interdigitation of a phospholipid/cholesterol bilayer. J Phys Chem B 122(9):2556–2563Google Scholar
  82. Slater JL, Huang C-H (1988) Interdigitated bilayer membranes. Prog Lipid Res 27(4):325–359Google Scholar
  83. Smith EA, Dea PK (2013) Differential scanning calorimetry studies of phospholipid membranes: the interdigitated gel phase. In: Applications of calorimetry in a wide context-differential scanning calorimetry, isothermal titration calorimetry and microcalorimetry. InTech, LondonGoogle Scholar
  84. Stone MB, Shelby SA, Núñez MF, Wisser K, Veatch SL (2017) Protein sorting by lipid phase-like domains supports emergent signaling function in b lymphocyte plasma membranes. Elife 6:e19891Google Scholar
  85. Su C-J, Wu S-S, Jeng U-S, Lee M-T, Su A-C, Liao K-F, Lin W-Y, Huang Y-S, Chen C-Y (2013) Peptide-induced bilayer thinning structure of unilamellar vesicles and the related binding behavior as revealed by X-ray scattering. Biochim Biophys Acta 1828(2):528–534Google Scholar
  86. Sun WJ, Tristram-Nagle S, Suter RM, Nagle JF (1996) Structure of the ripple phase in lecithin bilayers. Proc Natl Acad Sci 93(14):7008–7012Google Scholar
  87. Tardieu A, Vittorio L, Reman FC (1973) Structure and polymorphism of the hydrocarbon chains of lipids: a study of lecithin-water phases. J Mol Biol 75(4):711–733Google Scholar
  88. Vamparys L, Gautier R, Vanni S, Bennett WFD, Tieleman DP, Antonny B, Etchebest C, Fuchs PFJ (2013) Conical lipids in flat bilayers induce packing defects similar to that induced by positive curvature. Biophys J 104(3):585–593Google Scholar
  89. Vanni S, Vamparys L, Gautier R, Drin G, Etchebest C, Fuchs PFJ, Antonny B (2013) Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J 104(3):575–584Google Scholar
  90. Vanni S, Hirose H, Barelli H, Antonny B, Gautier R (2014) A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment. Nat Commun 5:4916Google Scholar
  91. Varkey J, Isas JM, Mizuno N, Jensen MB, Bhatia VK, Jao CC, Petrlova J, Voss JC, Stamou DG, Steven AC et al (2010) Membrane curvature induction and tubulation are common features of synucleins and apolipoproteins. J Biol Chem 285(42):32486–32493Google Scholar
  92. Vasudevan SV, Schulz J, Zhou C, Cocco MJ (2010) Protein folding at the membrane interface, the structure of nogo-66 requires interactions with a phosphocholine surface. Proc Natl Acad Sci 107(15):6847–6851Google Scholar
  93. Verde AR, Sierra MB, Alarcón LM, Pedroni VI, Appignanesi GA, Morini MA (2018) Experimental and computational studies of the effects of free dha on a model phosphatidylcholine membrane. Chem Phys Lipids 217:12–18Google Scholar
  94. Wang D-C, Taraschi TF, Rubin E, Janes N (1993) Configurational entropy is the driving force of ethanol action on membrane architecture. Biochim Biophys Acta 1145(1):141–148Google Scholar
  95. Weikl TR (2018) Membrane-mediated cooperativity of proteins. Annu Rev Phys Chem 69:521–539Google Scholar
  96. Welker S, Rudolph B, Frenzel E, Hagn F, Liebisch G, Schmitz G, Scheuring J, Kerth A, Blume A, Weinkauf S et al (2010) Hsp12 is an intrinsically unstructured stress protein that folds upon membrane association and modulates membrane function. Mol cell 39(4):507–520Google Scholar
  97. Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM et al (2014) Charmm-gui membrane builder toward realistic biological membrane simulations. J Comput Chem 35(27):1997–2004Google Scholar
  98. Yang L, Fukuto M (2005) Modulated phase of phospholipids with a two-dimensional square lattice. Phys Rev E 72(1):010901Google Scholar
  99. Yin H, Flynn AD (2016) Drugging membrane protein interactions. Annu Rev Biomed Eng 18:51–76Google Scholar
  100. Zambrano F, Fleischer S, Fleischer B (1975) Lipid composition of the golgi apparatus of rat kidney and liver in comparison with other subcellular organelles. Biochim Biophys Acta 380(3):357–369Google Scholar

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Authors and Affiliations

  • T. Devanand
    • 1
    • 2
  • Sankaran Krishnaswamy
    • 1
  • Satyavani Vemparala
    • 1
    • 2
    Email author
  1. 1.The Institute of Mathematical Sciences, C.I.T. CampusChennaiIndia
  2. 2.Homi Bhabha National InstituteMumbaiIndia

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