We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach.

1.
R. B. Gennis, Biomembranes: Molecular Structure and Function (Springer, New York, 1989).
2.
M.
Bloom
,
E.
Evans
, and
O. G.
Mouritsen
,
Q. Rev. Biophys.
24
,
293
(
1991
).
3.
Structure and Dynamics of Membranes: From Cells to Vesicles, edited by R. Lipowsky and E. Sackmann (Elsevier, Amsterdam, 1995).
4.
Biological Membranes: A Molecular Perspective from Computation and Experiment, edited by J. K. M. Merz and B. Roux (Birkhäuser, Boston, 1996).
5.
B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson, Molecular Biology of the Cell, 3rd. ed. (Garland Publishing, New York, 1994).
6.
Lipid Bilayers: Structure and Interactions, edited by J. Katsaras and T. Gutberlet (Springer, Berlin, 2001).
7.
M. J.
Zuckermann
,
M.
Bloom
,
J. H.
Ipsen
et al.,
Methods Enzymol.
383
,
198
(
2004
).
8.
D. P.
Tieleman
,
S. J.
Marrink
, and
H. J. C.
Berendsen
,
Biochim. Biophys. Acta
1331
,
235
(
1997
).
9.
S. E.
Feller
,
Curr. Opin. Colloid Interface Sci.
5
,
217
(
2000
).
10.
H. L.
Scott
,
Curr. Opin. Struct. Biol.
12
,
495
(
2002
).
11.
L.
Saiz
,
S.
Bandyopadhyay
, and
M. L.
Klein
,
Biosci Rep.
22
,
151
(
2002
).
12.
L.
Saiz
and
M. L.
Klein
,
Acc. Chem. Res.
35
,
482
(
2002
).
13.
I. Vattulainen and M. Karttunen, in Computational Nanotechnology, edited by M. Rieth and W. Schommers (Americal Scientific Press, in press).
14.
S. W.
Chiu
,
S.
Vasudevan
,
E.
Jakobsson
,
R. J.
Mashl
, and
H. L.
Scott
,
Biophys. J.
85
,
3624
(
2003
).
15.
C.
Hofsäß
,
E.
Lindahl
, and
O.
Edholm
,
Biophys. J.
84
,
2192
(
2003
).
16.
A. H.
de Vries
,
A. E.
Mark
, and
S. J.
Marrink
,
J. Am. Chem. Soc.
126
,
4488
(
2004
).
17.
K.
Simons
and
E.
Ikonen
,
Nature (London)
387
,
569
(
1997
).
18.
S.
Mayor
and
M.
Rao
,
Traffic Q.
5
,
231
(
2004
).
19.
M.
Edidin
,
Annu. Rev. Biophys. Biomol. Struct.
32
,
257
(
2003
).
20.
R. F. M.
de Almeida
,
A.
Fedorov
, and
M.
Prieto
,
Biophys. J.
85
,
2406
(
2003
).
21.
O. G.
Mouritsen
,
B.
Dammann
,
H. C.
Fogedby
et al.,
Biophys. Chem.
55
,
55
(
1995
).
22.
Bridging Time Scales: Molecular Simulations for the Next Decade, edited by P. Nielaba, M. Mareschal, and G. Ciccotti (Springer, Berlin, 2002).
23.
Novel Methods in Soft Matter Simulations, edited by M. Karttunen, I. Vattulainen, and A. Lukkarinen (Springer, Berlin, 2004).
24.
S. J.
Marrink
,
A. H.
de Vries
, and
A. E.
Mark
,
J. Phys. Chem. B
108
,
750
(
2004
).
25.
R.
Goetz
and
R.
Lipowsky
,
J. Chem. Phys.
108
,
7397
(
1998
).
26.
R.
Goetz
,
G.
Gompper
, and
R.
Lipowsky
,
Phys. Rev. Lett.
82
,
221
(
1999
).
27.
A.
Imparato
,
J. C.
Shillcock
, and
R.
Lipowsky
,
Eur. Phys. J. E
11
,
21
(
2003
).
28.
R. D.
Groot
and
K. L.
Rabone
,
Biophys. J.
81
,
725
(
2001
).
29.
M.
Kranenburg
,
M.
Venturoli
, and
B.
Smit
,
Phys. Rev. E
67
,
06090
(R) (
2003
).
30.
M.
Kranenburg
,
M.
Venturoli
, and
B.
Smit
,
J. Phys. Chem. B
107
,
11491
(
2003
).
31.
J. C.
Shelley
,
M. Y.
Shelley
,
R. C.
Reeder
,
S.
Bandyopadhyay
, and
M. L.
Klein
,
J. Phys. Chem. B
105
,
4464
(
2001
).
32.
J. C.
Shelley
,
M. Y.
Shelley
,
R. C.
Reeder
,
S.
Bandyopadhyay
,
P. B.
Moore
, and
M. L.
Klein
,
J. Phys. Chem. B
105
,
9785
(
2001
).
33.
S. O.
Nielsen
,
C. F.
Lopez
,
P. B.
Moore
,
J. C.
Shelley
, and
M. L.
Klein
,
J. Phys. Chem. B
107
,
13911
(
2003
).
34.
G.
Ayton
,
S. G.
Bardenhagen
,
P.
McMurtry
,
D.
Sulsky
, and
G. A.
Voth
,
J. Chem. Phys.
114
,
6913
(
2001
).
35.
G.
Ayton
,
A. M.
Smondyrev
,
S. G.
Bardenhagen
,
P.
McMurtry
, and
G. A.
Voth
,
Biophys. J.
82
,
1226
(
2002
).
36.
G.
Ayton
and
G. A.
Voth
,
Biophys. J.
83
,
3357
(
2002
).
37.
G.
Ayton
,
A. M.
Smondyrev
,
S. G.
Bardenhagen
,
P.
McMurtry
, and
G. A.
Voth
,
Biophys. J.
83
,
1026
(
2002
).
38.
L.
Miao
,
M.
Nielsen
,
J.
Thewalt
,
J. H.
Ipsen
,
M.
Bloom
,
M. J.
Zuckermann
, and
O. G.
Mouritsen
,
Biophys. J.
82
,
1429
(
2002
).
39.
M.
Nielsen
,
L.
Miao
,
J. H.
Ipsen
,
M. J.
Zuckermann
, and
O. G.
Mouritsen
,
Phys. Rev. E
59
,
5790
(
1999
).
40.
M.
Nielsen
,
L.
Miao
,
J. H.
Ipsen
,
O. G.
Mouritsen
, and
M. J.
Zuckermann
,
Phys. Rev. E
54
,
6889
(
1996
).
41.
M.
Nielsen
,
J.
Thewalt
,
L.
Miao
,
J. H.
Ipsen
,
M.
Bloom
,
M. J.
Zuckermann
, and
O. G.
Mouritsen
,
Europhys. Lett.
52
,
368
(
2000
).
42.
J. M.
Polson
,
I.
Vattulainen
,
H.
Zhu
, and
M. J.
Zuckermann
,
Eur. Phys. J. E
5
,
485
(
2001
).
43.
A. P.
Lyubartsev
and
A.
Laaksonen
,
Phys. Rev. E
52
,
3730
(
1995
).
44.
A. P.
Lyubartsev
,
M.
Karttunen
,
I.
Vattulainen
, and
A.
Laaksonen
,
Soft Materials
1
,
121
(
2003
).
45.
A.
Lyubartsev
and
A.
Laaksonen
,
J. Phys. Chem.
100
,
16410
(
1996
).
46.
A.
Lyubartsev
and
A.
Laaksonen
,
J. Chem. Phys.
111
,
11207
(
1999
).
47.
M. R.
Vist
and
J. H.
Davis
,
Biochemistry
29
,
451
(
1990
).
48.
J. P.
Slotte
,
Biochim. Biophys. Acta
1235
,
419
(
1995
).
49.
B.
Cannon
,
G.
Heath
,
J.
Hyang
,
P.
Somerharju
,
J. A.
Virtanen
, and
K. H.
Cheng
,
Biophys. J.
84
,
3777
(
2003
).
50.
E.
Falck
,
M.
Patra
,
M.
Karttunen
,
M. T.
Hyvönen
, and
I.
Vattulainen
,
Biophys. J.
87
,
1076
(
2004
).
51.
M.
Patra
,
M.
Karttunen
,
M. T.
Hyvönen
,
E.
Falck
,
P.
Lindqvist
, and
I.
Vattulainen
,
Biophys. J.
84
,
3636
(
2003
).
52.
M.
Patra
,
M.
Karttunen
,
M. T.
Hyvönen
,
E.
Falck
, and
I.
Vattulainen
,
J. Phys. Chem. B
108
,
4485
(
2004
).
53.
D. P.
Tieleman
and
H. J. C.
Berendsen
,
J. Chem. Phys.
105
,
4871
(
1996
).
54.
O.
Berger
,
O.
Edholm
, and
F.
Jahnig
,
Biophys. J.
72
,
2002
(
1997
).
55.
M.
Höltje
,
T.
Förster
,
B.
Brandt
,
T.
Engels
,
W.
von Rybinski
, and
H.-D.
Höltje
,
Biochim. Biophys. Acta
1511
,
156
(
2001
).
56.
E.
Lindahl
,
B.
Hess
, and
D.
van der Spoel
,
J. Mol. Model. [Electronic Publication]
7
,
306
(
2001
).
57.
U.
Essman
,
L.
Perera
,
M. L.
Berkowitz
,
H. L. T.
Darden
, and
L. G.
Pedersen
,
J. Chem. Phys.
103
,
8577
(
1995
).
58.
H. J. C.
Berendsen
,
J. P. M.
Postma
,
A.
DiNola
, and
J. R.
Haak
,
J. Chem. Phys.
81
,
3684
(
1984
).
59.
D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic, San Diego, 2002).
60.
B. J.
Thijsse
,
M. A.
Hollanders
, and
J.
Hendrikse
,
Comput. Phys.
12
,
393
(
1998
).
61.
S. W.
Chiu
,
E.
Jakobsson
,
R. J.
Mashl
, and
H. L.
Scott
,
Biophys. J.
83
,
1842
(
2002
).
62.
H. M.
McConnell
and
A.
Radhakrishnan
,
Biochim. Biophys. Acta
1610
,
159
(
2003
).
63.
GROMACS manual; see www.gromacs.org (2004).
64.
A. H.
de Vries
,
A. E.
Mark
, and
S. J.
Marrink
,
J. Phys. Chem. B
108
,
2454
(
2004
).
65.
P.
Somerharju
,
J. A.
Virtanen
, and
K. H.
Cheng
,
Biochim. Biophys. Acta
1440
,
32
(
1999
).
66.
D.
Bach
and
E.
Wachtel
,
Biochim. Biophys. Acta
1610
,
187
(
2003
).
67.
D. L.
Ermak
and
H.
Buckholtz
,
J. Comput. Phys.
35
,
169
(
1980
).
68.
H. C.
Andersen
,
J. Chem. Phys.
72
,
2384
(
1980
).
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