269
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
61. Ozdirekcan S, Rijkers DTS, Killian JA (2004) Influence of flanking residues on tilt and
rotation angles of transmembrane peptides in lipid bilayers. A solid-state
2
H NMR study.
Biochemistry 44(3):1004–1012. doi:10.1021/bi0481242
62. Strandberg E, Ozdirekcan S, Killian JA (2004) Tilt angles of transmembrane model peptides
in oriented and non-oriented lipid bilayers as determined by
2
H solid-state NMR. Biophys J
86(6):3709–3721
63. Ozdirekcan S, Etchebest C, Fuchs PF (2007) On the orientation of a designed transmembrane
peptide: toward the right tilt angle? J Am Chem Soc 129(49):15174–15181
64. Esteban-Martın S, Salgado J (2007) The dynamic orientation of membrane-bound peptides:
bridging simulations and experiments. Biophys J 93(12):4278–4288
65. Holt A, Koehorst RBM, Killian JA (2009) Tilt and rotation angles of a transmembrane model
peptide as studied by fluorescence spectroscopy. Biophys J 97(8):2258–2266
66. Monticelli L, Tieleman DP, Fuchs PFJ (2010) Interpretation of
2
H-NMR experiments on
the orientation of the transmembrane helix WALP23 by computer simulations. Biophys J
99(5):1455–1464
67. Holt A, Killian JA (2010) Orientation and dynamics of transmembrane peptides: the power of
simple models. Eur Biophys J 39(4):609–621. doi:10.1007/s00249–009-0567-1
68. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7(8):306–317
69. Van Gunsteren WF, Berendsen HJC (1987) Gromos-87 manual. Biomos BV, Nijenborgh 4,
9747 AG Groningen, Netherlands, p 331–342
70. Van Buuren AR, Marrink SJ, Berendsen HJC (1993) A molecular dynamics study of the
decane/water interface. J Phys Chem 97(36):9206–9212
71. Mark AE, van Helden SP, Smith PE, Janssen LHM, van Gunsteren WF (1994) Convergence
properties of free energy calculations: α-cyclodextrin complexes as a case study. J Am Chem
Soc 116(14):6293–6302
72. HyperChem(TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA
73. Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes:
molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331(3):235–
270
74. Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta
1469(3):159–195
75. Berger O, Edholm O, Jahnnig F (1997) Molecular dynamics simulations of a fluid bilayer of
dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72(5):2002–2013
76. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) Procheck—a program
to check the stereochemical quality of protein structures. J Appl Cryst 26(2):283–291
doi:10.1107/S0021889892009944
77. Tristam-Nagle S, Liu Y, Legleiter J, Nagle JF (2002) Structure of gel phase DMPC determined by X-ray diffraction. Biophys J 83(6):3324–3335
78. Tu K, Tobias DJ, Blasie JK, Klein ML (1996) Molecular dynamics investigation of structure
of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. Biophys J 70(2):595–
608
79. Tieleman DP, Berendsen HJC (1996) Molecular dynamics simulations of fully hydrated
DPPC with different macroscopic boundary conditions and parameters. J Chem Phys
105(11):4871–4880
80. Egberts E (1988) Molecular dynamics simulation of multibilayer membranes, Ph.D. Thesis,
University of Groningen, Netherlands
81. Nagle JF (1993) Area/lipid of bilayers from NMR. Biophys J 64(5):1476–1481
82. Damodaran KV, Merz KM Jr (1994) A comparison of DMPC- and DLPE-based lipid bilayers. Biophys J 66(4):1076–1067
83. Small DM (1986) The physical chemistry of lipids: from alkanes to phospholipids plenum.
Plenum Press, New York
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
61. Ozdirekcan S, Rijkers DTS, Killian JA (2004) Influence of flanking residues on tilt and
rotation angles of transmembrane peptides in lipid bilayers. A solid-state
2
H NMR study.
Biochemistry 44(3):1004–1012. doi:10.1021/bi0481242
62. Strandberg E, Ozdirekcan S, Killian JA (2004) Tilt angles of transmembrane model peptides
in oriented and non-oriented lipid bilayers as determined by
2
H solid-state NMR. Biophys J
86(6):3709–3721
63. Ozdirekcan S, Etchebest C, Fuchs PF (2007) On the orientation of a designed transmembrane
peptide: toward the right tilt angle? J Am Chem Soc 129(49):15174–15181
64. Esteban-Martın S, Salgado J (2007) The dynamic orientation of membrane-bound peptides:
bridging simulations and experiments. Biophys J 93(12):4278–4288
65. Holt A, Koehorst RBM, Killian JA (2009) Tilt and rotation angles of a transmembrane model
peptide as studied by fluorescence spectroscopy. Biophys J 97(8):2258–2266
66. Monticelli L, Tieleman DP, Fuchs PFJ (2010) Interpretation of
2
H-NMR experiments on
the orientation of the transmembrane helix WALP23 by computer simulations. Biophys J
99(5):1455–1464
67. Holt A, Killian JA (2010) Orientation and dynamics of transmembrane peptides: the power of
simple models. Eur Biophys J 39(4):609–621. doi:10.1007/s00249–009-0567-1
68. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7(8):306–317
69. Van Gunsteren WF, Berendsen HJC (1987) Gromos-87 manual. Biomos BV, Nijenborgh 4,
9747 AG Groningen, Netherlands, p 331–342
70. Van Buuren AR, Marrink SJ, Berendsen HJC (1993) A molecular dynamics study of the
decane/water interface. J Phys Chem 97(36):9206–9212
71. Mark AE, van Helden SP, Smith PE, Janssen LHM, van Gunsteren WF (1994) Convergence
properties of free energy calculations: α-cyclodextrin complexes as a case study. J Am Chem
Soc 116(14):6293–6302
72. HyperChem(TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA
73. Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes:
molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331(3):235–
270
74. Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta
1469(3):159–195
75. Berger O, Edholm O, Jahnnig F (1997) Molecular dynamics simulations of a fluid bilayer of
dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72(5):2002–2013
76. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) Procheck—a program
to check the stereochemical quality of protein structures. J Appl Cryst 26(2):283–291
doi:10.1107/S0021889892009944
77. Tristam-Nagle S, Liu Y, Legleiter J, Nagle JF (2002) Structure of gel phase DMPC determined by X-ray diffraction. Biophys J 83(6):3324–3335
78. Tu K, Tobias DJ, Blasie JK, Klein ML (1996) Molecular dynamics investigation of structure
of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. Biophys J 70(2):595–
608
79. Tieleman DP, Berendsen HJC (1996) Molecular dynamics simulations of fully hydrated
DPPC with different macroscopic boundary conditions and parameters. J Chem Phys
105(11):4871–4880
80. Egberts E (1988) Molecular dynamics simulation of multibilayer membranes, Ph.D. Thesis,
University of Groningen, Netherlands
81. Nagle JF (1993) Area/lipid of bilayers from NMR. Biophys J 64(5):1476–1481
82. Damodaran KV, Merz KM Jr (1994) A comparison of DMPC- and DLPE-based lipid bilayers. Biophys J 66(4):1076–1067
83. Small DM (1986) The physical chemistry of lipids: from alkanes to phospholipids plenum.
Plenum Press, New York