A crucial process in biological cells is the translocation of newly synthesized proteins across cell membranes via integral membrane protein pores termed translocons. Recent improved techniques now allow producing artificial membranes with pores of similar dimensions of a few nm as the translocon system. For the translocon system, the protein has to be unfolded, whereas the artificial pores are wide enough so that small proteins can pass through even when folded. To study how proteins permeate through such membrane pores, we used coarse-grained Brownian dynamics simulations where the proteins were modeled as single beads or bead-spring polymers for both folded and unfolded states. The pores were modeled as cylindrical holes through the membrane with various radii and lengths. Diffusion was driven by a concentration gradient created across the porous membrane. Our results for both folded and unfolded configurations show the expected reciprocal relation between the flow rate and the pore length in agreement with an analytical solution derived by Brunn et al [Q. J. Mech. Appl. Math.37, 311 (1984)]

. Furthermore, we find that the geometric constriction by the narrow pore leads to an accumulation of proteins at the pore entrance, which in turn compensates for the reduced diffusivity of the proteins inside the pore.

1.
S. P.
Adiga
,
C.
Jin
,
L. A.
Curtiss
,
N. A.
Monteiro-Riviere
, and
R. J.
Narayan
,
Wiley Interdiscip. Rev.: Nanomed. Nanobiotechnol.
1
,
568
(
2009
).
3.
M.
Firnkes
,
D.
Pedone
,
J.
Knezevic
,
M.
Doblinger
, and
U.
Rant
,
Nano Lett.
10
,
2162
(
2010
).
4.
R.
Zimmermann
,
S.
Eyrisch
,
M.
Ahmad
, and
V.
Helms
,
Biochim. Biophys. Acta
1808
,
912
(
2011
).
5.
W.
Wickner
and
R.
Schekman
,
Science
310
,
1452
(
2005
).
6.
C. C.
Striemer
,
T. R.
Gaborski
,
J. L.
McGrath
, and
P. M.
Fauchet
,
Nature (London)
445
,
749
(
2007
).
7.
P.
Tian
and
G. D.
Smith
,
J. Chem. Phys.
119
,
11475
(
2003
).
8.
A. J.
Storm
,
C.
Storm
,
J.
Chen
,
H.
Zandbergen
,
J. F.
Joanny
, and
C.
Dekker
,
Nano Lett.
5
,
1193
(
2005
).
9.
I.
Huopaniemi
,
K.
Luo
,
T.
Ala-Nissila
, and
S. C.
Ying
,
J. Chem. Phys.
125
,
124901
(
2006
).
10.
N.
Nikoofard
and
H.
Fazli
,
Phys. Rev. E
83
,
050801
(
2011
).
11.
H. S.
Yong
,
Y. L.
Wang
,
S. C.
Yuan
,
B.
Xu
, and
K. F.
Luo
,
Soft Matter
8
,
2769
(
2012
).
12.
R.
Metzler
and
K.
Luo
,
Eur. Phys. J. Spec. Top.
189
,
119
(
2010
).
13.
E.
Slonkina
and
A. B.
Kolomeisky
,
J. Chem. Phys.
118
,
7112
(
2003
).
14.
C. T. A.
Wong
and
M.
Muthukumar
,
J. Chem. Phys.
128
,
154903
(
2008
).
15.
C. M.
Edmonds
,
Y. C.
Hudiono
,
A. G.
Ahmadi
,
P. J.
Hesketh
, and
S.
Nair
,
J. Chem. Phys.
136
,
065105
(
2012
).
16.
K. H.
Zhang
and
K. F.
Luo
,
J. Chem. Phys.
136
,
185103
(
2012
).
17.
L.
Javidpour
,
M. R. R.
Tabar
, and
M.
Sahimi
,
J. Chem. Phys.
128
,
115105
(
2008
).
18.
L.
Javidpour
,
M. R. R.
Tabar
, and
M.
Sahimi
,
J. Chem. Phys.
130
,
085105
(
2009
).
19.
R.
Moussavi-Baygi
,
Y.
Jamali
,
R.
Karimi
, and
M. R. K.
Mofrad
,
PLOS Comput. Biol.
7
,
e1002049
(
2011
).
20.
P. O.
Brunn
,
V. I.
Fabrikant
, and
T. S.
Sankar
,
Q. J. Mech. Appl. Math.
37
,
311
(
1984
).
21.
L. D.
Eltis
,
R. G.
Herbert
,
P. D.
Barker
,
A. G.
Mauk
, and
S. H.
Northrup
,
Biochemistry
30
,
3663
(
1991
).
22.
T.
Frembgen-Kesner
and
A. H.
Elcock
,
J. Chem. Theory Comput.
5
,
242
(
2009
).
24.
D. J.
Segel
,
A. L.
Fink
,
K. O.
Hodgson
, and
S.
Doniach
,
Biochemistry
37
,
12443
(
1998
).
25.
M.
Medinanoyola
and
D. A.
McQuarrie
,
J. Chem. Phys.
73
,
6279
(
1980
).
26.
U.
Winter
and
T.
Geyer
,
J. Chem. Phys.
131
,
104102
(
2009
).
27.
28.
D. L.
Ermak
and
J. A.
McCammon
,
J. Chem. Phys.
69
,
1352
(
1978
).
29.
T.
Geyer
,
C.
Gorba
, and
V.
Helms
,
J. Chem. Phys.
120
,
4573
(
2004
).
30.
B.
Cichocki
and
R. B.
Jones
,
Physica A
258
,
273
(
1998
).
You do not currently have access to this content.