Molecular dynamics simulations of unsaturated lipid bilayers: effects of varying the numbers of double bonds

Akutsu H, Nagamori T (1991) Conformational analysis of the polar head group in phosphatidylcholine bilayers. A structural change induced by cations. Biochemistry 30:4510–4516

Anezo C, de Vries AH, Höltje H-D, Tieleman DP, Marrink S-J (2003) Methodological issues in lipid bilayer simulations. J Phys Chem B 107:9424–9433

Bachar M, Brunelle P, Tieleman DP, Rauk A (2004) Molecular dynamics simulation of a polyunsaturated lipid bilayer susceptible to lipid peroxidation. J Phys Chem B 108:7170–7179

Baenziger JE, Jarrel HC, Hill RJ, Smith ICP (1991) Average structural and motional properties of a diunsaturated acyl chain in a lipid bilayer: effects of two cis-unsaturated double bonds. Biochemistry 30:894–903

Bandyopadhyay S,Tarek M, Klein ML (1998) Computer simulation studies of amphiphilic interfaces. Curr Opin Colloid Interface Sci 3:242–246

Berendsen HJC,Tieleman DP (1998) Molecular dynamics: studies of lipid bilayers. In: Encyclopedia of computational chemistry. Wiley, London, pp 1639–1650

Berger O, Edholm O, Jähnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002–2013

Birukov KG, Leitinger N, Bochkov VN, Garcia JGN (2004) Signal transduction pathways activated in human pulmonary endothelial cells by OxPAPC, a bioactive component of oxidized lipoproteins. Microvasc Res 67:18–28

Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217

Ceccarelli M, Marchi M (1998) Molecular dynamics simulation of POPC at low hydration near the liquid crystal phase transition. Biochimie 80:415–419

Darden T, York D, Pedersen LG (1993) Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

Demel RA, Geurts van Kessel WSM, van Deenen LLM (1972) The properties of polyunsaturated lecithins in monolayers and liposomes and the interactions of these lecithins with cholesterol. Biochim Biophys Acta 266:26–40

Douliez J-P, Leonard A,Dufourc EJ (1995) Restatement of order parameters in biomembranes: Calculation of C-C bond order parameters from CD quadrupolar splittings. Biophys J 68:1727–1739

Eldho NV, Feller SE, Tristam-Nagle S, Polozov IV,Gawrisch K (2003) Polyunsaturated docosahexaenoic vs docosapentaenoic acid—differences in lipid matrix properties from the loss of one double bond. J Am Chem Soc 125:6409–6421

Essmann U, Berkowitz ML (1999) Dynamical properties of phospholipid bilayers from computer simulation. Biophys J 76:2081–2089

Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593

Esterbauer H, Dieber-Rotheneder M, Waeg G, Striegl G, Jürgens G (1990) Biochemical, structural and functional properties of oxidized low-density lipoprotein. Chem Res Toxicol 3:77–92

Evans RW, Williams MA, Tinoco J (1987) Surface areas of 1-palmitoyl phosphatidylcholines and their interactions with cholesterol. Biochem J 245:455–462

Feller SE (2000) Molecular dynamics simulations of lipid bilayers. Curr Opin Colloid Interface Sci 5:217–223

Feller SE, MacKerell AD Jr (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B 104:7510–7515

Feller SE, Zhang Y, Pastor Y, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613–4621

Feller SE, Pastor M, Rojnuckarin A, Bogusz S, Brooks BR (1996) Effect of electrostatic force truncation on interfacial and transport properties of water. J Phys Chem 100 :17011–17020

Feller SE, Gawrisch K, MacKerell AD Jr (2002) Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties. J Am Chem Soc 124:318–326

Fettiplace R, Haydon DA, (1980) Water permeability of lipid membranes. Physiol Rev 60:510–550

Flewelling R, Hubbell W (1986) The membrane dipole potential in a total membrane potential model. Applications to hydrophobic ion interactions with membranes. Biophys J 49:541–552

Gawrisch K, Ruston D, Zimmerberg J, Parsegian VA, Rand RP, Fuller N (1992) Membrane dipole potentials, hydration forces, and the ordering of water at membrane surfaces. Biophys J 61:1213–1223

Gawrisch K, Eldho NV, Holte LL (2003) The structure of DHA in phospholipid membranes. Lipids 38:445–452

Heller H, Schaefer M, Schulten K (1993) Molecular dynamics simulation of a bilayer of 200 lipids in a gel and in the liquid-crystal phase. J Phys Chem 97:8343–8360

Holte LL, Senaka AP, Sinnwell T, Gawrisch K (1995) 2H nuclear magnetic resonance order parameter profiles suggest a change of molecular shape for phosphatidylcholines containing a polyunsaturated acyl chain. Biophys J 68:2396–2403

Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697

Huang P, Perez JJ, Loew GH (1994) Molecular dynamics simulations of phospholipid bilayers. J Biomol Struct Dyn 11:927–956

Huber T, Rajamoorthi K, Kurze V, Beyer K, Brown MF (2002) Structure of docosahexaenoic acid-containing phospholipid bilayers studied by 2H NMR and molecular dynamics simulations. J Am Chem Soc 124:298–309

Huster D, Jin AJ, Arnold K, Gawrisch K (1997) Water permeability of polyunsaturated lipid membranes measured by 17 O NMR. Biophys J 73:855–864

Hyvönen MT, Kovanen PT (2003) Molecular dynamics simulation of sphingomyelin bilayer. J Phys Chem B 107:9102–9108

Hyvönen MT, Ala-Korpela M, Vaara J, Rantala TT,Jokisaari J (1995) Effects of two double bonds on the hydrocarbon interior of a phospholipid bilayer. Chem Phys Letters 246:300–306

Hyvönen MT, Rantala TT,Ala-Korpela M (1997a) Structure and dynamic properties of diunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine lipid bilayer from molecular dynamics simulation. Biophys J 73:2907–2923

Hyvönen MT, Ala-Korpela M, Vaara J,Rantala TT,Jokisaari J (1997b) Inequivalence of single CHa and CHb methylene bonds in the interior of a diunsaturated lipid bilayer from a molecular dynamics simulation. Chem Phys Lett 268:55–60

In’t Veld G, Driessen AJM, Konings WN (1992) Effect of the unsaturation of phospholipid acyl chains on leucine transport of Lactococcus lactis and membrane permeability. Biochim Biophys Acta 1108:31–39

Jensen MO, Mouritsen OG, Peters GH (2004) Simulations of a membraneanchored peptide: structure, dynamics, and influence on bilayer properties. Biophys J 86:3556–3575

Jorgensen WL, Chandrasekhar L, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

Koenig BW, Strey HH,Gawrisch K (1997) Membrane lateral compressibility determined by NMR and X-ray diffraction: effect of acyl chain polyunsaturation. Biophys J 73:1954–1966

Koubi L, Saiz L, Tarek M,Scharf D, Klein ML (2003) Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer. J Phys Chem B 107:14500–14508

Marrink S-J, Jähnig F, Berendsen HJC (1996b) Proton transfer across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys J 71:632–647

Marrink SJ, Sok RM, Berendsen HJC (1996a) Free volume properties of a simulated lipid membrane. J Chem Phys 104:9090–9099

McIntosh TJ, Simon SA (1986) Hydration force and bilayer deformation: A reevaluation. Biochemistry 25:4058–4066

McIntosh TJ, Simon SA, Needham D, Huang C (1992) Interbilayer interactions between sphongomyelin and sphingomyeli/cholesterol bilayers. Biochemistry 31:2020–2024

Mendelsohn R, Davies MA, Schuster HF, Zu ZG, Bittman R (1991) CD2 rocking modes as quantitative infrared probes of one-, two-, and three-bond conformational disorder in dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylcholine/cholesterol mixtures. Biochemistry 30:8558–8563

Merz KM Jr (1997) Molecular dynamics simulations of lipid bilayers. Curr Opin Struct Biol 7:511–517

Mitchell DC, Litman BJ (1998) Molecular order and dynamics in bilayers consisting of highly polyunsaturated phospholipids. Biophys J 74:879–891

Murzyn K, Rog T, Jezierski G, Takaoka Y, Pasenkiewicz-Gierula M (2001) Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys J 81:170–183

Nagle JF, Tristam-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469:159–195

Pasenkiewicz-Gierula M, Rog T, Grochowski J,Serda P, Czarnecki R, Librowski T, Lochynski S (2003) Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation. Biophys J 85:1248–1258

Pastor RW (1994) Molecular dynamics and Monte Carlo simulations of lipid bilayers. Curr Opin Struct Biol 4:486–492

Patra M, Karttunen M, Hyvönen MT, Falck E, Lindqvist P, Vattulainen I (2003) Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J 84:3636–3645

Peterson U, Mannock DA,Lewis RNAH, Pohl P, McElhaney RN, Pohl EE (2002) Origin of membrane dipole potential: contribution of the phospholipid fatty acid chains. Chem Phys Lipids 117:19–27

Rabinovich AL, Ripatti PO, Balabaev NK, Leermakers FAM (2003) Molecular dynamics simulations of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to self-consistent field modeling. Phys Rev E 67:11909–11923

Rog T, Murzyn K, Gurbiel R, Takaoka Y,Kusumi A, Pasenkiewicz-Gierula M (2004) Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study. J Lipid Res 45:326–336

Sachs JN, Nanda H, Petrache HI, Woolf TB (2004) Changes in phosphatidylcholine headgrouptilt anf water order induced by monovalent salts: molecular dynamics simulation. Biophys J 86:3772–3782

Saiz L, Bandyopadhyay S, Klein ML (2001) Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations. Biosci Rep 22:151–173

Saiz L, Klein ML (2001a) Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations. Biophys J 81:204–216

Saiz L, Klein ML (2001b) Influence of highly polyunsaturated lipid acyl chains of biomembranes on the NMR order parameters. J Am Chem Soc 123:7381–7387

Schamberger J, Clarke RJ (2002) Hydrophobic ion hydrationand the magnitude of the dipole potential. Biophys J 82:3081–3088

Schlenkrich M, Brickmann J, MacKerell Jr AD, Karplus M (1996) An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In: Merz KM Jr , Roux B (eds) Biological membranes: a molecular perspective from computation and experiment. Birkhäuser, Boston, pp 31–81

Seelig A, Niederberger W (1974) Deuterium-labeled lipids as structural probes in liquid-crystalline bilayers: a deuterium magnetic resonance study. J Am Chem Soc 96:2069–2072

Seelig A, Seelig J (1974) The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry 13:4839–4845

Seelig A, Seelig J (1977) Effect of single cis double bond on the structure of a phospholipid bilayer. Biochemistry 16:45–50

Seelig J,Waespe-Sarcevic N (1978) Molecular order in cis and trans unsaturated phospholipid bilayer. Biochemistry 17:3311–3315

Seelig J, Seelig A (1980) Lipid conformation in model membranes and biological membranes. Q Rev Biophys 13:19–61

Shinoda W, Shimizu M, Okazaki S (1998) Molecular dynamics study on electrostatic properties of a lipid bilayer: polarization, electrostatic potential, and the effects on structure and dynamics of water near the interface. J Phys Chem B 102:6647–6654

Simon SA, McIntosh TJ (1989) Magnitude of the solvation pressure depends on dipole potential. Proc Natl Acad Sci USA 86:9263–9267

Stillwell W, Wassal SR (2003) Docosahexaenoic acid: membrane properties of a unique fatty acid. Chem Phys Lipids 126:1–27

Tieleman DP, Marrink S-J,Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235–270

Tobias DJ, Tu K, Klein ML (1997) Atomic-scale molecular dynamics simulations of lipid membranes. Curr Opin Colloid Interface Sci 2:15–26

Tomita M, Baker RC, Ando S, Santoro TJ (2004) Arachidonoyl-phospholipid remodeling in proliferating murine T cells. Lipids Health Dis 3:1–12

Venable RM, Pastor RW (2002) Molecular dynamics simulation of water wires in a lipid bilayer and water/octane model systems. J Chem Phys 116:2663–2664

Vorobyov I, Yappert MC, DuPre DB (2002) Energetic and topological analyses of cooperative sH and pH-bonding interactions. J Phys Chem A 106:10691–10699

Walter L, Stella N (2003) Endothelin-1 increases 2-arachidonoyl glycerol (2-AG) production in astrocytes. Glia 44:85–90

Walton KA, Hsieh X, Gharavi N, Wang S, Wang G, Yeh M, Cole AL, Berliner JA (2003) Receptors involved in the oxidized 1-palmitoyl-2-arachidonoylsn-glycero-3-phosphorylcholine-mediated synthesis of interleukin-8. J Biol Chem 278:29661–29666

Wiener MC, White SH (1992) Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of X-ray and neutron diffraction data. III. Complete structure. Biophys J 61:434–447

Zeng Y,Han X,Gross RW (1998) Phospholipid subclass specific alterations in the passive ion permeability of membrane bilayers: separation of enthalpic and entropic contributions to transbilayer ion flux. Biochemistry 37:2346–2355