-
1
-
-
4143138518
-
Methodological issues in lipid bilayer simulations
-
Anézo C, de Vries AH, Höltje HD, Tieleman DP, Marrink SJ (2003) Methodological issues in lipid bilayer simulations. J Phys Chem B 107:9424-9433
-
(2003)
J Phys Chem B
, vol.107
, pp. 9424-9433
-
-
Anézo, C.1
De Vries, A.H.2
Höltje, H.D.3
Tieleman, D.P.4
Marrink, S.J.5
-
2
-
-
77957046824
-
Molecular theory of chain packing, elasticity and lipid-protein interaction in lipid bilayers
-
Lipowsky R, Sackmann E (eds), Elsevier, Amsterdam
-
Ben-Shaul A (1995) Molecular theory of chain packing, elasticity and lipid-protein interaction in lipid bilayers. In: Lipowsky R, Sackmann E (eds) Handbook of biological physics, vol 1. Elsevier, Amsterdam, pp 359-401
-
(1995)
Handbook of Biological Physics
, vol.1
, pp. 359-401
-
-
Ben-Shaul, A.1
-
3
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B (ed). Reidel, Dordrecht
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht, pp 331-342
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
4
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
5
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger O, Edholm O, Jahnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002-2013. The force field description is available at http://moose.bio.ucalgary.ca/Downloads/files/lipid. itp
-
(1997)
Biophys J
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
6
-
-
0033729495
-
Functional consequences of lipid packing stress
-
Bezrukov SM (2000) Functional consequences of lipid packing stress. Curr Opin Colloid Interface Sci 5:237-243
-
(2000)
Curr Opin Colloid Interface Sci
, vol.5
, pp. 237-243
-
-
Bezrukov, S.M.1
-
7
-
-
0000316648
-
Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics
-
Bishop TC, Skeel RD, Schulten K (1997) Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics. J Comput Chem 18:1785-1791
-
(1997)
J Comput Chem
, vol.18
, pp. 1785-1791
-
-
Bishop, T.C.1
Skeel, R.D.2
Schulten, K.3
-
8
-
-
0031027931
-
The lateral pressure profile in membranes: A physical mechanism of general anesthesia
-
Cantor RS (1997a) The lateral pressure profile in membranes: a physical mechanism of general anesthesia. Biochemistry 36:2339-2344
-
(1997)
Biochemistry
, vol.36
, pp. 2339-2344
-
-
Cantor, R.S.1
-
9
-
-
0001098317
-
Lateral pressures in cell membranes: A mechanism for modulation of protein function
-
Cantor RS (1997b) Lateral pressures in cell membranes: a mechanism for modulation of protein function. J Phys Chem 101:1723-1725
-
(1997)
J Phys Chem
, vol.101
, pp. 1723-1725
-
-
Cantor, R.S.1
-
10
-
-
0032857624
-
The influence of membrane lateral pressures on simple geometric models of protein conformational equilibria
-
Cantor RS (1999a) The influence of membrane lateral pressures on simple geometric models of protein conformational equilibria. Chem Phys Lipids 101:45-56
-
(1999)
Chem Phys Lipids
, vol.101
, pp. 45-56
-
-
Cantor, R.S.1
-
11
-
-
0033028551
-
Lipid composition and the lateral pressure profile in bilayers
-
Cantor RS (1999b) Lipid composition and the lateral pressure profile in bilayers. Biophys J 76:2625-2639
-
(1999)
Biophys J
, vol.76
, pp. 2625-2639
-
-
Cantor, R.S.1
-
12
-
-
0031566307
-
Lipids beyond the bilayer
-
de Kruijff B (1997) Lipids beyond the bilayer. Nature 386:129-130
-
(1997)
Nature
, vol.386
, pp. 129-130
-
-
De Kruijff, B.1
-
13
-
-
0000655837
-
Promiscuous ligands and attractive cavities: How do the inhaled anesthetics work?
-
Eckenhoff RG (2001) Promiscuous ligands and attractive cavities: How do the inhaled anesthetics work? Mol Interv 1:258-268
-
(2001)
Mol Interv
, vol.1
, pp. 258-268
-
-
Eckenhoff, R.G.1
-
14
-
-
0037195264
-
Anisotropic motion and molecular dynamics of cholesterol, lanosterol, and ergosterol in lecithin bilayers studied by quasi-elastic neutron scattering
-
Endress E, Heller H, Casalta H, Brown MF, Bayerl TM (2002) Anisotropic motion and molecular dynamics of cholesterol, lanosterol, and ergosterol in lecithin bilayers studied by quasi-elastic neutron scattering. Biochemistry 41:13078-13086
-
(2002)
Biochemistry
, vol.41
, pp. 13078-13086
-
-
Endress, E.1
Heller, H.2
Casalta, H.3
Brown, M.F.4
Bayerl, T.M.5
-
15
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8592
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8592
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
16
-
-
22944452126
-
Impact of cholesterol on voids in phospholipid membranes
-
Falck E, Patra M, Karttunen M, Hyvönen MT, Vattulainen I (2004a) Impact of cholesterol on voids in phospholipid membranes. J Chem Phys 121:12676-12689
-
(2004)
J Chem Phys
, vol.121
, pp. 12676-12689
-
-
Falck, E.1
Patra, M.2
Karttunen, M.3
Hyvönen, M.T.4
Vattulainen, I.5
-
17
-
-
4143051192
-
Lessons of slicing membranes: Interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers
-
Falck E, Patra M, Karttunen M, Hyvönen MT, Vattulainen I (2004b) Lessons of slicing membranes: Interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers. Biophys J 87:1076-1091
-
(2004)
Biophys J
, vol.87
, pp. 1076-1091
-
-
Falck, E.1
Patra, M.2
Karttunen, M.3
Hyvönen, M.T.4
Vattulainen, I.5
-
19
-
-
0000206982
-
Computer simulations of bilayer membranes: Self-assembly and interfacial tension
-
Goetz R, Lipowsky R (1998) Computer simulations of bilayer membranes: Self-assembly and interfacial tension. J Chem Phys 108:7397-7409
-
(1998)
J Chem Phys
, vol.108
, pp. 7397-7409
-
-
Goetz, R.1
Lipowsky, R.2
-
20
-
-
2942675244
-
Lipid bilayer pressure profiles and mechanosensitive channel gating
-
Gullingsrud J, Schulten K (2004) Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys J 86:3496-3509
-
(2004)
Biophys J
, vol.86
, pp. 3496-3509
-
-
Gullingsrud, J.1
Schulten, K.2
-
22
-
-
0035069134
-
Molecular basis of mechanotransduction in living cells
-
Hamill OP, Martinac B (2001) Molecular basis of mechanotransduction in living cells. Physiol Rev 81:685-740
-
(2001)
Physiol Rev
, vol.81
, pp. 685-740
-
-
Hamill, O.P.1
Martinac, B.2
-
23
-
-
0001653388
-
Conformational chain statistics in a model lipid bilayer: Comparison between mean field and Monte Carlo calculations
-
Harries D, Ben-Shaul A (1997) Conformational chain statistics in a model lipid bilayer: Comparison between mean field and Monte Carlo calculations. J Chem Phys 106:1609-1619
-
(1997)
J Chem Phys
, vol.106
, pp. 1609-1619
-
-
Harries, D.1
Ben-Shaul, A.2
-
26
-
-
0037381939
-
Molecular dynamics simulations of phospholipid bilayers with cholesterol
-
Hofsäß C, Lindahl E, Edholm O (2003) Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophys J 84:2192-2206
-
(2003)
Biophys J
, vol.84
, pp. 2192-2206
-
-
Hofsäß, C.1
Lindahl, E.2
Edholm, O.3
-
27
-
-
0035831092
-
Molecular dynamics simulations of stratum corneum lipid models: Fatty acids and cholesterol
-
Höltje M, Förster T, Brandt B, Engels T, von Rybinski W, Höltje HD (2001) Molecular dynamics simulations of stratum corneum lipid models: fatty acids and cholesterol. Biochim Biophys Acta 1511:156-167. The topology file is available from http://www.gromacs.org/topologies/ uploaded_molecules/cholesterol.tgz
-
(2001)
Biochim Biophys Acta
, vol.1511
, pp. 156-167
-
-
Höltje, M.1
Förster, T.2
Brandt, B.3
Engels, T.4
Von Rybinski, W.5
Höltje, H.D.6
-
28
-
-
0035098389
-
The "double lives" of membrane lipids
-
Killian JA, van Meer G (2001) The "double lives" of membrane lipids. EMBO Rep 21:91-95
-
(2001)
EMBO Rep
, vol.21
, pp. 91-95
-
-
Killian, J.A.1
Van Meer, G.2
-
29
-
-
0034535076
-
Lipid bilayers as osmotic response elements
-
Kinnunen PKJ (2000) Lipid bilayers as osmotic response elements. Cell Physiol Biochem 10:243-250
-
(2000)
Cell Physiol Biochem
, vol.10
, pp. 243-250
-
-
Kinnunen, P.K.J.1
-
30
-
-
27944458633
-
The triple layer model: A different perspective on lipid bilayers
-
Lee CC, Petersen NO (2004) The triple layer model: a different perspective on lipid bilayers. J Chin Chem Soc 51:1183-1191
-
(2004)
J Chin Chem Soc
, vol.51
, pp. 1183-1191
-
-
Lee, C.C.1
Petersen, N.O.2
-
31
-
-
0034271962
-
Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations
-
Lindahl E, Edholm O (2000) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J Chem Phys 113:3882-3893
-
(2000)
J Chem Phys
, vol.113
, pp. 3882-3893
-
-
Lindahl, E.1
Edholm, O.2
-
32
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306-317
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
33
-
-
33751158845
-
Simulation of water transport through a lipid membrane
-
Marrink SJ, Berendsen HJC (1994) Simulation of water transport through a lipid membrane. J Phys Chem 98:4155-4168
-
(1994)
J Phys Chem
, vol.98
, pp. 4155-4168
-
-
Marrink, S.J.1
Berendsen, H.J.C.2
-
34
-
-
0030264744
-
Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations
-
Marrink SJ, Berendsen HJC (1996) Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. J Phys Chem 100:16729-16738
-
(1996)
J Phys Chem
, vol.100
, pp. 16729-16738
-
-
Marrink, S.J.1
Berendsen, H.J.C.2
-
35
-
-
0030606012
-
Lateral pressure in membranes
-
Marsh D (1996) Lateral pressure in membranes. Biochim Biophys Acta 1286:183-223
-
(1996)
Biochim Biophys Acta
, vol.1286
, pp. 183-223
-
-
Marsh, D.1
-
36
-
-
0036975483
-
Membrane water-penetration profiles from spin labels
-
Marsh D (2002) Membrane water-penetration profiles from spin labels. Eur Biophys J 31:559-562
-
(2002)
Eur Biophys J
, vol.31
, pp. 559-562
-
-
Marsh, D.1
-
38
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto S, Kollman PA (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952-962
-
(1992)
J Comput Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
39
-
-
0038440700
-
Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions
-
Patra M, Karttunen M, Hyvönen M, 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
-
(2003)
Biophys J
, vol.84
, pp. 3636-3645
-
-
Patra, M.1
Karttunen, M.2
Hyvönen, M.3
Falck, E.4
Lindqvist, P.5
Vattulainen, I.6
-
40
-
-
2342422492
-
Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions
-
Patra M, Karttunen M, Hyvönen MT, Falck E, Vattulainen I (2004a) Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions. J Phys Chem B 108:4485-4494
-
(2004)
J Phys Chem B
, vol.108
, pp. 4485-4494
-
-
Patra, M.1
Karttunen, M.2
Hyvönen, M.T.3
Falck, E.4
Vattulainen, I.5
-
42
-
-
0030734157
-
The cholesterol dependance of activation and fast desensitization of the nicotinic acetylcholine receptor
-
Rankin SE, Addona GH, Kloczewiak MA, Bugge B, Miller KW (1997) The cholesterol dependance of activation and fast desensitization of the nicotinic acetylcholine receptor. Biophys J 73:2446-2455
-
(1997)
Biophys J
, vol.73
, pp. 2446-2455
-
-
Rankin, S.E.1
Addona, G.H.2
Kloczewiak, M.A.3
Bugge, B.4
Miller, K.W.5
-
43
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J Comp Phys 23:327-341
-
(1977)
J Comp Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
44
-
-
0242580832
-
The potential of fluorescent and spin-labeled steroid analogs to mimic natural cholesterol
-
Scheidt HA, Müller P, Herrmann A, Huster D (2003) The potential of fluorescent and spin-labeled steroid analogs to mimic natural cholesterol. J Biol Chem 278:45563-45569
-
(2003)
J Biol Chem
, vol.278
, pp. 45563-45569
-
-
Scheidt, H.A.1
Müller, P.2
Herrmann, A.3
Huster, D.4
-
45
-
-
0037044173
-
Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations
-
Shillcock JC, Lipowsky R (2002) Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations. J Chem Phys 117:5048-5061
-
(2002)
J Chem Phys
, vol.117
, pp. 5048-5061
-
-
Shillcock, J.C.1
Lipowsky, R.2
-
46
-
-
0023662998
-
The effect of cholesterol on lipid dynamics and packing in diether phosphatidylcholine bilayers. X-ray diffraction and 2H-NMR study
-
Siminovitch DJ, Ruocco MJ, Makriyannis A, Griffin RG (1987) The effect of cholesterol on lipid dynamics and packing in diether phosphatidylcholine bilayers. X-ray diffraction and 2H-NMR study. Biochim Biophys Acta 901:191-200
-
(1987)
Biochim Biophys Acta
, vol.901
, pp. 191-200
-
-
Siminovitch, D.J.1
Ruocco, M.J.2
Makriyannis, A.3
Griffin, R.G.4
-
47
-
-
0034529050
-
How cells handle cholesterol
-
Simons K, Ikonen E (2000) How cells handle cholesterol. Science 290:1721-1726
-
(2000)
Science
, vol.290
, pp. 1721-1726
-
-
Simons, K.1
Ikonen, E.2
-
48
-
-
0030901623
-
Mechanosensitive channels of escheria coli - The MscL gene, protein and activities
-
Sukharev SI, Blount P, Martinac B, Kung C (1997) Mechanosensitive channels of escheria coli - the MscL gene, protein and activities. Annu Rev Physiol 59:633-657
-
(1997)
Annu Rev Physiol
, vol.59
, pp. 633-657
-
-
Sukharev, S.I.1
Blount, P.2
Martinac, B.3
Kung, C.4
-
49
-
-
3843063595
-
Correlation of membrane order and dynamics derived from time-resolved fluorescence measurements with solute permeability
-
Sutter M, Fiechter T, Imanidis G (2004) Correlation of membrane order and dynamics derived from time-resolved fluorescence measurements with solute permeability. J Pharmaceut Sci 93:2090-2107
-
(2004)
J Pharmaceut Sci
, vol.93
, pp. 2090-2107
-
-
Sutter, M.1
Fiechter, T.2
Imanidis, G.3
-
50
-
-
0032228279
-
Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylchlonine
-
Templer RH, Castle SJ, Curran AR, Rumbles G, Klug DR (1998) Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylchlonine. Faraday Discuss 111:41-53
-
(1998)
Faraday Discuss
, vol.111
, pp. 41-53
-
-
Templer, R.H.1
Castle, S.J.2
Curran, A.R.3
Rumbles, G.4
Klug, D.R.5
-
51
-
-
0000112789
-
Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
-
Tieleman DP, Berendsen HJC (1996) Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys 105:4871-4880. The topology file is available from http://moose.bio.ucalgary.ca/Downloads/files/dppc.itp
-
(1996)
J Chem Phys
, vol.105
, pp. 4871-4880
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
-
52
-
-
0031438285
-
A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
-
Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270
-
(1997)
Biochim Biophys Acta
, vol.1331
, pp. 235-270
-
-
Tieleman, D.P.1
Marrink, S.J.2
Berendsen, H.J.C.3
-
53
-
-
4544369164
-
A generalized reaction field method for molecular dynamics simulations
-
Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451-5459
-
(1995)
J Chem Phys
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Van Gunsteren, W.F.4
-
54
-
-
0031752966
-
Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer
-
Tu K, Klein ML, Tobias DJ (1998) Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer. Biophys J 75:2147-2156
-
(1998)
Biophys J
, vol.75
, pp. 2147-2156
-
-
Tu, K.1
Klein, M.L.2
Tobias, D.J.3
-
55
-
-
7044232102
-
Nonbilayer lipids affect peripheral and integral membrane proteins via changes in the lateral pressure profile
-
van den Brink-van der Laan E, Killian JA, de Kruijff B (2004) Nonbilayer lipids affect peripheral and integral membrane proteins via changes in the lateral pressure profile. Biochim Biophys Acta 1666:275-288
-
(2004)
Biochim Biophys Acta
, vol.1666
, pp. 275-288
-
-
Van Den Brink-Van Der Laan, E.1
Killian, J.A.2
De Kruijff, B.3
-
56
-
-
0022389171
-
Cholesterol and the cell membrane
-
Yeagle PL (1985) Cholesterol and the cell membrane. Biochim Biophys Acta 822:267-287
-
(1985)
Biochim Biophys Acta
, vol.822
, pp. 267-287
-
-
Yeagle, P.L.1
|