Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields
Lula Rosso,
Ian R. Gould,
Lula Rosso
Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
Search for more papers by this authorCorresponding Author
Ian R. Gould
Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
Department of Chemistry, Imperial College London, SW7 2AZ, United KingdomSearch for more papers by this authorLula Rosso,
Ian R. Gould,
Lula Rosso
Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
Search for more papers by this authorCorresponding Author
Ian R. Gould
Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
Department of Chemistry, Imperial College London, SW7 2AZ, United KingdomSearch for more papers by this authorAbstract
Two fully hydrated pure-species phospholipids bilayers, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphorylcholine (DOPC), in the fluid phase and explicit solvent have been studied using molecular dynamics simulation. Atom interactions were modeled using recently developed force fields based on AMBER with full atomistic details. Several representative liquid phase properties for the structure and dynamics of lipids with different length of hydrocarbon chains and different level of saturation have been reproduced without artificially biasing the system in order to match experimental data. In particular, as the new GAFF (General Amber Force Field) has not been explicitly developed to reproduce lipid characteristics and is naturally compatible with standard AMBER nucleic acids and proteins parameters, it is here proven a promising tool to study mixed lipid–protein processes as protein activity dependence on membrane composition, permeation of solute across membranes, and other cellular processes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
References
- 1 Ash, W.;Zlomislic, M.;Oloo, E.;Tieleman, D. Biochim Biophys Acta 2004, 1666, 158.
- 2 Feller, S. Curr Opin Coll Interafce Sci 2000, 5, 217.
- 3 Roux, B.;Woolf, T. B. Molecular Dynamics Simulation of Pf1 Coat Protein in a Phospholipid Bilayer, In: K. Merz; B. Roux, Eds. Biological Membranes: A Molecular Perspective from Computation and Experiments. Birkhauser: Cambridge, MA. 1996; pp. 555–587.
- 4 Saiz, L.;Bandyopadhyay, S.;Klein, M. Bioscience Rep 2002, 22, 151.
- 5 Tieleman, D;Marrink, S.;Berendsen, H. Biochim Biophys Acta 1997, 1331, 235.
- 6 Nagle, J.;Tristam-Nagle, S. Biochim Biophys Acta 2000, 1469, 159.
- 7 Chiu, S.;Clark, M.;Jakobsson, E.;Subramaniam, S.;Scott, H. J Phys Chem B 1999, 103, 6323.
- 8 van Gunsteren, W.;Berendsen, H. Gromos96. Biomos; ETH Hnggerberg: Zürich, CH, 1996.
- 9 Repakova, J.;Holopainen, J.;Karttunen, M.;Vattulainen, I. J Phys Chem B 2006, 110, 15403.
- 10 Xu, Y.;Barrantes, F.;Luo, X.;Chen, K.;Shen, J.;Jiang, H. J Am Chem Soc 2005, 127, 1291.
- 11 Smondyrev, A.;Berkowitz, M. J Comp Chem 1998, 20, 531.
- 12 Feller, S.;MacKerell, A. J Phys Chem B 2000, 104, 7510.
- 13 Feller, S.;Yin, D.;Pastor, R.;MacKerell, A.,Jr. Biophys J 1997, 73, 2269.
- 14 Pitman, M.;Grossfield, A.;Suits, F.;Feller, S. J Am Chem Soc 2005, 127, 4576.
- 15 Cornell, W. D.;Cieplak, P.;Bayly, C. I.;Gould, I. R.;Merz, K. M.,Jr.;Ferguson, D. M.;Spellmeyer, D. C.;Fox, T.;Caldwell, J. W.;Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
- 16 Lopez, C.;Nielsen, S.;Klein, M.;Moore, P. J Phys Chem B 2004, 108, 6603.
- 17 Moore, P.;Lopez, C.;Klein, M. Biophys J 2001, 81, 2484.
- 18 Liu, Y.;Nagle, J. Phys Rev E 2004, 69, 040901.
- 19 Kuĉerka, N.;Liu, Y.;Chu, N.;Petrache, H.;Tristam-Nagle, S.;Nagle, J. Biophys J 2005, 88, 2626.
- 20 Wang, J.;Wolf, R.;Caldwell, J.;Kollman, P.;Case, D. J Comp Chem 2004, 25, 1157.
- 21 Huang, P.;Perez, J.;Loew, G. J Biomol Struct Dyn 1994, 11, 927.
- 22 Lindahl, E.;Edholm, O. Biophys J 2000, 79, 426.
- 23 Wang, W.;Donini, O.;Reyes, C.;Kollman, P. Annu Rev Biophys Biomol Struct 2001, 30, 211.
- 24 Wiener, M.;White, S. Biophys J 1992, 61, 433.
- 25 Chiu, S.;Jakobsson, E.;Subramaniam, S.;Scott, H. Biophys J 1999, 77, 2462.
- 26 Mashl, R.;Scott, H.;Subramaniam, S.;Jakobsson, E. Biophys J 2001, 81, 3005.
- 27 Zubrzycki, I.;Xu, Y.;Madrid, M.;Tang, P. J Chem Phys 2000, 112, 3437.
- 28 Gurtovenko, A.;Patra, M.;Karttunen, M.;Vattulainen, I. Biophys J 2004, 86, 3461.
- 29 Pasenkiewicz-Gierula, M.;Takaoka, Y.;Miyagawa, H.;Kitamura, K.;Kusumi, A. Biophys J 1999, 76, 1228.
- 30 de Vries, A.;Mark, A.;Marrink, S. Phys Chem B 2004, 108, 2454.
- 31 Tristam-Nagle, S.;Petrache, H.;Nagle, J. Biophys J 1998, 75, 917.
- 32 Costigan, S.;Booth, P.;Templer, R. Biochim Biophys Acta 2000, 1468, 41.
- 33 Tuckerman, M. E.;Yarne, D. A.;Samuelson, S. O.;Martyna.G. J. Comp Phys Comm 2000, 128, 333.
- 34 Rog, T.;Murzyn, K.;Gurbiel, R.;Takaoka, Y.;Kusumi, A.;Pasenkiewicz-Gierula M. J Lipid Res 2004, 45, 326.
- 35 Jorgensen, W.;Tirado-Rives, J. J Am Chem Soc 1988, 110, 1657.
- 36 Anézo, C.;de Vries, A.;Höltje, H.;Tieleman, D.;Marrink, S. J Phys Chem 2003, 107, 9424.
- 37 Patra, M.;Karttunen, M.;Hyvönen, M.;Falck, E.;Lindqvist, P.;Vattulainen, I. Biophys J 2003, 84, 3636.
- 38 Case, D.;Darden, T.;Cheatham, T.III;Simmerling, C.;Wang, J.;Duke, R.;Luo, R.;Merz, K.;Wang, B.;Pearlman, D.;Crowley, M.;Brozell, S.;Tsui, V.;Gohlke, H.;Mongan, J.;Hornak, V.;Cui, G.;Beroza, P.;Shafmeister, C.;Caldwell, J.;Ross, W.;Kollman, P. Amber 8. University of California; San Francisco, CA, 2004.
- 39 Cornell, W. D.;Cieplak, P.;Bayly, C. I.;Kollman, P. J Am Chem Soc 1993, 115, 9620.
- 40 Wang, J.;Cieplak, P.;Kollman, P. J Comp Chem 2000, 21, 1049.
- 41 Frisch, M. J.;Trucks, G. W.;Schlegel, H. B.;Scuseria, G. E.;Robb, M. A.;Cheeseman, J. R.;Montgomery, J. A.,Jr.;Vreven, T.;Kudin, K. N.;Burant, J. C.;Millam, J. M.;Iyengar, S. S.;Tomasi, J.;Barone, V.;Mennucci, B.;Cossi, M.;Scalmani, G.;Rega, N.;Petersson, G. A.;Nakatsuji, H.;Hada, M.;Ehara, M.;Toyota, K.;Fukuda, R.;Hasegawa, J.;Ishida, M.;Nakajima, T.;Honda, Y.;Kitao, O.;Nakai, H.;Klene, M.;Li, X.;Knox, J. E.;Hratchian, H. P.;Cross, J. B.;Bakken, V.;Adamo, C.;Jaramillo, J.;Gomperts, R.;Stratmann, R. E.;Yazyev, O.;Austin, A. J.;Cammi, R.;Pomelli, C.;Ochterski, J. W.;Ayala, P. Y.;Morokuma, K.;Voth, G. A.;Salvador, P.;Dannenberg, J. J.;Zakrzewski, V. G.;Dapprich, S.;Daniels, A. D.;Strain, M. C.;Farkas, O.;Malick, D. K.;Rabuck, A. D.;Raghavachari, K.;Foresman, J. B.;Ortiz, J. V.;Cui, Q.;Baboul, A. G.;Clifford, S.;Cioslowski, J.;Stefanov, B. B.;Liu, G.;Liashenko, A.;Piskorz, P.;Komaromi, I.;Martin, R. L.;Fox, D. J.;Keith, T.;Al-Laham, M. A.;Peng, C. Y.;Nanayakkara, A.;Challacombe, M.;Gill, P. M. W.;Johnson, B.;Chen, W.;Wong, M. W.;Gonzalez, C.;Pople, J. A. Gaussian 03, Revision C. 01. Gaussian, Inc.; Wallinford, CT, 2004.
- 42 Jorgensen, W. J Chem Phys 1983, 79, 926.
- 43 Essman, U.;Perera, L.;Berkowitz, M.;Darden, T.;Lee, H.;Pedersen, L. J Chem Phys 1995, 103, 8577.
- 44 Press, W.;Teukolsky, S.;Vetterling, W.;Flannery, B. Numerical Recipes, 2nd edn., Cambridge: Cambridge University Press, 1992.
- 45 Pastor, R.;Brooks, B.;Szabo, A. Mol Phys 1988, 65, 1409.
- 46 Pastor, R. L. R.;Brooks, B. Biopolimers 1992, 32, 523.
- 47 Berendsen, H.;Postma, W. v. G. J. P. M.;Nola, A. D.;Haak, J. Chem Phys 1984, 81, 3684.
- 48 Ryckaert, J.-P.;Ciccotti, G.;Berendsen, H. J. C. J Comp Phys 1977, 23, 327.
- 49 Izaguirre, J.;Catarello, D.;Wozniak, J.;Skeel, R. J Chem Phys 2001, 114, 2090.
- 50 Petrache, H.;Dodd, S.;Brown, M. Biophys J 2000, 79, 3172.
- 51 Simon, S.;McIntosh, T. Methods Enzymol 1986, 127, 511.
- 52 Tristam-Nagle, S.;J. L.;Liu, Y.;Nagle, J. Biophys J 2002, 83, 332.
- 53 Benz, R.;Cástro-Roman, F.;Tobias, D.;White, S. Biophys J 2005, 88, 805.
- 54 Petrache, H.;Feller, S.;Nagle, J. Biophys J 1997, 70, 2237.
- 55 Lynch, D.;Reggio, P. J Med Chem 2005, 48, 4824.
- 56 Seelig, J.;Waespe-Ŝarĉević N. Biochemistry 1978, 17, 3310.
- 57 Urbina, J.;Moreno, B.;Arnold, W.;Taron, C.;Orlean, P.;Oldfield, E. Biophys J 1998, 75, 1372.
- 58 Habiger, R.;Cassal, J.;Kempen, H. J. M.;Seelig, J. Biochim Biophys Acta 1992, 1103, 69.
- 59 Hristova, K.;White, S. Biophys J 1998, 74, 2419.
- 60 Ulrich, A.;Watts, A. Biophys J 1994, 66, 1441.
- 61 Marrink, S.;Berendsen, H. J. C. J Phys Chem 1994, 98, 4155.
- 62 Lee, C.;McCammon, J.;Rossky, P. J Chem Phys 1984, 80, 4448.
- 63 Filippov, A.;Oradd, G.;Lindblom, G. Langmuir 2003, 19, 6397.
- 64 Benda, A.;Benes, M.;Marecek, V.;Lhotsky, A.;Hermens, W.;Hof, M. Langmuir 2003, 19, 4120.
- 65 Kusba, J.;Li, L.;Gryczynski, I.;Piszczek, G.;Johnson, M.;Lakowicz, J. Biophys J 2002, 82, 1358.
- 66 Chiu, S.;Clark, M.;Balaji, V.;Subramaniam, S.;Scott, H.;Jakobsson, E. Biophys J 1995, 69, 1230.
