References
- Abercrombie, M., & Ambrose, E. J. (1962). The surface properties of cancer cells: A review. Cancer Research, 22, 525–548.
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. Softwarex, 1–2, 19–25. https://doi.org/https://doi.org/10.1016/j.softx.2015.06.001
- Allen, M. P., & Tildesley, D. J. (2017). Computer simulation of liquids. In Computer simulation of liquids (2nd ed.). Oxford: Oxford University Press. https://doi.org/https://doi.org/10.1093/oso/9780198803195.001.0001
- Almeida, P. F. F., & Vaz, W. L. C. (1995). Chapter 6 Lateral diffusion in membranes. In Handbook of Biological Physics (Vol. 1(C), pp. 305–357. Amsterdam: Elsevier: https://doi.org/https://doi.org/10.1016/S1383-8121(06)80023-0
- Anézo, C., De Vries, A. H., Höltje, H. D., Tieleman, D. P., & Marrink, S. J. (2003). Methodological issues in lipid bilayer simulations. The Journal of Physical Chemistry B, 107(35), 9424–9433. https://doi.org/https://doi.org/10.1021/jp0348981
- Arcamone, F., Franceschi, G., Penco, S., & Selva, A. (1969). Adriamycin (14-hydroxydaunomycin), a novel antitumor antibiotic. Tetrahedron Letters, 10(13), 1007–1010. https://doi.org/https://doi.org/10.1016/S0040-4039(01)97723-8
- Baumgart, T., Hunt, G., Farkas, E. R., Webb, W. W., & Feigenson, G. W. (2007). Fluorescence probe partitioning between Lo/Ld phases in lipid membranes. Biochimica et Biophysica Acta, 1768(9), 2182–2194. https://doi.org/https://doi.org/10.1016/j.bbamem.2007.05.012
- Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
- Bitensky, L. (1989). Introduction to biological membranes. 2nd edn. Mahendra K. Jain. John Wiley and Sons: New York. vii + 423 pages, £47.50 (1988. ). Cell Biochemistry and Function, 7(1), 78–78. https://doi.org/https://doi.org/10.1002/cbf.290070118
- Bostick, D., & Berkowitz, M. L. (2003). The implementation of slab geometry for membrane-channel molecular dynamics simulations. Biophysical Journal, 85(1), 97–107. https://doi.org/https://doi.org/10.1016/S0006-3495(03)74458-0
- Bretscher, M. S. (1985). The molecules of the cell membrane. Scientific American, 253(4), 100–108. https://doi.org/https://doi.org/10.1038/scientificamerican1085-100
- Briegel, A., Ortega, D. R., Tocheva, E. I., Wuichet, K., Zhuo, L., Songye, C., Müller, A., Iancu, C. V., Murphy, G. E., Dobro, M. J., Zhulin, I. B., & Jensen, G. J. (2009). Universal architecture of bacterial chemoreceptor arrays. Proceedings of the National Academy of Sciences of the United States of America, 106(40), 17181–17186. https://doi.org/https://doi.org/10.1073/pnas.0905181106
- Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126(1), 014101. https://doi.org/https://doi.org/10.1063/1.2408420
- Chien, S., Sung, K. L., Skalak, R., Usami, S., & Tözeren, A. (1978). Theoretical and experimental studies on viscoelastic properties of erythrocyte membrane. Biophysical Journal, 24(2), 463–487. https://doi.org/https://doi.org/10.1016/S0006-3495(78)85395-8
- Clarke, R. J. (2001). Dipole potential of phospholipid membranes and methods for its detection. Advances in Colloid and Interface Science, 89–90, 263–281. https://doi.org/https://doi.org/10.1016/S0001-8686(00)00061-0
- Comfurius, P., & Zwaal, R. F. A. (1977). The enzymatic synthesis of phosphatidylserine and purification by CM-cellulose column chromatography. Biochimica et Biophysica Acta (Bba) - Lipids and Lipid Metabolism, 488(1), 36–42. https://doi.org/https://doi.org/10.1016/0005-2760(77)90120-5
- Cooper, G. M., & Hausman, R. E. (2007). The cell: A molecular approach (4th ed.). In Sinauer Associates.
- Demel, R. A., Geurts van Kessel, W. S. M., Zwaal, R. F. A., Roelofsen, B., & van Deenen, L. L. M. (1975). Relation between various phospholipase actions on human red cell membranes and the interfacial phospholipid pressure in monolayers. Biochimica et Biophysica Acta, 406(1), 97–107. https://doi.org/https://doi.org/10.1016/0005-2736(75)90045-0
- Demel, R. A., Paltauf, F., & Hauser, H. (1987). Monolayer characteristics and thermal behavior of natural and synthetic phosphatidylserines. Biochemistry, 26(26), 8659–8665. https://doi.org/https://doi.org/10.1021/bi00400a025
- Einstein, A. (1906). Zur Theorie der Brownschen Bewegung. Annalen Der Physik, 324(2), 371–381. https://doi.org/https://doi.org/10.1002/andp.19063240208
- Engelman, D. M. (1969). Surface area per lipid molecule in the intact membrane of the human red cell. Nature, 223(5212), 1279–1280. https://doi.org/https://doi.org/10.1038/2231279a0
- Evans, C. J., Phillips, R. M., Jones, P. F., Loadman, P. M., Sleeman, B. D., Twelves, C. J., & Smye, S. W. (2009). A mathematical model of doxorubicin penetration through multicellular layers. Journal of Theoretical Biology, 257(4), 598–608. https://doi.org/https://doi.org/10.1016/j.jtbi.2008.11.031
- Ewald, P. P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen Der Physik, 369(3), 253–287. https://doi.org/https://doi.org/10.1002/andp.19213690304
- Filippov, A., Orädd, G., & Lindblom, G. (2003). Influence of cholesterol and water content on phospholipid lateral diffusion in bilayers. Langmuir, 19(16), 6397–6400. https://doi.org/https://doi.org/10.1021/la034222x
- Filippov, A., Orädd, G., & Lindblom, G. (2006). Sphingomyelin structure influences the lateral diffusion and raft formation in lipid bilayers. Biophysical Journal, 90(6), 2086–2092. https://doi.org/https://doi.org/10.1529/biophysj.105.075150
- Herrera, F. E., & Pantano, S. (2009). Salt induced asymmetry in membrane simulations by partial restriction of ionic motion. Journal of Chemical Physics, 130(19). https://doi.org/https://doi.org/10.1063/1.3132705
- Hicks, B. (1998). Instant Notes in Biochemistry by B. D. Hames, N. M. Hooper & J. D. Houghton. The Chemical Educator, 3(2), 1–2. https://doi.org/https://doi.org/10.1007/s00897980195a
- Himbert, S., Alsop, R. J., Rose, M., Hertz, L., Dhaliwal, A., Moran-Mirabal, J. M., Verschoor, C. P., Bowdish, D. M. E., Kaestner, L., Wagner, C., & Rheinstädter, M. C. (2017). The molecular structure of human red blood cell membranes from highly oriented, solid supported multi-lamellar membranes. Scientific Reports, 7, 39661. https://doi.org/https://doi.org/10.1038/srep39661
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Ivanova, N., & Ivanova, A. (2018). Testing the limits of model membrane simulations-bilayer composition and pressure scaling. Journal of Computational Chemistry, 39(8), 387–396. https://doi.org/https://doi.org/10.1002/jcc.25117
- Jämbeck, J. P. M., & Lyubartsev, A. P. (2013). Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers. Physical Chemistry Chemical Physics, 15(13), 4677–4686. https://doi.org/https://doi.org/10.1039/c3cp44472d
- Jo, S., Lim, J. B., Klauda, J. B., & Im, W. (2009). CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophysical Journal, 97(1), 50–58. https://doi.org/https://doi.org/10.1016/j.bpj.2009.04.013
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/https://doi.org/10.1063/1.445869
- Khalid, S., Bond, P. J., Holyoake, J., Hawtin, R. W., & Sansom, M. S. P. (2008). DNA and lipid bilayers: Self-assembly and insertion. Journal of the Royal Society Interface, 5(suppl_3), 241–250. https://doi.org/https://doi.org/10.1098/rsif.2008.0239.focus
- Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D., & Pastor, R. W. (2010). Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types. The Journal of Physical Chemistry B, 114(23), 7830–7843. https://doi.org/https://doi.org/10.1021/jp101759q
- Kučerka, N., Nagle, J. F., Sachs, J. N., Feller, S. E., Pencer, J., Jackson, A., & Katsaras, J. (2008). Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophysical Journal, 95(5), 2356–2367. https://doi.org/https://doi.org/10.1529/biophysj.108.132662
- Kučerka, N., Nieh, M. P., & Katsaras, J. (2011). Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. Biochimica et Biophysica Acta, 1808(11), 2761–2771. https://doi.org/https://doi.org/10.1016/j.bbamem.2011.07.022
- Lewis, B. A., & Engelman, D. M. (1983). Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. Journal of Molecular Biology, 166(2), 211–217. https://doi.org/https://doi.org/10.1016/S0022-2836(83)80007-2
- Lindblom, G., & Orädd, G. (2009). Lipid lateral diffusion and membrane heterogeneity. Biochimica et Biophysica Acta, 1788(1), 234–244. https://doi.org/https://doi.org/10.1016/j.bbamem.2008.08.016
- Lipkowski, J. (2014). Biomimetic membrane supported at a metal electrode surface. A molecular view. In Advances in Planar Lipid Bilayers and Liposomes, 20, 1–49. https://doi.org/https://doi.org/10.1016/B978-0-12-418698-9.00001-0
- Lukat, G., Krüger, J., & Sommer, B. (2013). APL@Voro: A voronoi-based membrane analysis tool for GROMACS trajectories. Journal of Chemical Information and Modeling, 53(11), 2908–2925. https://doi.org/https://doi.org/10.1021/ci400172g
- Luna, E. J., & Hitt, A. L. (1992). Cytoskeleton-plasma membrane interactions. Science (New York, N.Y.), 258(5084), 955–964. https://doi.org/https://doi.org/10.1126/science.1439807
- Marrink, S. J., Risselada, J., & Mark, A. E. (2005). Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry and Physics of Lipids, 135(2), 223–244. https://doi.org/https://doi.org/10.1016/j.chemphyslip.2005.03.001
- Marsh, D. (1996). Lateral pressure in membranes. Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, 1286(3), 183–223. https://doi.org/https://doi.org/10.1016/S0304-4157(96)00009-3
- Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/https://doi.org/10.1002/jcc.540130805
- Nagle, J. F., & Tristram-Nagle, S. (2000). Structure of lipid bilayers. Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, 1469(3), 159–195. https://doi.org/https://doi.org/10.1016/S0304-4157(00)00016-2 https://doi.org/https://doi.org/10.1016/S0304-4157(00)00016-2
- Nakase, I., Akita, H., Kogure, K., Gräslund, A., Langel, Ü., Harashima, H., & Futaki, S. (2012). Efficient intracellular delivery of nucleic acid pharmaceuticals using cell-penetrating peptides. Accounts of Chemical Research, 45(7), 1132–1139. https://doi.org/https://doi.org/10.1021/ar200256e
- Peter Tieleman, D., Hess, B., & Sansom, M. S. P. (2002). Analysis and evaluation of channel models: Simulations of alamethicin. Biophysical Journal, 83(5), 2393–2407. https://doi.org/https://doi.org/10.1016/S0006-3495(02)75253-3
- Prochiantz, A. (2000). Messenger proteins: Homeoproteins, TAT and others. Current Opinion in Cell Biology, 12(4), 400–406. https://doi.org/https://doi.org/10.1016/S0955-0674(00)00108-3
- Ramos, J., Cruz, V. L., Martínez-Salazar, J., Campillo, N. E., & Páez, J. A. (2011). Dissimilar interaction of CB1/CB2 with lipid bilayers as revealed by molecular dynamics simulation. Physical Chemistry Chemical Physics, 13(9), 3660–3668. https://doi.org/https://doi.org/10.1039/c0cp01456g
- Ramstedt, B., & Slotte, J. P. (2002). Membrane properties of sphingomyelins. FEBS Letters, 531(1), 33–37. https://doi.org/https://doi.org/10.1016/S0014-5793(02)03406-3
- Rawicz, W., Olbrich, K. C., McIntosh, T., Needham, D., & Evans, E. A. (2000). Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophysical Journal, 79(1), 328–339. https://doi.org/https://doi.org/10.1016/S0006-3495(00)76295-3
- Rose, H. G., & Oklander, M. (1965). Improved procedure for the extraction of lipids from human erythrocytes. Journal of Lipid Research, 6, 428–431.
- Seelig, A., & Seelig, J. (1974). The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry, 13(23), 4839–4845. https://doi.org/https://doi.org/10.1021/bi00720a024
- Shushkov, P., Tzvetanov, S., Velinova, M., Ivanova, A., & Tadjer, A. (2010). Structural aspects of lipid monolayers: Computer simulation analyses. Langmuir: The ACS Journal of Surfaces and Colloids, 26(11), 8081–8092. https://doi.org/https://doi.org/10.1021/la904734b
- Singleton, W. S., Gray, M. S., Brown, M. L., & White, J. L. (1965). Chromatographically homogeneous lecithin from egg phospholipids. Journal of the American Oil Chemists' Society, 42(1), 53–56. https://doi.org/https://doi.org/10.1007/BF02558256
- Tabujew, I., Lelle, M., & Peneva, K. (2015). Cell-penetrating peptides for nanomedicine-how to choose the right peptide. BioNanoMaterials, 16(1), 59–72. https://doi.org/https://doi.org/10.1515/bnm-2015-0001
- Tardieu, A., Luzzati, V., & Reman, F. C. (1973). Structure and polymorphism of the hydrocarbon chains of lipids: A study of lecithin-water phases. Journal of Molecular Biology, 75(4), 711–733. https://doi.org/https://doi.org/10.1016/0022-2836(73)90303-3
- Tieleman, D. P. (2004). The molecular basis of electroporation. BMC Biochemistry, 5, 10–12. https://doi.org/https://doi.org/10.1186/1471-2091-5-10
- Tieleman, D. P., & Berendsen, H. J. C. (1996). Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. The Journal of Chemical Physics, 105(11), 4871–4880. https://doi.org/https://doi.org/10.1063/1.472323
- Tsoneva, Y., Jonker, H. R. A., Wagner, M., Tadjer, A., Lelle, M., Peneva, K., & Ivanova, A. (2015). Molecular structure and pronounced conformational flexibility of doxorubicin in free and conjugated state within a drug-peptide compound. The Journal of Physical Chemistry B, 119(7), 3001–3013. https://doi.org/https://doi.org/10.1021/jp509320q
- Vaz, W. L. C., Clegg, R. M., & Hallmann, D. (1985). Translational diffusion of lipids in liquid crystalline phase phosphatidylcholine multibilayers. A comparison of experiment with theory. Biochemistry, 24(3), 781–786. https://doi.org/https://doi.org/10.1021/bi00324a037
- Virtanen, J. A., Cheng, K. H., & Somerharju, P. (1998). Phospholipid composition of the mammalian red cell membrane can be rationalized by a superlattice model. Proceedings of the National Academy of Sciences of the United States of America, 95(9), 4964–4969. https://doi.org/https://doi.org/10.1073/pnas.95.9.4964
- Vist, M. R., & Davis, J. H. (1990). Phase equilibria of cholesterol/dipalmitoylphosphatidylcholine mixtures: 2H nuclear magnetic resonance and differential scanning calorimetry. Biochemistry, 29(2), 451–464. https://doi.org/https://doi.org/10.1021/bi00454a021
- Wadia, J. S., Stan, R. V., & Dowdy, S. F. (2004). Transducible TAT-HA fusogenic peptide enhances escape of TAT-fusion proteins after lipid raft macropinocytosis. Nature Medicine, 10(3), 310–315. https://doi.org/https://doi.org/10.1038/nm996
- Zaccai, G., Bagyan, I., Combet, J., Cuello, G. J., Demé, B., Fichou, Y., Gallat, F. X., Josa, V. M. G., Von Gronau, S., Haertlein, M., Martel, A., Moulin, M., Neumann, M., Weik, M., & Oesterhelt, D. (2016). Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane. Scientific Reports, 6, 31434. https://doi.org/https://doi.org/10.1038/srep31434