Cholesterol, sphingolipids, and glycolipids: What do we know about their role in raft-like membranes?

Chemistry and Physics of Lipids

Volumn 184, Issue , 2014, Pages 82-104

  Róg, Tomasz ^a   Vattulainen, Ilpo ^a,b  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Coarse grained simulations; Lipid raft; Membrane domain; Membrane protein; Molecular dynamics simulations; Peptide; Receptor

Indexed keywords

CEREBROSIDE; CHOLESTEROL; CHOLESTEROL HYDROGEN SUCCINATE; DRUG CARRIER; GALACTOSYLCEREBROSIDE; GLYCEROL; GLYCOLIPID; LIPOPOLYSACCHARIDE; MEMBRANE PROTEIN; PEPTIDE; PHOSPHATIDYLCHOLINE; SPHINGOLIPID; SUGAR; UNCLASSIFIED DRUG; LIPID BILAYER; PROTEIN; SPHINGOMYELIN;

ADSORPTION; CHEMICAL STRUCTURE; DESORPTION; HYDROPHOBICITY; LENS; LIPID BILAYER; LIPID RAFT; MEMBRANE PERMEABILITY; MOLECULAR DYNAMICS; OXIDATIVE STRESS; REVIEW; SIMULATION; STEROL ANALYSIS; CELL MEMBRANE; CHEMISTRY; HUMAN; METABOLISM;

CHOLESTEROL; GLYCOLIPIDS; HUMANS; LIPID BILAYERS; MEMBRANE MICRODOMAINS; PEPTIDES; PHOSPHATIDYLCHOLINES; PROTEINS; SPHINGOLIPIDS; SPHINGOMYELINS;

EID: 84910019812     PISSN: 00093084     EISSN: 18732941     Source Type: Journal    
DOI: 10.1016/j.chemphyslip.2014.10.004     Document Type: Review

References (346)

1. Aittoniemi, J., Niemela, P.S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., 2007. Insight into the putative specific interactions between cholesterol, sphingomyelin, and palmitoyl-oleoyl phosphatidylcholine. Biophys. J. 92, 1125-1137.
2. Aittoniemi, J., Róg, T., Niemelä, P.S., Pasenkiewicz-Gierula, M., Karttunen, M., Vattulainen, I., 2006. Tilt: major factor in sterols' ordering capability in membranes. J. Phys. Chem. B 110, 25562-25564.
3. Almeida, P.F.F., 2009. Thermodynamics of lipid interactions in complex bilayers. Biochim. Biophys. Acta 1788, 72-85.
4. Alwarawrah, M., Dai, J., Huang, J., 2010. A molecular view of the cholesterol condensing effect in DOPC lipid bilayers. J. Phys. Chem. B 114, 7516-7523.
5. Alwarawrah, M., Dai, J., Huang, J., 2012. Modification of lipid bilayer structure by diacylglycerol: a comparative study of diacylglycerol and cholesterol. J. Chem. Theory Comput. 8, 749-758.
6. Antila, H.S., Salonen, E., 2012. Polarizable force fields. In: Monticelli, L., Salonen, E. (Eds.), Biomolecular Simulations Methods and Protocols Series: Methods in Molecular Biology, vol. 924. Springer, New York, pp. 215-242.
7. Apajalahti, T., Niemela, P.S., Govindan, P.N., Miettinen, M.S., Salonen, E., Marrink, S.- J., Vattulainen, I., 2010. Concerted diffusion of lipids in raft-like membranes. Faraday Discuss. 144, 411-430.
8. Arnarez, C., Marrink, S.-J., Periole, X., 2013a. Identification of cardiolipin binding sites oncytochrome c oxidase at the entrance of proton channels. Sci. Rep. 3, 1263.
9. Arnarez, C., Mazat, J.-P., Elezgaray, J., Marrink, S.-J., Periole, X., 2013b. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1. J. Am. Chem. Soc. 135, 3112-3120.
10. Bauer, B.A., Lucas, T.R., Meninger, D.J., Patel, S., 2011. Water permeation through DMPC lipid bilayers using polarizable charge equilibration force fields. Chem. Phys. Lett. 508, 289-294.
11. Beattie, M.E., Veatch, S.L., Stottrup, B.L., Keller, S.L., 2005. Sterol structure determines miscibility versus melting transitions in lipid vesicles. Biophys. J. 89, 1760-1768.
12. Bennett, W.F.D., Tieleman, D.P., 2012. Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes. J. Lipid Res. 53, 421-429.
13. Bennett, W.F.D., MacCallum, J.L., Tieleman, D.P., 2009a. Thermodynamic Analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes. J. Am. Chem. Soc. 131, 1972-1978.
14. Bennett, W.F.D., MacCallum, J.L., Hinner, M.J., Marrink, S.J., Tieleman, D.P., 2009b. Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. J. Am. Chem. Soc. 131, 12714-12720.
15. Bennett, W.F.D., Tieleman, D.P., 2013. Computer simulations of lipid membrane domains. Biochim. Biophys. Acta 1828, 1765-1776.
16. Berkowitz, M.L., 2009. Detailed molecular dynamics simulations of model biological membranes containing cholesterol. Biochim. Biophys. Acta 1788, 86-96.
17. Berkowitz, M.L., Vacha, R., 2012. Aqueous solutions at the interface with phospholipid bilayers. Acc. Chem. Res. 45, 74-82.
18. Bhatnagar, N., Kamath, G., Potoff, J.J., 2013. Biomolecular simulations with the transferable potentials for phase equilibria: extension to phospholipids. J. Phys. Chem. B 117, 9910-9921.
19. Bhide, S.Y., Zhang, Z., Berkowitz, M.L., 2007. Molecular dynamics simulations of SOPS and sphingomyelin bilayers containing cholesterol. Biophys. J. 92, 1284-1295.
20. Bielska, A.A., Olsen, B.N., Gale, S.E., Mydock-McGrane, L., Krishnan, K., Baker, N.A., Schlesinger, P.H., Covey, D.F., Ory, D.S., 2014. Side-chain oxysterols modulate cholesterol accessibility through membrane remodeling. Biochemistry 53, 3042-3051.
21. Björkbom, A., Róg, T., Kankaanpää, P., Lindroos, D., Kaszuba, K., Kurita, M., Yamaguchi, S., Yamamoto, T., Jaikishan, S., Paavolainen, L., Päivärinne, J., Nyholm, T.K.M., Katsumura, S., Vattulainen, I., Slotte, J.P., 2011. N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol. Biochim. Biophys. Acta 1808, 1179-1186.
22. Björkbom, A., Róg, T., Kaszuba, K., Kurita, M., Yamaguchi, S., Lonnfors, M., Nyholm, T. K.M., Vattulainen, I., Katsumura, S., Slotte, J.P., 2010. Effect of sphingomyelin headgroup size on molecular properties and interactions with cholesterol. Biophys. J. 99, 3300-3308.
23. Boggara, M.B., Mihailescu, M., Krishnamoorti, R., 2012. Structural association of nonsteroidal anti-inflammatory drugs with lipid membranes. J. Am. Chem. Soc. 134, 19669-19676.
24. Bunker, A., 2012. Poly(ethylene glycol) in drug delivery, why does it work, and can we do better? All atom molecular dynamics simulation provides some answers. Phys. Procedia 34, 24-33.
25. Busch, S., Smuda, C., Pardo, L.C., Unruh, T., 2010. Molecular mechanism of long-range diffusion in phospholipid membranes studied by quasi-elastic neutron scattering. J. Am. Chem. Soc. 132, 3232-3233.
26. Cang, X., Du, Y., Mao, Y., Wang, Y., Yang, H., Jiang, H., 2013. Mapping the functional binding sites of cholesterol in β2-adrenergic receptor by long-time molecular dynamics simulations. J. Phys. Chem. B 117, 1085-1094.
27. Cantor, R.S., 1997. The lateral pressure profile in membranes: a physical mechanism of general anesthesia. Biochemistry 36, 2339-2344.
28. Cantor, R.S., 1999a. The influence of membrane lateral pressures on simple geometric models of protein conformational equilibria. Chem. Phys. Lipids 101, 45-56.
29. Cantor, R.S., 1999b. Lipid composition and the lateral pressure profile in bilayers. Biophys. J. 76, 2625-2639.
30. Casciola, M., Bonhenry, D., Liberti, M., Apollonio, F., Tarek, M., 2014. A molecular dynamic study of cholesterol rich lipid membranes: comparison of electroporation protocols. Bioelectrochemistry 100, 11-17.
31. Chaban, V.V., Khandelia, H., 2014a. Lipid structure in triolein lipid droplets. J. Phys. Chem. B 118, 10335-10340.
32. Chaban, V.V., Khandelia, H., 2014b. Distribution of neutral lipids in the lipid droplet core. J. Phys. Chem. B 118, 11145-11151.
33. Chen, C., Tripp, C.P., 2012. A comparison of the behavior of cholesterol, 7-dehydrocholesterol and ergosterol in phospholipid membranes. Biochim. Biophys. Acta 1818, 1673-1681.
34. Cheng, M.H., Xu, Y., Tang, P., 2009. Anionic lipid and cholesterol interactions with α4β2 nAChR: insights from MD simulations. J. Phys. Chem. B 113, 6964-6970.
35. Cherezov, V., Rosenbaum, D.M., Hanson, M.A., Rasmussen, S.G.F., Thian, F.S., Sun, T., Choi, H.-J., Kuhn, P., Weis, W.I., Kobilka, B.K., Stevens, R.C., 2007. High resolution crystal structure of an engineered human β2-adrenergic G-protein coupled receptor. Science 318, 1258-1265.
36. Chiu, S.W., Vasudevan, S., Jakobsson, E., Mashl, R.J., Scott, H.L., 2003. Structure of sphingomyelin bilayers: a simulation study. Biophys. J. 85, 3624-3635.
37. Choi, Y., Attwood, S.J., Hoopes, M.I., Drolle, E., Karttunen, M., Leonenko, Z., 2014. Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers. Soft Matter 10, 206-213.
38. Chowdhary, J., Harder, E., Lopes, P.E.M., Huang, L., MacKerell Jr., A.D., Roux, 2013. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J. Phys. Chem. B 117, 9142-9160.
39. Christopher, J., Brown, J., Dore, A., Errey, J., Koglin, M., Marshall, F.H., Myszka, D., Rich, R.L., Tate, C.G., Tehan, B., Warne, T., Congreve, M., 2013. Biophysical fragment screening of the β1-adrenergic receptor: identification of high affinity arylpiperazine leads using structure-based drug design. J. Med. Chem. 56, 3446-3455.
40. Coetzee, T., Fujita, N., Dupree, J., Shi, R., Blight, A., Suzuki, K., Suzuki, K., Popko, B., 1996. Myelination in the absence of galactocerebroside and sulfatide: normal structure with abnormal function and regional instability. Cell 86, 209-219.
41. Coskun, U., Grzybek, M., Drechsel, D., Simons, K., 2011. Regulation of human EGF receptor by lipids. Proc. Natl. Acad. Sci. USA 108, 9044-9048.
42. Cramariuc, O., Róg, T., Vattulainen, I., 2012. Drug-lipid membrane interaction mechanisms revealed through molecular simulations. Curr. Phys. Chem. 2, 379-400.
43. Curatolo, W., 1987. Glycolipid function. Biochim. Biophys. Acta 906, 137-160.
44. Curdova, J., Capkova, P., Plasek, J., Repakova, J., Vattulainen, I., 2007. Free pyrene probes in gel and fluid membranes: perspective through atomistic simulations. J. Phys. Chem. B 111, 3640-3650.
45. Dai, J., Alwarawrah, M., Huang, J., 2010. Instability of cholesterol clusters in lipid bilayers and the cholesterol's umbrella effect. J. Phys. Chem. B 114, 840-848.
46. Daily, M.D., Olsen, B.N., Schlesinger, P.H., Ory, D.S., Baker, N.A., 2014. Improved coarse-grained modeling of cholesterol-containing lipid bilayers. J. Chem. Theory Comput. 10, 2137-2150.
47. Damm, W., Frontera, A., Tirado-Rives, J., Jorgensen, W.L., 1997. OPLS all-atom force field for carbohydrates. J. Comput. Chem. 18, 1955-1970.
48. Davis, J.E., Patel, S., 2009. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J. Phys. Chem. B. 113, 9183-9196.
49. de Joannis, J., Coppock, P.S., Yin, F., Mori, M., Zamorano, A., Kindt, J.T., 2011. Atomistic simulation of cholesterol effects on miscibility of saturated and unsaturated phospholipids: implications for liquid-ordered/liquid-disordered phase coexistence. J. Am. Chem. Soc. 133, 3625-3634.
50. de Meyer, F., Smit, B., 2009. Effect of cholesterol on the structure of a phospholipid bilayer. Proc. Nat. Acad. Sci. USA 106, 3654-3658.
51. de Meyer, F.J.M., Benjamini, A., Rodgers, J.M., Misteli, Y., Smit, B., 2010a. Molecular simulation of the DMPC-cholesterol phase diagram. J. Phys. Chem. B 114, 10451-10461.
52. de Meyer, F.J.-M., Rodgers, J.M., Willems, T.F., Smit, B., 2010b. Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions. Biophys. J 99, 3629-3638.
53. Degroote, S., Wolthoorn, J., van der Meer, G., 2004. The cell biology of glycosphingolipids. Cell Develop. Biol. 15, 375-387.
54. DeMarco, M.L., 2012. Three-dimensional structure of glycolipids in biological membranes. Biochemistry 51, 5725-5732.
55. DeMarco, M.L., Woods, R.J., 2009. Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces. Glycobiology 19, 344-355.
56. DeMarco, M.L., Woods, R.J., Prestegard, J.H., Tian, F., 2010. Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement. J. Am. Chem. Soc. 132, 1334-1338.
57. Dickson, C.J., Madej, B.D., Skjevik A˚, A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., 2014. Lipid14: the Amber lipid force field. J. Chem. Theory Comput. 10, 865-879.
58. do Canto, A.M.T.M., Carvalho, A.J.P., Ramalho, J.P.P., Loura, L.M.S., 2011. Molecular dynamics simulations of T-20HIV fusion inhibitor interacting with model membranes. Biophys. Chem. 159, 275-286.
59. do Canto, A.M.T.M., Carvalho, A.J.P., Ramalho, J.P.P., Loura, L.M.S., 2012. Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction. Comput. Math. Methods Med Article ID 1151854.
60. Dopico, A.M., Bukiya, A.N., Singh, A.K., 2012. Large conductance, calcium- and voltage-gated potassium (BK) channels: regulation by cholesterol. Pharmaco. Therap. 135, 133-150.
61. Drolle, E., Kučerka, N., Hoopes, M.I., Choi, Y., Katsaras, J., Karttunen, M., Leonenko, Z., 2013. Effect of melatonin and cholesterol on the structure of DOPC and DPPC membranes. Biochim. Biophys. Acta 1828, 2247-2254.
62. Duncan, S.L., Dalal, I.S., Larson, R.G., 2011. Molecular dynamics simulation of phase transitions in model lung surfactant monolayers. Biochim. Biophys. Acta 1808, 2450-2465.
63. Dörmann, P., Benning, C., 2002. Galactolipids rule in seed plants. Trends Plant Sci. 7, 112-118.
64. Edholm, O., Nagle, J.F., 2005. Areas of molecules in membranes consisting of mixtures. Biophys. J. 89, 1827-1832.
65. Ekholm, O., Jaikishan, S., Lonnfors, M., Nyholm, T.K.M., Slotte, J.P., 2011. Membrane bilayer properties of sphingomyelins with amide-linked 2- or 3-hydroxylated fatty acids. Biochim. Biophys. Acta 1808, 727-732.
66. Eriksson, E.S.E., Eriksson, L.A., 2011. The influence of cholesterol on the properties and permeability of hypericin derivatives in lipid membranes. J. Chem. Theory Comput. 7, 560-574.
67. Fadda, E., Woods, R.J., 2010. Carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug Discov. Today 15, 596-609.
68. Falck, E., Patra, M., Karttunen, M., Hyvonen, M.T., Vattulainen, I., 2004. Lessons of slicing membranes Interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers. Biophys. J. 87, 1076-1091.
69. Falck, E., Róg, T., Karttunen, M., Vattulainen, I., 2008. Lateral diffusion in lipid membranes through collective flows. J. Am. Chem. Soc. 130, 44-45.
70. Fantini, J., Yahi, N., 2010. Molecular insights into amyloid regulation by membrane cholesterol and sphingolipids: common mechanisms in neurodegenerative diseases. Expert Rev. Mol. Med. 12, e27.
71. Fantini, J., Yahi, N., 2011. Molecular basis for the glycosphingolipid-binding specificity of α-synuclein: key role of tyrosine 39 in membrane insertion. J. Mol. Biol. 408, 654-669.
72. Fernandez, M.L., Marshall, G., Sagues, F., Reigada, R., 2010. Structural and kinetic molecular dynamics study of electroporation in cholesterol-containing bilayers. J. Phys. Chem. B 114, 6855-6865.
73. Forst, G., Cwiklik, L., Jurkiewicz, P., Schubert, R., Hof, M., 2014. Interactions of beta-blockers with model lipid membranes: molecular view of the interaction of acebutolol, oxprenolol, and propranolol with phosphatidylcholine vesicles by time-dependent fluorescence shift and molecular dynamics simulations. Eur. J. Pharma. Biopharma. 87, 559-569.
74. Franova, M., Repakova, J., Capkova, P., Holopainen, J.M., Vattulainen, I., 2010. Effects of DPH on DPPC-cholesterol membrane with varying concentration of cholesterol: from local perturbations to limitations in fluorescence anisotropy experiments. J. Phys. Chem. B 114, 2704-2711.
75. Gabizon, A., Catane, R., Uziely, B., Kaufman, B., Safra, T., Cohen, R., Martin, F., Huang, A., Barenholz, Y., 1994. Prolonged circulation time and enhanced accumulation in malignant exudates of doxorubicin encapsulated in polyethylene-glycol coated liposomes. Cancer Res. 54, 987-992.
76. Gallova, J., Uhrikova, D., Kucerka, N., Teixeirac, J., Balgavy, P., 2010. Partial area of cholesterol in monounsaturated diacylphosphatidylcholine bilayers. Chem. Phys. Lipids 163, 765-770.
77. Gapsys, V., de Groot, B.L., Briones, R., 2013. Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. 27, 845-858.
78. Gupta, G., Surolia, A., 2010. Glycosphingolipids in microdomain formation and their spatial organization. FEBS Lett. 584, 1634-1641.
79. Gurtovenko, A.A., Anwar, J., Vattulainen, I., 2010. Defect-mediated trafficking across cell membranes: insights from in silico modeling. Chem. Rev. 110, 6077-6103.
80. Haas, D., Kelley, R.J., Hoffmann, G.F., 2001. Inherited disorders of cholesterol biosynthesis. Neuropediatrics 32, 113-122.
81. Hadley, K.R., McCabe, C., 2010. A structurally relevant coarse-grained model for cholesterol. Biophys. J 99, 2896-2905.
82. Hadley, K.R., McCabe, C., 2012. A simulation study of the self-assembly of coarsegrained skin lipids. Soft Matter 8, 4802-4814.
83. Hakobyan, D., Heuer, A., 2013. Phase separation in a lipid/cholesterol system: comparison of coarse-grained and united-atom simulations. J. Phys. Chem. B 117, 3841-3851.
84. Hakobyan, D., Heuer, A., 2014. Key molecular requirements for raft formation in lipid/cholesterol membranes. PLoS One 9, e87369.
85. Hakomori, S., 1981. Glycosphingolipids in cellular interaction differentiation, and oncogenesis. Annu. Rev. Biochem. 50, 733-764.
86. Hakomori, S., Handa, K., Iwabuchi, K., Yamamura, S., Prinetti, A., 1998. New insights in glycosphingolipid function: glycosignaling domain, a cell surface assembly of glycosphingolipids with signal transducer molecules, involved in cell adhesion coupled with signaling. Glycobiology 8, XI-XIX.
87. Hakomori, S.I., 2007. Structure and function of glycosphingolipids and sphingolipids: recollections and future trends. Biochim. Biophys. Acta 1780, 325-346.
88. Haldar, S., Kanaparthi, R.K., Samanta, A., Chattopadhyay, A., 2012. Differential effect of cholesterol and its biosynthetic precursors on membrane dipole potential. Biophys J. 102, 1561-1569.
89. Hall, A., Róg, T., Karttunen, M., Vattulainen, I., 2010. Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylcer- amide. J. Chem. Phys. B 114, 7797-7807.
90. Hall, A., Róg, T., Vattulainen, I., 2011. Effect of galactosylceramide on dynamics of cholesterol-rich lipid membranes. J. Phys. Chem. B 115, 14424-14434.
91. Hanson, M.A., Cherezov, V., Roth, C.B., Griffith, M.T., Jaakola, V.-P., Chien, E.Y.T., Velasquez, J., Kuhn, P., Stevens, R.C., 2008. A specific cholesterol binding site is established by the 2.8 A˚ structure of the human β2-adrenergic receptor in an alternate crystal form. Structure 16, 897-905.
92. Harouse, J.M., 1991. Inhibition of entry of HIV-1 in neural cell-lines by antibodies against galactosyl ceramide. Science 253, 320-323.
93. Holt, A., Killian, J.A., 2010. Orientation and dynamics of transmembrane peptides: the power of simple models. Eur. Biophys. J. 39, 609-621.
94. Hong, C., Tieleman, D.P., Wang, Y., 2014. Microsecond molecular dynamics simulations of lipid mixing. Langmuir 30, 11993-12001.
95. Horta, B.A.C., Peric-Hassler, L., Hünenberger, P.H., 2010. Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: a comparative molecular dynamics study. J. Mol. Graphics Model. 29, 331-346.
96. Huang, J.Y., Feigenson, G.W., 1999. A microscopic interaction model of maximum solubility of cholesterol in lipid bilayers. Biophys. J. 76, 2142-2157.
97. Hug, S., 2012. Classical molecular dynamics in a nutshell. In: Monticelli, L., Salonen, E. (Eds.), Biomolecular Simulations Methods and Protocols Series: Methods in Molecular Biology, vol. 924. Springer, New York, pp. 127-252.
98. Hughes, Z.E., Malajczuk, C.J., Mancera, R.L., 2013. The effects of cryosolvents on DOPC-β-Sitosterol bilayers determined from molecular dynamics simulations. J. Phys. Chem. B 117, 3362-3375.
99. Hung, A., Yarovsky, I., 2011. Gap junction hemichannel interactions with zwitterionic lipid, anionic lipid, and cholesterol: molecular simulation studies. Biochemistry 50, 1492-1504.
100. Hunte, C., 2005. Specific protein-lipid interactions in membrane proteins. Biochem. Soc. Trans. 33, 938-942.
101. Hyvönen, M.T., Kovanen, P.T., 2003. Molecular dynamics simulation of sphingomyelin bilayer. J. Phys. Chem. B 107, 9102-9108.
102. Hölttävuori, M., Uronen, R.L., Repakova, J., Salonen, E., Vattulainen, I., Panula, P., Li, Z., Bittman, R., Ikonen, E., 2008. BODIPY-cholesterol: a new tool to visualize sterol trafficking in living cells and organisms. Traffic 9, 1839-1849.
103. Iida-Tanaka, N., Fukase Koichi Utsumi, H., Ishizuka, I., 2000. Conformational studies on a unique bis-sulfated glycolipid using NMR spectroscopy and molecular dynamics simulations. Eur. J. Biochem. 267, 6790-6797.
104. Ingolfsson, H.I., Melo, M.N., van Eerden, F.J., Arnarez, C., Lopez, C., Wassenaar, T.A., Periole, X., de Vries, A.H., Tieleman, D.P., Marrink, S.J., 2014. Lipid organization of the plasma membrane. J. Am. Chem. Soc. 136, 14554-14559.
105. Jafurulla, Md., Rao, B.D., Sreedevi, S., Ruysschaert, J.-M., Covey, D.F., Chattopadhyay, A., 2013. Stereospecific requirement of cholesterol in the function of the 2 serotonin -1A receptor. Biochim. Biophys. Acta 1838, 158-163.
106. Jaikishan, S., Björkbom, A., Slotte, J.P., 2010. Sphingomyelin analogs with branched N-acyl chains: the position of branching dramatically affects acyl chain order and sterol interactions in bilayer membranes. Biochim. Biophys. Acta 1798, 1987-1994.
107. Jaikishan, S., Slotte, J.P., 2011. Effect of hydrophobic mismatch and interdigitation on sterol/sphingomyelin interaction in ternary bilayer membranes. Biochim. Biophys. Acta 1808, 1940-1945.
108. Jedlovszky, P., Sega, M., Vallauri, R., 2009. GM1 ganglioside embedded in a hydrated DOPC membrane: a molecular dynamics simulation study. J. Phys. Chem. B 113, 4876-4886.
109. Jerabek, H., Pabst, G., Rappolt, M., Stockner, T., 2010. Membrane mediated effect on ion channels induced by the anesthetic drug ketamine. J. Am. Chem. Soc. 132, 7990-7997.
110. Jo, S., Rui, H., Lim, J.B., Klauda, J.B., Im, W., 2010. Cholesterol flip-flop: insights from free energy simulation studies. J. Phys. Chem. B 114, 13342-13348.
111. Johansson, A.C.V., Lindahl, E., 2009. The role of lipid composition for insertion and stabilization of amino acids in membranes. J. Chem. Phys. 130, 185101.
112. Jungwirth, P., 2014. Ions at biological interfaces. Encyclopedia of Applied Electrochemistry. Springer, Berlin, pp. 1131.
113. Jurkiewicz, P., Cwiklik, L., Jungwirth, P., Hof, M., 2012. Lipid hydration and mobility: an interplay between fluorescence solvent relaxation experiments and molecular dynamics simulations. Biochimie 94, 26-32.
114. Jämbeck, J.P.M., Lyubartsev, A.P., 2012a. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J. Phys. Chem. B 116, 3164-3179.
115. Jambeck, J.P.M., Lyubartsev, A.P., 2012b. An extension and further validation of an all-atomistic force field for biological membranes. J. Chem. Theory Comput. 8, 2938-2948.
116. Jambeck, J.P.M., Lyubartsev, A.P., 2013. Another piece of the membrane puzzle: extending Slipids further. J. Chem. Theory Comput. 9, 774-784.
117. Kaiser, H.-J., Orlowski, A., Róg, T., Nyholm, T.K.M., Chai, W., Feizi, T., Lingwood, D., Vattulainen, I., Simons, K., 2011. Lateral sorting in model membranes by cholesterol mediated hydrophobic matching. Proc. Natl. Acad. Sci. USA 108, 16628-16633.
118. Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C., 2013. Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state. Nature 502, 201-206.
119. Kang, H., Klauda, J.B., 2014. Molecular dynamics simulations of palmitoyloleoyl- phosphatidylglycerol bilayers. Mol. Sim doi:http://dx.doi.org/10.1080/08927022.2014.926548 in press.
120. Kapla, J., Stevensson, B., Dahlberg, M., Maliniak, A., 2012. Molecular dynamics simulations of membranes composed of glycolipids and phospholipids. J. Phys. Chem. B 116, 244-252.
121. Kasahara, K., Sanai, Y., 1999. Possible roles of glycosphingolipids in lipid rafts. Biophys. Chem. 82, 121-127.
122. Kasahara, K., Sanai, Y., 2000. Functional roles of glycosphingolipids in signal transduction via lipid rafts. Glycoconjug. J. 17, 153-162.
123. Kemmerer, S., Voss, J.C., Faller, R., 2013. Molecular dynamics simulation of dipalmitoylphosphatidylcholine modified with a MTSL nitroxide spin label in a lipid membrane. Biochim. Biophys. Acta 1828, 2770-2777.
124. Khajeh, A., Modarress, H., 2014a. The influence of cholesterol on interactions and dynamics of ibuprofen in a lipid bilayer. Biochim. Biophys. Acta 1838, 2431-2438.
125. Khajeh, A., Modarress, H., 2014b. Effect of cholesterol on behavior of 5-fluorouracil (5-FU) in a DMPC lipidbilayer a molecular dynamics study. Biophys. Chem. 187, 43-50.
126. Khandelia, H., Loubet, B., Olzynska, A., Jurkiewicz, P., Hof, M., 2014. Pairing of cholesterol with oxidized phospholipid species in lipid bilayers. Soft Matter 10, 639-647.
127. Khelashvili, G., Grossfield, A., Feller, S.E., Pitman, M.C., Weinstein, H., 2009. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins 76, 403-417.
128. Khelashvili, G., Harries, D., 2013a. How cholesterol tilt modulates the mechanical properties of saturated and unsaturated lipid membranes. J. Phys. Chem. B 117, 2411-2421.
129. Khelashvili, G., Harries, D., 2013b. How sterol tilt regulates properties and organization of lipid membranes and membrane insertions. Chem. Phys. Lipids 169, 113-123.
130. Khelashvili, G., Johner, N., Zhao, G., Harries, D., Scott, H.L., 2014. Molecular origins of bending rigidity in lipids with isolated and conjugated double bonds: the effect of cholesterol. Chem. Phys. Lipids 178, 18-26.
131. Khelashvili, G., Mondal, S., Andersen, O.S., Weinstein, H., 2010b. Cholesterol modulates the membrane effects and spatial organization of membrane-penetrating ligands for G-protein coupled receptors. J. Phys. Chem. B 114, 12046-12057.
132. Khelashvili, G., Pabst, G., Harries, D., 2010a. Cholesterol orientation and tilt modulus in DMPC bilayers. J. Phys. Chem. B 114, 7524-7534.
133. Khelashvili, G.A., Pandit, S.A., Scott, H.L., 2005. Self-consistent mean-field model based on molecular dynamics: application to lipid-cholesterol bilayers. J. Chem. Phys. 123, 034910.
134. Kirschner, K.N., Yongye, A.B., Tschampel, S.M., Daniels, C.R., Foley, B.L., Woods, R.J., 2008. GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J. Comput. Chem. 29, 622-655.
135. Klauda, J.B., Garrison, S.L., Arora, G., Jiang, J., Sandler, S.I., 2004. HM-IE: a quantum chemical hybrid method for accurate interaction energies. J. Phys. Chem. A 108, 107-112.
136. Klauda, J.B., Monje, V., Kim, T., Im, W., 2012. Improving the CHARMM force field for polyunsaturated fatty acid chains. J. Phys. Chem. B 116, 9424-9431.
137. Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon- Ramirez, C., Vorobyov, I., MacKerell Jr., A.D., Pastor, 2010. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830-7843.
138. Kopec, W., Khandelia, H., 2014. Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations. J. Comput. Aided. Mol. Des. 28, 123-134.
139. Krause, M.R., Wang, M., Mydock-McGrane, L., Covey, D.F., Tejada, E., Almeida, P.F., Regen, S.L., 2014. Eliminating the roughness in cholesterol's β-face: does it matter? Langmuir 30, 12114-12118.
140. Kucerka, N., Marquard, D., Harroun, T.A., Wassall, Nieh M.-P., de Jong, S.R., Schafer, D. H., Marrink, L.V., Katsaras, S.J., 2010. Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane- domain formation. Biochemistry 49, 7485-7493.
141. Kulig, W., Jurkiewicz, P., Olẓyńska, A., Tynkkynen, J., Javanainen, M., Manna, M., Róg, T., Hof, M., Vattulainen, I., Jungwirth, P., 2014a. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. Biochim Biophys Acta doi:http://dx. doi.org/10.1016/j.bbamem.2014.10.032 in press.
142. Kulig, W., Tynkkynen, J., Javanainen, M., Manna, M., Róg, T., Vattulainen, I., Jungwirth, P., 2014b. How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers? J. Mol. Model. 20, 2121.
143. Kulovesi, P., Telenius, J., Koivuniemi, A., Brezesinski, G., Vattulainen, I., Holopainen, J. M., 2012. The impact of lipid composition on the stability of the tear fluid lipid layer. Soft Matter 8, 5826-5834.
144. Kuo, A.-T., Chang, C.-H., 2014. Cholesterol-induced condensing and disordering effects on a rigid catanionic bilayer: a molecular dynamics study. Langmuir 30, 55-62.
145. Kwon, H.J., Abi-Mosleh, L., Wang, M.L., Deisenhofer, J., Goldstein, J.L., Brown, M.S., Infante, R.E., 2009. Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol. Cell 137, 1213-1224.
146. Köberl, M., Hinz, H.J., Rapp, G., 1998. Temperature scanning simultaneous small- and wide-angle X-ray scattering studies on glycolipid vesicles: areas, expansion coefficients and hydration. Chem. Phys. Lipids 91, 13-37.
147. 2+ bound in the cation binding site. Proc. Natl. Acad. Sci. USA 110, 10958-10963.
148. Lee, J.Y., Patel, R., Lyman, E., 2013. Ligand-dependent cholesterol interactions with the human A2A adenosine receptor. Chem. Phys. Lipids 169, 39-45.
149. Lehtinen, J., Magarkar, A., Stepniewski, M., Hakola, S., Bergman, M., Róg, T., Yliperttula, M., Urtti, A., Bunker, A., 2012. Analysis of cause of failure of new targeting peptide in PEGylated liposome: molecular modeling as rational design tool for nanomedicine. Eur. J. Pharma. Sci. 46, 121-130.
150. Li, L.B., Vorobyov, I., Allen, T.W., 2012. The role of membrane thickness in charged protein-lipid interactions. Biochim. Biophys. Acta 1818, 135-145.
151. Lim, J.B., Rogaski, B., Klauda, J.B., 2012. Update of the cholesterol force field parameters in CHARMM. J. Phys. Chem. B 116, 203-210.
152. Lingwood, C.A., 2011a. Glycosphingolipid functions. Cold Spring Harbor Persp. Biol. 3, 149-174.
153. Lingwood, D., Binnington, B., Róg, T., Vattulainen, I., Chai, W., Feizi, T., Grzybek, M., Coskun, U., Lingwood, C., Simons, K., 2011b. Cholesterol regulates glycolipid conformation and receptor activity. Nature Chem. Biol. 7, 260-262.
154. Lingwood, D., Kaiser, H.-J., Levental, I., Simons, K., 2009. Lipid rafts as functional heterogeneity in cell membranes. Biochem. Soc. Trans. 37, 955-960.
155. Lingwood, D., Simons, K., 2010. Lipid rafts as a membrane-organizing principle. Science 327, 46-50.
156. Lins, R.D., Straatsma, T.P., 2001. Computer simulation of the rough lipopolysaccha- ride membrane of Pseudomonas aeruginosa. Biophys. J. 81, 1037-1046.
157. Liu, W., Chun, E., Thompson, A.A., Chubukov, P., Xu, F., Katritch, V., Han, G.W., Roth, C. B., Heitman, L.H., Jzerman, I., Cherezov, A.P., Stevens, V., 2012. Structural basis for allosteric regulation of GPCRs by sodium ions. Science 337, 232-236.
158. Liu, W., Wacker, D., Gati, C., Han, G.W., James, D., Wang, D., Nelson, G., Weierstall, U., Katritch, V., Barty, A., Zatsepin, N.A., Li, D., Messerschmidt, M., Boutet, S., Williams, G.J., Koglin, J.E., Seibert, M.M., Wang, C., Shah, S.T., Basu, S., Fromme, R., Kupitz, C., Rendek, K.N., Grotjohann, I., Fromme, P., Kirian, R.A., Beyerlein, K.R., White, T.A., Chapman, H.N., Caffrey, M., Spence, J.C., Stevens, R.C., Cherezov, V., 2013. Serial femtosecond crystallography of G protein-coupled receptors. Science 342, 1521-1524.
159. Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S., 2011. The effects of 7-dehydrocholesterol on the structural properties of membranes. Phys. Biol. 8, 056005.
160. Lopez, C.A., de Vries, A.H., Marrink, S.J., 2011. Molecular mechanism of cyclodextrin mediated cholesterol extraction. PLoS Comput. Biol. 7, e1002020.
161. Lopez, C.A., Rzepiela, A.J., de Vries, A.H., Dijkhuizen, L., Hunenberger, P.H., Marrink, S. J., 2009. Martini coarse-grained force field: extension to carbohydrates. J. Chem. Theory Comput. 5, 3195-3210.
162. Lopez, C.A., Sovova, Z., van Eerden, F.J., de Vries, A.H., Marrink, S.J., 2013. Martini force field parameters for glycolipids. J. Chem. Theory Comput. 9, 1694-1708.
163. Loubet, B., Lomholt, M.A., Khandelia, H., 2013. Tension moderation and fluctuation spectrum in simulated lipid membranes under an applied electric potential. J. Chem. Phys. 139, 164902.
164. Loura, L.M.S., Martins do Canto, A.M.T., Martins, J., 2013. Sensing hydration and behavior of pyrene in POPC and POPC/cholesterol bilayers: a molecular dynamics study. Biochim. Biophys. Acta 1828, 1094-1101.
165. Loura, L.M.S., Ramalho, J.P.P., 2011. Recent developments in molecular dynamics simulations of fluorescent membrane probes. Molecules 16, 5437-5452.
166. Lu, L., Voth, G.A., 2009. Systematic coarse-graining of a multicomponent lipid bilayer. J. Phys. Chem. B 113, 1501-1510.
167. Lyman, E., Higgs, C., Kim, B., Lupyan, D., Shelley, J.C., Farid, R., Voth, G.A., 2009. A role for a specific cholesterol interaction in stabilizing the apo configuration of the human A2A adenosine receptor. Structure 17, 1660-1668.
168. Lyubartsev, A.P., Rabinovich, A.L., 2011. Recent development in computer simulations of lipid bilayers. Soft Matter 7, 25-39.
169. MacCallum, J.L., Bennett, W.F.D., Tieleman, D.P., 2008. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94, 3393-3404.
170. Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., Róg, T., 2014. Refined OPLS-AA force field for saturated phosphatidylcholine bilayers at full hydration. J. Phys. Chem. B 118, 4571-4581.
171. Magarkar, A., Róg, T., Bunker, A., 2014a. Molecular dynamics simulation of PEGylated membranes with cholesterol: building towards the DOXILR formulation. J. Phys. Chem. C 118, 15541-15549.
172. Magarkar, A., Dhawan, V., Kallinteri, P., Viitala, T., Elmowafy, M., Róg, T., Bunker, A., 2014b. Cholesterol level affects surface charge of lipid membranes in physiological environment. Sci. Rep. 4, 5005.
173. Magarkar, A., Karakas, E., Stepniewski, M., Rog, T., Bunker, A., 2012. Molecular dynamics simulation of PEGylated bilayer interacting with salt ions: a model of the liposome surface in the bloodstream. J. Phys. Chem. B 116, 4212-4219.
174. Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Mathiesen, J.M., Sunahara, R.K., Pardo, L., Weis, W.I., Kobilka, B.K., Granier, S., 2012. Crystal structure of the μ-opioid receptor bound to a morphinan antagonist. Nature 485, 321-326.
175. Manickam Achari, V., Seng Nguan, H., Heidelberg, T., Bryce, R.A., Hashim, R., 2012. Molecular dynamics study of anhydrous lamellar structures of synthetic glycolipids: effects of chain branching and disaccharide headgroup. J. Phys. Chem. B 116, 11626-11634.
176. Manna, M., Mukhopadhyay, C., 2011. Cholesterol driven alteration of the conformation and dynamics of phospholamban in model membrane. Phys Chem. Chem. Phys. 13, 20188-20198.
177. Manna, M., Róg, T., Vattulainen, I., 2014. The challenges of understanding glycolipid functions: an open outlook based on molecular simulations. Biochim. Biophys. Acta 1841, 1130-1145.
178. Mannock, D.A., Lewis, R.N.A.H., McMullen, T.P.W., McElhaney, R.N., 2010. The effect of variations in phospholipid and sterol structure on the nature of lipid-sterol interactions in lipid bilayer model membranes. Chem. Phys. Lipids 163, 403-448.
179. Markiewicz, M., Pasenkiewicz-Gierula, M., 2011. Comparative model studies of gastric toxicity of nonsteroidal anti-inflammatory drugs. Langmuir 27, 6950-6961.
180. Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H., 2007. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111, 7812-7824.
181. Marrink, S.J., Risselada, J., Mark, A.E., 2005. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem. Phys. Lipids 135, 223-244.
182. Marrink, S.J., Tieleman, D.P., 2013. Perspective on the Martini model. Chem. Soc. Rev. 42, 6801-6822.
183. Marsh, D., 2012. Bilayer dimensions and hydration of glycolipids. Chem. Phys. Lipids 165, 23-31.
184. Martinez-Seara, H., Róg, T., Karttunen, M., Vattulainen, I., Reigada, R., 2010. Cholesterol induces specific spatial and orientational order in cholesterol/ phospholipid membranes. PLoS One 5, e11162.
185. Martinez-Seara, H., Róg, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M., Reigada, R., 2008. Interplay of unsaturated phospholipids and cholesterol in membranes: Effect of double bond position. Biophys. J. 95, 3295-3305.
186. Massey, J.B.,1998. Effect of cholesteryl hemisuccinate on the interfacial properties of phosphatidylcholine bilayers. Biochim. Biophys. Acta 1415, 193-204.
187. Matsuzaki, K., Kato, K., Yanagisawa, K., 2010. Aβ polymerization through interaction with membrane gangliosides. Biochim. Biophys. Acta 1801, 868-877.
188. Maula, T., Kurita, M., Yamaguchi, S., Yamamoto, T., Katsumura, S., Slotte, J.P., 2011. Effects of sphingosine 2N- and 3O-methylation on palmitoyl ceramide properties in bilayer membranes. Biophys. J 101, 2948-2956.
189. Maxfield, F.R., Mondal, M., 2006. Sterol and lipid trafficking in mammalian cells Biochem. Soc. Trans. 34, 335-339.
190. Mendes Ferreira, T., Coreta-Gomes, F., Ollila, O.H.S., Joao Moreno, M., Vaz, W.L.C., Topgaard, D., 2013. Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H-13C NMR and MD simulation studies. Phys. Chem. Chem. Phys. 15, 1976-1989.
191. Metcalf, R., Pandit, S.A., 2012. Mixing properties of sphingomyelin ceramide bilayers: a simulation study. J. Phys. Chem. B 116, 4500-4509.
192. Mombelli, E., Morris, R., Taylor, W., Fraternali, F., 2003. Hydrogen bonding propensities of sphingomyelin in solution and in a bilayer assembly: a molecular dynamics study. Biophys. J. 84, 1507-1517.
193. Mondal, S., Mukhopadhyay, C., 2008. Molecular level investigation of organization in ternary lipid bilayer: a computational approach. Langmuir 24, 10298-10305.
194. Monticelli, L., Kandasamy, S.K., Periole, X., Larson, R.G., Tieleman, D.P., Marrink, S.J., 2008. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 4, 819-834.
195. Monticelli, L., Tieleman, D.P., 2012. Force fields for classical molecular dynamics. In: Monticelli, L., Salonen, E. (Eds.), Biomolecular Simulations Methods and Protocols Series Methods in Molecular Biology, vol. 924. Springer, New York, pp. 197-214.
196. Mori, K., Mahmood, M.I., Neya, S., Matsuzaki, K., Hoshino, T., 2012. Formation of GM1 ganglioside clusters on the lipid membrane containing sphingomyeline and cholesterol. J. Phys. Chem. B 116, 5111-5121.
197. Morth, J.P., Pedersen, B.P., Toustrup-Jensen, M.S., Sorensen, T.L., Petersen, J., Andersen, J.P., Vilsen, B., Nissen, P., 2007. Crystal structure of the sodium- potassium pump. Nature 450, 1043-1049.
198. Murtola, T., Vuorela, T., Hyvonen, M.T., Marrink, S.J., Karttunen, M., Vattulainen, I., 2011. Low-density lipoprotein: structure, dynamics and lipid-apoB-100 interactions. Soft Matter 7, 8135-8141.
199. Murzyn, K., Róg, T., Pasenkiewicz-Gierula, M., 2004. Interactions of magainin- 2 amide with membrane lipids. Lect. Notes Comput. Sci. 3037, 325-331.
200. Mydock-McGrane, L.N., Rath, P., Covey, D.F., 2014. Synthesis of a smoothened cholesterol: 18,19-Di-nor-cholesterol. J. Org. Chem. 79, 5636-5643.
201. Neale, C., Bennett, W.F.D., Tieleman, D.P., Pomes, R., 2011. Statistical convergence of equilibrium properties in simulations of molecular solutes embedded in lipid bilayers. J. Chem. Theory Comput. 7, 4175-4188.
202. Neuvonen, M., Manna, M., Mokkila, S., Javanainen, M., Róg, T., Liu, Z., Bittman, R., Vattulainen, I., Ikonen, E., 2014. Enzymatic oxidation of cholesterol: properties and functional effects of cholestenone in cell membranes. PLoS ONE 9, e103743.
203. Niemela, P.S., Castillo, S., Sysi-Aho, M., Oresic, M., 2009. Bioinformatics and computational methods for lipidomics. J. Chromatogr. B 877, 2855-2862.
204. Niemela, P.S., Hyvonen, M.T., Vattulainen, I., 2004. Structure and dynamics of sphingomyelin bilayer Insight gained through systematic comparison to phosphatidylcholine. Biophys. J. 87, 2976-2989.
205. Niemela, P.S., Hyvonen, M.T., Vattulainen, I., 2006. Influence of chain length and unsaturation on sphingomyelin bilayers. Biophys. J. 90, 851-863.
206. Niemela, P.S., Miettinen, M.S., Monticelli, L., Hammaren, H., Bjelkmar, P., Murtola, T., Lindahl, E., Vattulainen, I., 2010. Membrane proteins diffuse as dynamic complexes with lipids. J. Am. Chem. Soc. 132, 7574.
207. Niemela, P.S., Ollila, S., Hyvonen, M.T., Karttunen, M., Vattulainen, I., 2007. Assessing the nature of lipid raft membranes. PLoS Comput. Biol. 3, e34.
208. Nyblom, M., Poulsen, H., Gourdon, P., Reinhard, L., Andersson, M., Lindahl, E., Fedosova, N., Nissen, P., 2013. Crystal structure of Na+, K(+)-ATPase in the Na (+)-bound state. Science 342, 123-127.
209. Nyholm, T.K.M., Ozdirekcan, S., Killian, J.A., 2007. How protein transmembrane segments sense the lipid environment. Biochemistry 46, 1457-1465.
210. O'Connor, J.W., Klauda, J.B., 2011. Lipid membranes with a majority of cholesterol: applications to the ocular lens and aquaporin 0. J. Phys. Chem. B 115, 6455-6464.
211. Ogawa, H., Shinoda, T., Cornelius, F., Toyoshima, C., 2009. Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain. Proc. Natl. Acad. Sci. USA 106, 13742-13747.
212. Ogushi, F., Ishitsuka, R., Kobayashi, T., Sugita, Y., 2012. Rapid flip-flop motions of diacylglycerol and ceramide in phospholipid bilayers. Chem. Phys. Lett. 522, 96-102.
213. Ohvo-Rekila, H., Ramstedt, B., Leppimaki, P., Slotte, J.P., 2002. Cholesterol interactions with phospholipids in membranes. Prog. Lip. Res. 41, 66-97.
214. Ollila, O.H.S., Louhivuori, M., Marrink, S.J., Vattulainen, I., 2011. Protein shape change has a major effect on the gating energy of a mechanosensitive channel. Biophys. J. 100, 1651-1659.
215. Ollila, O.H.S., Róg, T., Karttunen, M., Vattulainen, I., 2007. Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: comparison between cholesterol, desmosterol, 7-dehydrocho- lesterol and ketosterol. J. Struc. Biol. 159, 311-323.
216. Olsen, B.N., Schlesinger, P.H., Baker, N.A., 2009. Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. J. Am. Chem. Soc. 131, 4854-4865.
217. Olsen, B.N., Schlesinger, P.H., Ory, D.S., Baker, N.A., 2011. 25-hydroxycholesterol increases the availability of cholesterol in phospholipid membranes. Biophys. J. 100, 948-956.
218. Orlowski, A., Bunker, A., Pasenkiewicz-Gierula, M., Vattulainen, I., Männistö, P.T., Róg, T., 2012. Strong preferences of dopamine and L-dopa towards lipid head group: importance of phosphatidylserine and its implication for neurotransmitters metabolism. J. Neurochem. 122, 681-690.
219. Orsi, M., Essex, J.W., 2011. The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One 6, e28637.
220. Pan, J., Cheng, X., Heberle, F.A., Mostofian, B., Kucerka, N., Drazba, P., Katsaras, J., 2012. Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations. J. Phys. Chem. B 116, 14829-14838.
221. Pandit, S.A., Jakobsson, E., Scott, H.L., 2004b. Simulation of the early stages of nanodomain formation in mixed bilayers of sphingomyelin cholesterol, and dioleylphosphatidylcholine. Biophys. J. 87, 3312-3322.
222. Pandit, S.A., Scott, H.L., 2009. Multiscale simulations of heterogeneous model membranes. Biochim. Biophys. Acta 1788, 136-148.
223. Pandit, S.A., Vasudevan, S., Chiu, S.W., Mashl, R.J., Jakobsson, E., Scott, H.L., 2004a. Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation. Biophys. J 87, 1092-1100.
224. Paradies, G., Paradies, V., De Benedictis, V., Ruggiero, F.M., Petrosillo, G., 2014. Functional role of cardiolipin in mitochondrial bioenergetics. Biochi. Biophys. Acta 1837, 408-417.
225. Parisio, G., Ferrarini, A., 2010. Solute partitioning into lipid bilayers: an implicit model for nonuniform and ordered environment. J. Chem. Theory Comput. 6, 2267-2280.
226. Parisio, G., Sperotto, M.M., Ferrarini, A., 2012. Flip-Flop of steroids in phospholipid bilayers: effects of the chemical structure on transbilayer diffusion. J. Am. Chem. Soc. 134, 12198-12208.
227. Parthasarathi, R., Tian, J., Redondo, A., Gnanakaran, S., 2011. Quantum chemical study of carbohydrate-phospholipid interactions. J. Phys. Chem. A 115, 12826-12840.
228. Pasenkiewicz-Gierula, M., Baczyński, K., Murzyn, K., Markiewicz, M., 2012. Orientation of lutein in a lipid bilayer-revisited. Acta Biochim. Polon. 59, 115-118.
229. Pasenkiewicz-Gierula, M., Róg, T., Kitamura, K., Kusumi, A., 2000. Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study. Biophys. J. 78, 1376-1389.
230. Pastor, R.W., MacKerell Jr., R.Y., 2011. Development of the CHARMM force field for lipids. J. Phys. Chem. Lett. 2, 1526-1532.
231. Patel, Balaji, P.V., 2007. Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations. Biochim. Biophys. Acta 1768, 1628-1640.
232. Patel, R.Y., Balaji, P.V., 2008. Characterization of symmetric and asymmetric lipid bilayers composed of varying concentrations of ganglioside GM1 and DPPC. J. Phys. Chem. B 112, 3346-3356.
233. Patel, R.Y., Balaji, P.V., 2011. Structure and dynamics of glycosphingolipids in lipid bilayers: insights from molecular dynamics simulations. Int. J. Carbohydrate Chem Article ID 950256.
234. Patterson, G.H., Hirschberg, K., Polishchuk, R.S., Gerlich, D., Phair, R.D., Lippincott- Schwartz, J., 2008. Transport through the golgi apparatus by rapid partitioning within a two-phase membrane system. Cell 133, 1055-1067.
235. Penmatsa, A., Wang, K.H., Gouaux, E., 2013. X-ray structure of dopamine transporter elucidates antidepressant mechanism. Nature 503, 85-90.
236. Perlmutter, J.D., Sachs, J.N., 2009. Inhibiting lateral domain formation in lipid bilayers: simulations of alternative steroid headgroup chemistries. J. Am. Chem. Soc. 131, 16362-16363.
237. Pietilainen, K.H., Róg, T., Seppanen-Laakso, T., Virtue, S., Gopalacharyulu, P., Tang, J., Rodriguez-Cuenca, S., Maciejewski, A., Naukkarinen, J., Ruskeepaa, A.-L., Niemela, P.S., Yetukuri, L., Tan, C.Y., Velagapudi, V., Castillo, S., Nygren, H., Hyotylainen, T., Rissanen, A., Kaprio, J., Yki-Jarvinen, H., Vattulainen, I., Vidal- Puig, A., Oresic, M., 2011. Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans. PLoS Biol 9, e1000623.
238. Piggot, T.J., Holdbrook, D.A., Khalid, S., 2011. Electroporation of the E. coli and S. aureus membranes: molecular dynamics simulations of complex bacterial membranes. J. Phys. Chem. B 115, 13381-13388.
239. Plesnar, E., Subczynski, W.K., Pasenkiewicz-Gierula, M., 2013. Comparative computer simulation study of cholesterol in hydrated unary and binary lipid bilayers and in an anhydrous crystal. J. Phys. Chem. B 117, 8758-8769.
240. Plesnar, E., Subczynski, W.K., Pasenkiewicz-Gierula, M., 2012. Saturation with cholesterol increases vertical order and smoothes the surface of the phosphatidylcholine bilayer: a molecular simulation study. Biochim. Biophys. Acta 1818, 520-529.
241. Poger, D., Mark, A.E., 2013. The relative effect of sterols and hopanoids on lipid bilayers: when comparable is not identical. J. Phys. Chem. B 117, 16129-16140.
242. Polley, A., Vemparala, S., 2013. Partitioning of ethanol in multi-component membranes: effects on membrane structure. Chem. Phys. Lipids 166, 1-11.
243. Polley, A., Vemparala, S., Rao, M., 2012. Atomistic simulations of a multicomponent asymmetric lipid bilayer. J. Phys. Chem. B 116, 13403-13410.
244. Pourmousa, A.M., Róg, T., Mikkeli, R., Vattulainen, I., Solanko, L.M., Wustner, D., Holmgaard List, N., Kongsted, J., Karttunen, M., 2014. Cholesterol and its analogues: the effect of dehydroergosterol on cell membranes. J. Phys. Chem. B 118, 7345-7357.
245. Prakash, A., Janosi, L., Doxastakis, M., 2011. GxxxG motifs phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors. Biophys. J. 101, 1949-1958.
246. Puri, V., Watanabe, R., Dominguez, M., Sun, X.F., Wheatley, C.L., Marks, D.L., Pagano, R.E., 1999. Cholesterol modulates membrane traffic along the endocytic pathway in sphingolipid storage diseases. Nature Cell Biol. 1, 386-388.
247. Pöyry, S., Cramariuc, O., Postila, P.A., Kaszuba, K., Sarewicz, M., Osyczka, A., Vattulainen, I., Róg, T., 2013. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. Biochim. Biophys. Acta 1827, 769-778.
248. Pöyry, S., Róg, T., Karttunen, M., Vattulainen, I., 2008. Significance of cholesterol methyl groups. J. Phys. Chem. B 112, 2922-2929.
249. Qiu, L., Buie, C., Reay, A., Vaughn, M.W., Cheng, K.H., 2011. Molecular dynamics simulations reveal the protective role of cholesterol in β-amyloid protein-induced membrane disruptions in neuronal membrane mimics. J. Phys. Chem. B 115, 9795-9812.
250. Raguz, M., Mainali, L., Widomska, J., Subczynski, W.K., 2011. The immiscible cholesterol bilayer domain exists as an integral part of phospholipid bilayer membranes. Biochim. Biophys. Acta 1808, 1072-1080.
251. Ramadurai, S., Holt, A., Schafer, L.V., Krasnikov, V.V., Rijkers, D.T.S., Marrink, S.J., Killian, J.A., Poolman, B., 2010. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of AT peptides. Biophys. J. 99, 1447-1454.
252. Ramstedt, B., Slotte, J.P., 2002. Membrane properties of sphingomyelins. FEBS Lett. 531, 33-37.
253. Ramstedt, B., Slotte, J.P., 2006. Sphingolipids and the formation of sterol-enriched ordered membrane domains. Biochim. Biophys. Acta 1758, 1945-1956.
254. Rantamaki, A., Telenius, J., Koivuniemi, A., Vattulainen, I., Holopainen, J.M., 2011. Lessons from the biophysics of interfaces lung surfactant and tear fluid. Prog. Retinal Eye Res. 30, 204-215.
255. Reigada, R., 2014. Electroporation of heterogeneous lipid membranes. Biochim. Biophys. Acta 1838, 814-821.
256. Rheinstädter, M.C., Mouritsen, O.G., 2013. Small-scale structure in fluid cholesterol- lipid bilayers. Curr. Opin. Colloid Interface Sci. 18, 440-447.
257. Risselada, H.J., Marrink, S.J., 2008. The molecular face of lipid rafts in model membranes. Proc. Natl. Acad. Sci. USA 105, 17367-17372.
258. Risselada, H.J., Marrink, S.J., Muller, M., 2011. Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Phys. Rev. Lett. 106, 148102.
259. Robalo, J.R., Martins do Canto, A.M.T., Carvalho, A.J.P., Ramalho, J.P.P., Loura, L.M.S., 2013. Behavior of fluorescent cholesterol analogues dehydroergosterol and cholestatrienol in lipid bilayers: a molecular dynamics study. J. Phys. Chem. B 117, 5806-5819.
260. Robalo, J.R., Ramalho, J.P.P., Loura, L.M.S., 2013b. NBD-labeled cholesterol analogues in phospholipid bilayers: insights from molecular dynamics. J. Phys. Chem. B 117, 13731-13742.
261. Róg, T., Bunker, A., Vattulainen, I., Karttunen, M., 2007b. Effect of glucose and galactose headgroup on lipid bilayer properties. J. Phys. Chem. B 111, 10146-10154.
262. Róg, T., Murzyn, K., Karttunen, M., Pasenkiewicz-Gierula, M., 2008b. Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol molecular dynamics simulation studies. J. Pept. Sci. 14, 374-382.
263. Róg, T., Pasenkiewicz-Gierula, M., 2003. Comparison of effects of epicholesterol and cholesterol on the phosphatidylcholine bilayer: a molecular dynamics simulation study. Biophys. J. 84, 1818-1826.
264. Róg, T., Pasenkiewicz-Gierula, M., 2006. Cholesterol-sphingomyelin interactions: a molecular dynamics simulation study. Biophys. J. 91, 3756-3767.
265. Róg, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M., 2009a. Ordering effects of cholesterol and its analogues. Biochim. Biophys. Acta 1788, 97-121.
266. Róg, T., Stimson, L.M., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M., 2008a. Replacing the cholesterol hydroxyl group with the ketone group facilitates sterol flip-flop and promotes membrane fluidity. J. Phys. Chem. B 112, 1946-1952.
267. Róg, T., Vattulainen, I., Jansen, M., Ikonen, E., Karttunen, M., 2008. Comparison of cholesterol and its direct precursors along the biosynthetic pathway: effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers. J. Chem. Phys 129, 154508.
268. Róg, T., Vattulainen, I., Karttunen, M., 2005. Modeling glycolipids: take one. Cell. Mol. Biol. Lett. 10, 625-630.
269. Róg, T., Vattulainen, I., Pasenkiewicz-Gierula, M., Karttunen, M., 2007a. What happens if cholesterol is made smoother: importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction. Biophys. J 92, 3346-3357.
270. Rosenbaum, D.M., Zhang, C., Lyons, J.A., Holl, R., Aragao, D., Arlow, D.H., Rasmussen, S.G.F., Choi, H.J., Devree, B.T., Sunahara, R.K., Chae, P.S., Gellman, S.H., Dror, R.O., Shaw, D.E., Weis, W.I., Caffrey, M., Gmeiner, P., Kobilka, B.K., 2011. Structure and function of an irreversible agonist-β(2) adrenoceptor complex. Nature 469, 236-240.
271. Rosetti, C., Pastorino, C., 2012. Comparison of ternary bilayer mixtures with asymmetric or symmetric unsaturated phosphatidylcholine lipids by coarse grained molecular dynamics simulations. J. Phys. Chem. B 116, 3525-3537.
272. Roy, D., Mukhopadhyay, C., 2001. GD1a in phospholipid bilayer: a molecular dynamics simulation. J. Biomolec. Struc. Dyn. 18, 639-646.
273. Roy, D., Mukhopadhyay, C., 2002. Molecular dynamics simulation of GM1 in phospholipid bilayer. J. Biomolec. Struct. Dyn. 19, 1121-1132.
274. Sadiq, S.K., Guixà-González, R., Dainese, E., Pastor, M., De Fabritiis, G., Selent, J., 2013. Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. Curr. Med. Chem 20, 22-38.
275. Sáenz, J.P., Sezgin, E., Schwille, P., Simons, K., 2012. Functional convergence of hopanoids and sterols in membrane ordering. Proc. Natl. Acad. Sci. USA 109, 14236-14240.
276. Saito, H., Shinoda, W., 2011. Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study. J. Phys. Chem. B 115,15241-15250.
277. Sandvig, K., Bergan, J., Kavaliauskiene, S., Skotland, T., 2014. Lipid requirements for entry of protein toxins into cells. Prog. Lipid Res. 54, 1-13.
278. Saxena, R., Chattopadhyay, A., 2012. Membrane cholesterol stabilizes the human serotonin1A receptor. Biochim. Biophys. Acta 1818, 2936-2942.
279. Schmidt, U., Weiss, M., 2010. Hydrophobic mismatch-induced clustering as a primer for protein sorting in the secretory pathway. Biophys. Chem. 151, 34-38.
280. Sega, M., Jedlovszky, P., Vallauri, R., 2006. Molecular dynamics simulation of GM1 gangliosides embedded in a phospholipid membrane. J. Mol. Liq. 129, 86-91.
281. Sega, M., Vallauri, R., Brocca, P., Cantu, L., Melchionna, S., 2007. Short-range structure of a GM3 ganglioside membrane: comparison between experimental WAXS and computer simulation results. J. Phys. Chem. B 111, 10965-10969.
282. Sega, M., Vallauri, R., Brocca, P., Melchionna, S., 2004. Molecular dynamics simulation of a GM3 ganglioside bilayer. J. Phys. Chem. B 108, 20322-20330.
283. Sengupta, D., 2012. Cholesterol modulates the structure, binding modes, and energetics of caveolin-membrane interactions. J. Phys. Chem. B 116, 6-14564.
284. Sengupta, D., Chattopadhyay, A., 2012. Identification of cholesterol binding sites in the serotonin1A receptor. J. Phys. Chem. B 116, 12991-12996.
285. Sergelius, C., Niinivehmas, S., Maula, T., Kurita, M., Yamaguchi, S., Yamamoto, T., Katsumura, S., Pentikainen, O.T., Slotte, J.P., 2012. Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus. Biochim. Biophys. Acta 1818, 474-480.
286. Sergelius, C., Slotte, J.P., 2011. Membrane properties of and cholesterol's interactions with a biologically relevant three-chain sphingomyelin: 3O-palmitoyl-N-palmitoyl-D-erythro-sphingomyelin. Biochim. Biophys. Acta 1808, 2841-2848.
287. Shang, Z., Mao, Y., Tero, R., Liu, X., Hoshino, T., Tanaka, M., Urisu, T., 2010. Clustering effects of GM1 and formation mechanisms of interdigitated liquid disordered domains in GM1/SM/cholesterol-supported planar bilayers on mica surfaces. Chem. Phys. Lett. 497, 108-114.
288. Shigematsu, T., Koshiyama, K., Wada, S., 2014. Molecular dynamics simulations of pore formation in stretched phospholipid/cholesterol bilayers. Chem. Phys. Lipids 183, 43-49.
289. Shinoda, T., Ogawa, H., Cornelius, F., Toyoshima, C., 2009. Crystal structure of the sodium-potassium pump at 2.4 A resolution. Nature 459, 446-450.
290. Shintre, C.A., Pike, A.C.W., Li, Q., Kim, J., Barr, A.J., Von Delft, F., Shrestha, S., Gou, L., Yang, J., Berridge, G., Ross, J., Stansfeld, P.J., Edwards, M.S.P., Sans, A.M., Bountra, C., Marsden, B.D., Von Delft, F., Bullock, A.N., Gileadi, O., Burgess-Brown, N., Carpenter, E.P., 2013. Structures of ABCB10: a human ATP-binding cassette transporter in apo- and nucleotide-bound states. Proc. Natl. Acad. Sci. USA 110, 9710-9715.
291. Shipley, G.G., Green, J.P., Nichols, B.W., 1973. Phase behavior of monogalactosyl digalactosyl, and sulfoquinovosyl diglycerides. Biochim. Biophys. Acta 311, 531-544.
292. Shrivastava, S., Devi Paila, Y., Dutta, A., Chattopadhyay, A., 2008. Differential effects of cholesterol and its immediate biosynthetic precursors on membrane organization. Biochemistry 47, 5668-5677.
293. Shroll, R.M., Straatsma, T.P., 2002. Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation. Biopolymers 65, 395-407.
294. Shroll, R.M., Straatsma, T.P., 2003. Molecular basis for microbial adhesion to geochemical surfaces: computer simulation of Pseudomonas aeruginosa adhesion to goethite. Biophys. J. 84, 1765-1772.
295. Slotte, J.P., 2013. Molecular properties of various structurally defined sphingomye- lins-correlation of structure with function. Prog. Lip. Res 52, 206-219.
296. Smith, A.W., 2012. Lipid-protein interactions in biological membranes: a dynamic perspective. Biochim. Biophys. Acta 1818, 172-177.
297. Smondyrev, A.M., Berkowitz, M.L., 2000. Molecular dynamics simulation of dipalmitoylphosphatidylcholine membrane with cholesterol sulfate. Biophys. J. 78, 1672-1680.
298. Soares, T.A., Straatsma, T.P., Lins, R.D., 2008. Influence of the B-band O-antigen chain in the structure and electrostatics of the lipopolysaccharide membrane of Pseudomonas aeruginosa. J. Braz. Chem. Soc. 19, 312-320.
299. Sodt, A.J., Logan Sandar, M., Gawrisch, K., Pastor, R.W., Lyman, E., 2014. The molecular structure of the liquid-ordered phase of lipid bilayers. J. Am. Chem. Soc. 136, 725-732.
300. Song, Y., Kenworthy, A.K., Sanders, C.R., 2014. Cholesterol as a co-solvent and a ligand for membrane proteins. Protein Sci. 23, 1-22.
301. Soubias, O., Gawrisch, K., 2012. The role of the lipid matrix for structure and function of the GPCR rhodopsin. Biochim. Biophys. Acta 1818, 234-240.
302. Sparr, E., Ash, W.L., Nazarov, P.V., Rijkers, D.T.S., Hemminga, M.A., Tieleman, D.P., Killian, J.A., 2005. Self-association of transmembrane-helices in model membranes. Importance of helix orientation and role of hydrophobic mismatch. J. Biol. Chem. 280, 39324-39331.
303. Stansfeld, P.J., Sansom, M.S.P., 2011. From coarse grained to atomistic: a serial multiscale approach to membrane protein simulations. J. Chem. Theory Comput. 7, 1157-1166.
304. Štefl, M., Šachl, R., Olẓyńska, A., Amaro, M., Savchenko, D., Deyneka, A., Hermetter, A., Cwiklik, L., Humpolíčková, J., Hof, M., 2014. Comprehensive portrait of cholesterol containing oxidized membrane. Biochim. Biophys. Acta 1838, 1769-1776.
305. Stepniewski, M., Bunker, A., Pasenkiewicz-Gierula, M., Karttunen, M., Róg, T., 2010. Effects of the lipid bilayer phase state on the water membrane interface. J. Chem. Phys. B. 114, 11784-11792.
306. Stetter, F.W.S., Cwiklik, L., Jungwirth, P., Hugel, T., 2014. Single lipid extraction: The anchoring strength of cholesterol in liquid-ordered and liquid-disordered phases. Biophys. J. 107, 1167-1175.
307. Stoffel, W., Bosio, A., 1997. Myelin glycolipids and their functions. Curr. Opin. Neurobio. 7, 654-661.
308. Straubinger, R.M., 1993. pH-Sensitive liposomes for delivery of macromolecules into cytoplasm of cultured-cells. Methods Enzymol. 221, 361-376.
309. Subczynski, W.K., Raguz, M., Widomska, J., Mainali, L., Konovalov, A., 2012b. Functions of cholesterol and the cholesterol bilayer domain specific to the fiber-cell plasma membrane of the eye lens. J. Membrane Biol. 245, 51-68.
310. Subczynski, W.K., Wisniewska-Becker, A., Widomska, J., 2012a. Can macular xanthophylls replace cholesterol in formation of the liquid-ordered phase in lipid-bilayer membranes. Acta Biochim. Polon 59, 109-114.
311. Sun, D., Lin, X., Gu, N., 2014. Cholesterol affects C translocation across lipid bilayers. Soft Matter 10, 2160-2168.
312. Teixeira, V., Feio, M.J., Bastos, M., 2012. Role of lipids in the interaction of antimicrobial peptides with membranes. Progr. Lip. Res. 51, 149-177.
313. Tessier, M.B., DeMarco, M.L., Yongye, A.B., Woods, R.J., 2008. Extension of the Glycam06 biomolecular force field to lipids lipid bilayers and glycolipids. Mol. Simul. 34, 349-364.
314. Tieleman, D.P., MacCallum, J.L., Ash, W.L., Kandt, C., Xu, Z.T., Monticelli, L., 2006. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J. Phys. Cond. Matt. 18, 1221-1234.
315. Timr, S., Bondar, A., Cwiklik, L., Stefl, M., Hof, M., Vazdar, M., Lazar, J., Jungwirth, P., 2014. Accurate determination of the orientational distribution of a fluorescent molecule in a phospholipid membrane. J. Phys. Chem. B 118, 855-863.
316. Tumaneng, P.W., Pandit, S.A., Zhao, G., Scott, H.L., 2011. Self-consistent mean-field model for palmitoyloleoylphosphatidylcholine-palmitoyl sphingomyelin-cholesterol lipid bilayers. Phys. Rev. E 83, 031925.
317. Vacha, R., Siu, S.W.I., Petrov, M., Bockmann, R.A., Barucha-Kraszewska, J., Jurkiewicz, P., Hof, M., Berkowitz, M.L., Jungwirth, P., 2009. Effects of alkali cations and halide anions on the DOPC lipid membrane. J. Phys. Chem. A 113, 7235-7243.
318. Wacker, D., Fenalti, G., Brown, M.A., Katritch, V., Abagyan, R., Cherezov, V., Stevens, R. C., 2010. Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J. Am. Chem. Soc. 132, 11443-11445.
319. Wacker, D., Wang, C., Katritch, V., Han, G.W., Huang, X.P., Vardy, E., McCorvy, J.D., Jiang, Y., Chu, M., Siu, F.Y., Liu, W., Xu, H.E., Cherezov, V., Roth, B.L., Stevens, R.C., 2013. Structural features for functional selectivity at serotonin receptors. Science 340, 615-619.
320. Wada, T., Shimono, K., Kikukawa, T., Hato, M., Shinya, N., Kim, S.Y., Kimura-Someya, T., Shirouzu, M., Tamogami, J., Miyauchi, S., Jung, K.-H., Kamo, N., Yokoyama, S., 2011. Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin: acetabularia rhodopsin II from marine alga. J. Mol. Biol. 411, 986-998.
321. Vainio, S., Jansen, M., Koivusalo, M., Róg, T., Karttunen, M., Vattulainen, I., Ikonen, E., 2006. J. Biol. Chem. 281, 348-355.
322. van Meer, G., Voelker, D.R., Feigenson, G.W., 2008. Membrane lipids: where they are and how they behave. Nature Rev. Mol. Cell Biol. 9, 112-124.
323. Warne, A., Moukhametzianov, R., Baker, J.G., Nehme, R., Edwards, P.C., Leslie, A.G.W., Schertler, G.F.X., Tate, C.G., 2011. The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor. Nature 469, 241-244.
324. Vasudevan, S.V., Balaji, P.V., 2001. Dynamics of ganglioside headgroup in lipid environment: molecular dynamics simulations of GM1 embedded in dodecylphosphocholine micelle. J. Phys. Chem. B 105, 7033-7041.
325. Vattulainen, I., Róg, T., 2011. Lipid simulations: a perspective on lipids in action. Cold Spring Harbor Perspect. Biol. 3, a004655.
326. Venable, R.M., Sodt, A.J., Rogaski, B., Rui, H., Hatcher, E., MacKerell Jr., A.D., Pastor, R. W., Klauda, J.B., 2014. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophys. J. 107, 134-145.
327. Wennberg, C.L., van der Spoel, D., Hub, J.S., 2012. Large influence of cholesterol on solute partitioning into lipid membranes. J. Am. Chem. Soc. 134, 5351-5361.
328. Wenz, J.J., 2012. Predicting the effect of steroids on membrane biophysical properties based on the molecular structure. Biochim. Biophys. Acta 1818, 896-906.
329. Westerlund, B., Slotte, J.P., 2009. How the molecular features of glycosphingolipids affect domain formation in fluid membranes. Biochim. Biophys. Acta 1788, 194-201.
330. Wizert, D., Iskander, R., Cwiklik, L., 2014. Organization of lipids in the tear film: a molecular-level view. PLoS One 9, e92461.
331. Woods, R.J., Tessier, M.B., 2010. Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr. Struct. Biol. 20, 575-583.
332. Wu, H., Wang, C., Gregory, K.J., Han, G.W., Cho, H.P., Xia, Y., Niswender, C.M., Katritch, V., Meiler, J., Cherezov, V., Conn, P.J., Stevens, R.C., 2014. Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science 344, 58-64.
333. Vyas, A.A., 2002. Gangliosides are functional nerve cell ligands for myelin- associated glycoprotein (MAG): an inhibitor of nerve regeneration. Proc. Natl. Acad. Sci. USA 99, 8412-8417.
334. Wydro, P., Knapczyk, S., Lapczynska, M., 2011. Variations in the condensing effect of cholesterol on saturated versus unsaturated phosphatidylcholines at low and high sterol concentration. Langmuir 27, 5433-5444.
335. Yahi, N., Aulas, A., Fantini, J., 2010. How cholesterol constrains glycolipid conformation for optimal recognition of Alzheimer's b amyloid peptide (Ab1-40). PLoS ONE 5, e9079.
336. Yamashita, T., 1999. A vital role for glycosphingolipid synthesis during development and differentiation. Proc. Natl. Acad. Sci. USA 96, 9142-9147.
337. Yamashita, T., 2014. Properties of a hydrated excess proton near the cholesterol- containing phospholipid bilayer. JPS Conf. Proc. 1, 013086.
338. Yesylevskyy, S.O., Demchenko, A.P., 2012. How cholesterol is distributed between monolayers in asymmetric lipid membranes. Eur. Biophys. J. 41, 1043-1054.
339. Yesylevskyy, S.O., Ramseyer, C., 2014. Determination of mean and Gaussian curvatures of highly curved asymmetric lipid bilayers: the case study of the influence of cholesterol on the membrane shape. Phys. Chem. Chem. Phys. 16, 17052-17061.
340. Yethiraj, T., Weisshaar, 2007. Why are lipid rafts not observed in vivo? Biophys. J. 93, 3113-3119.
341. Zaraiskaya, Jeffrey, K.R., 2005. Molecular dynamics simulations and 2H NMR study of the GalCer/DPPG lipid bilayer. Biophys. J. 88, 4017-4031.
342. Zhang, J., Zhang, K., Gao, Z.G., Paoletta, S., Zhang, D., Han, G.W., Li, T., Ma, L., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., 2014b. Agonist-bound structure of the human P2Y12 receptor. Nature 509, 119-122.
343. Zhang, K., Zhang, J., Gao, Z.-G., Zhang, D., Zhu, L., Han, G.W., Moss, S.M., Paoletta, S., Kiselev, E., Lu, W., Fenalti, G., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., 2014a. Structure of the human P2Y12 receptor in complex with an antithrombotic drug. Nature 509, 115-118.
344. Zhang, Z., Bhide, S.Y., Berkowitz, M.L., 2007. Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol. J. Phys. Chem. B 111, 12888-12897.
345. Zhao, G., Subbaiah, P.V., Mintzer, E., Chiu, S.-W., Jakobsson, E., Scott, H.L., 2011. Molecular dynamic simulation study of cholesterol and conjugated double bonds in lipid bilayers. Chem. Phys. Lipids 164, 811-818.
346. Zidar, J., Merzel, F., Hodoscek, M., Rebolj, K., Sepcic, K., Macek, P., Janezic, D., 2009. Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers: allatom molecular dynamics simulations. J. Phys. Chem. B 113, 15795-15802.