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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 038 01 - Diskussion
Zuletzt bearbeitet: 2016-03-15 20:12:39 WiseWoman
Anézo 2003, Fragment, Gesichtet, KomplettPlagiat, Ry, SMWFragment, Schutzlevel sysop

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[In 1992 and 1993, several research groups reported simulation studies of single component membranes consisting, for instance, of dipalmitoylphosphatidylcholine (DPPC), dilauroylphosphatidylethanolamine (DLPE), or palmitoyloleoylphosphatidylcholine (POPC) molecules, demonstrating that the MD] technique applied to patches of a few phospholipids in water has enormous potential and can give detailed insights into lipid motions and interactions.

During the past ten years, computer hardware has become faster and cheaper, software problems have found innovative solutions, so that impressive improvements in the size and complexity of the simulated systems as well as in calculation time have been achieved. These improvements enable one nowadays to simulate mixed lipid systems (mixing for instance two type of phospholipids [30] or introducing a certain amount of cholesterol [31]), to include small molecules like drugs into the bilayer [32,33], or to insert peptides or even membrane proteins to study their interactions with the lipid components [34,35]. These new applications have been performed with more or less success and the simulation of lipid-protein systems in particular still remains a very challenging area.


30. de Vries, A. H.; Mark, A. E.; Marrink, S. J. J. Phys. Chem. B 2003.

31. Robinson, A. J.; Richards, W. G.; Thomas, P. J.; Hann, M. M. Biophys. J. 1995, 68, 164.

32. Huang, P.; Bertaccini, E.; Loew, G. H. 1995, 12, 725. [sic]

33. Alper, H. E.; Stouch, T. R. 1995, 99, 5724. [sic]

34. Chiu, S. W.; Subramaniam, S.; Jakobson, E. Biophys. J. 1999, 76, 1929.

35. Tieleman, D. P.; Berendsen, H. J. C.; Sansom, M. S. P. Biophys. J. 1999, 76, 1757.

In 1992 and 1993, several research groups reported simulation studies of single component membranes consisting, for instance, of dipalmitoylphosphatidylcholine (DPPC), dilauroylphosphatidylethanolamine (DLPE), or palmitoyloleoylphosphatidylcholine (POPC) molecules, demonstrating that the MD technique applied to patches of a few phospholipids in water has enormous potential and can give detailed insights into lipid motions and interactions.

During the past ten years, computer hardware has become faster and cheaper, software problems have found innovative solutions, so that impressive improvements in the size and complexity of the simulated systems as well as in calculation time have been achieved. These improvements enable one nowadays to simulate mixed lipid systems (mixing for instance two type of phospholipids [57] or introducing a certain amount of cholesterol [58–64]), to include small molecules like drugs into the bilayer [65–73], or to insert peptides or even membrane proteins to study their interactions with the lipid components [61,74–85]. These new applications have been performed with more or less success and the simulation of lipid- protein systems in particular still remains a very challenging area, which can only benefit in the next years from the increase in simulation time scale and system size.


[57] A. H. de Vries, A. E. Mark, and S. J. Marrink. J. Phys. Chem. B, 2003. In press.

[58] A. J. Robinson, W. G. Richards, P. J. Thomas, and M. M. Hann. Biophys. J., 68:164–170, 1995.

[59] K. Tu, M. L. Klein, and D. J. Tobias. Biophys. J., 75:2147–2156, 1998.

[60] A. M. Smondyrev and M. L. Berkowitz. Biophys. J., 77:2075–2089, 1999.

[61] M. Pasenkiewicz-Gierula, K. Murzyn, T. Róg, and C. Czaplewski. Acta Biochim. Pol., 47:601–611, 2000.

[62] M. Pasenkiewicz-Gierula T. Róg, K. Kitamura, and A. Kusumi. Biophys. J., 78:1376– 1389, 2000.

[63] A. Léonard, C. Escrive, M. Laguerre, E. Pebay-Peyroula,W. Néri, T. Pott, J. Katsaras, and E. J. Dufourc. Langmuir, 17:2019–2030, 2001.

[64] A. M. Smondyrev and M. L. Berkowitz. Biophys. J., 80:1649–1658, 2001.

[65] H. E. Alper and T. R. Stouch. J. Phys. Chem., 99:5724–5731, 1995.

[66] P. Huang, E. Bertaccini, and G. H. Loew. J. Biomol. Struct. Dyn., 12:725–754, 1995.

[67] J. J. López Cascales, M. L. Huertas, and J. García de la Torre. Biophys. Chem., 69:1–8, 1997.

[68] M. Aiello, O. Moran, M. Pisciotta, and F. Gambale. Eur. Biophys. J., 27:211–218, 1998.

[69] K. Tu, M. Tarek, M. L. Klein, and D. Scharf. Biophys. J., 75:2123–2134, 1998.

[70] L. Koubi, M. Tarek, M. L. Klein, and D. Scharf. Biophys. J., 78:800–811, 2000.

[71] L. Koubi, M. Tarek, S. Bandyopadhyay, M. L. Klein, and D. Scharf. Biophys. J., 81:3339–3345, 2001.

[72] J. A. Söderhäll and A. Laaksonen. J. Phys. Chem. B, 105:9308–9315, 2001.

[73] A. Grossfield and T. B. Woolf. Langmuir, 18:198–210, 2002.

[74] D. P. Tieleman and H. J. C. Berendsen. Biophys. J., 74:2786–2801, 1998.

[75] D. P. Tieleman, H. J. C. Berendsen, and M. S. P. Sansom. Biophys. J., 76:1757–1769, 1999.

[76] S.-W. Chiu, S. Subramaniam, and E. Jakobsson. Biophys. J., 76:1929–1938, 1999.

[77] S.-W. Chiu, S. Subramaniam, and E. Jakobsson. Biophys. J., 76:1939–1950, 1999.

[78] Y. Z. Tang, W. Z. Chen, C. X. Wang, and Y. Y. Shi. Eur. Biophys. J., 28:478–488, 1999.

[79] M. Nina, S. Bernecke, and B. Roux. Eur. Biophys. J., 29:439–454, 2000.

[80] R. J. Law, L. R. Forrest, K. M. Ranatunga, P. La Rocca, D. P. Tieleman, and M. S. P. Sansom. Proteins: Struct. Func. Genet., 39:47–55, 2000.

[81] L. R. Forrest, A. Kukol, I. T. Arkin, D. P. Tieleman, and M. S. P. Samson. Biophys. J., 78:55–69, 2000.

[82] D. P. Tieleman and M. S. P. Sansom. Int. J. Quant. Chem., 83:166–179, 2001.

[83] J. Baudry, E. Tajkhorshid, F. Molnar, J. Phillips, and K. Schulten. J. Phys. Chem. B, 105:905–918, 2001.

[84] D. E. Elmore and D. A. Dougherty. Biophys. J., 81:1345–1359, 2001.

[85] C. M. Shepherd, H. J. Vogel, and D. J. Tieleman. Biochim. [sic] J., 370:233–243, 2003.

Anmerkungen

The source is not given.

Sichter
(Klgn), WiseWoman

[2.] Ry/Fragment 038 21 - Diskussion
Zuletzt bearbeitet: 2016-03-15 19:55:05 WiseWoman
Anézo 2003, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

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Untersuchte Arbeit:
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Quelle: Anézo 2003
Seite(n): 61, 62, 201, Zeilen: 61:29-32; 62:1-4; 201:8-11
Currently, simulations typically involve a few hundred of lipids and are confined to a few nanoseconds [40-43]. Lindahl and Edholm [44,45] reported the first 100-ns simulation of a bilayer consisting 64 DPPC molecules, and a larger system of 1024 DPPC molecules was simulated for 10 ns.

The reported MD simulations of lipid bilayers vary in different aspects. At first sight, they may be distinguished by different microscopic interaction parameters (i.e. force fields) and by different macroscopic boundary conditions (i.e. different ensembles). In addition, more technical issues like the choice of the method used for the computation of van der Waals and electrostatic interactions or the length of the time step may differ. This introduces the problem of combining the right conditions and parameters in order to [obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.]


40. Essman, U.; Berkowitz, M. L. Biophys. J. 1999, 76, 2081.

41. Feller, S. E.; Huster, D.; Gawrish, K. J. Am. Chem. Soc. 1999, 8963.

42. Moore, P. B.; Lopez, C. F.; Klein, M. L. Biophys. J. 2001, 81, 2484.

43. Pastor, R. W.; Venable, R. M.; Feller, S. E. Acc. Chem. Res. 2002, 35, 438.

44. Lindahl, E.; Edholm, O. J. Chem. Phys. 2001, 115, 4938.

45. Lindahl, E.; Edholm, O. Biophys. J. 2000, 79, 426.

[page 61]

The numerous MD simulations of lipid bilayers which have been reported vary in different aspects. At first sight, they may be distinguished by different microscopic interaction parameters (i.e. force fields) and by different macroscopic boundary conditions (i.e. different ensembles). In addition, more technical issues like the choice of the method used for the

[page 62]

computation of van der Waals and electrostatic interactions or the length of the time step may differ. This introduces the problem of combining the right conditions and parameters in order to obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.

[page 201]

Currently, simulations typically involve a few hundreds of lipids and are confined to a few nanoseconds [101,220–222]. Recently, Lindahl and Edholm reported the first 100 ns simulation of a bilayer consisting of 64 DPPC molecules, and a larger system containing 1024 lipids, with a linear size of 20 nm, was simulated for 10 ns [156,223].


[101] U. Essmann and M. L. Berkowitz. Biophys. J., 76:2081–2089, 1999.

[156] E. Lindahl and O. Edholm. J. Chem. Phys., 115:4938–4950, 2001.

[220] S. E. Feller, D. Huster, and K. Gawrisch. J. Am. Chem. Soc., 121:8963–8964, 1999.

[221] P. B. Moore, C. F. Lopez, and M. L. Klein. Biophys. J., 81:2484–2494, 2001.

[222] R. W. Pastor, R. M. Venable, and S. E. Feller. Acc. Chem. Res., 35:438–446, 2002.

[223] E. Lindahl and O. Edholm. Biophys. J., 79:426–433, 2000.

Anmerkungen

A source is not given.

Sichter
(Klgn), WiseWoman


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