Simple Solvent-Free Molecular Model to Simulate Bilayer Membrane - - PowerPoint PPT Presentation

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Simple Solvent-Free Molecular Model to Simulate Bilayer Membrane Hiroshi Noguchi ISSP, University of Tokyo ISSP/SOFT2010 Biomembrane Cell Plasma membrane 10nm ~10 m Large scale gap

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Hiroshi Noguchi

ISSP, University of Tokyo

ISSP/SOFT2010

Simple Solvent-Free Molecular Model   to Simulate Bilayer Membrane

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~10µm 10nm

・ Biomembrane

Plasma membrane Large scale gap Cell

http://upload.wikimedia.org/wikipedia/commons/1/10/Illu_cell_structure.jpg

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Membrane models

curved surface ( no bilayer structure） atomistic model

∼ µm

molecular model

~ nm

Numerically faster More detailed information

length and time scale

Tieleman, et al. BBA 1331, 225 (1997)

coarse grained molecule bottom up

Shinoda etc.

go down

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C1, C2:principal curvatures、C0:spontaneous curvature

curved surface
simulation: discretized surface
theory: continuous surface
mesh methods ● meshless methods

A particle represents a membrane patch.

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Ochanomizu Lecture (Aug. 23) by G. Gompper

mesh method

degrees of freedom: positions and connections of particles fluid membrane by bond flip (Monte Carlo) for fixed topology dynamics with topological changes disadvantage works very well

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meshless methods

Naturally applied to the topological changes Advantage: 1) degrees of freedom: positions and orientation 2) degrees of freedom: only positions

Drouffe, Maggs, S. Leibler Science 254, 1353 (1991). Del Popolo (2008); T. Kohyama (2009);

P. Liu (2009); H. Yuan (2010).

Noguchi and Gompper Phys. Rev. E 73, 021903 (2006).

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kα and ε dependence

1.45 1.5 20 40 60 18 19 20 4 6 2 4 6

ε / T

A /Nσ 2

K σ / T Γσ / T κ / T

1.2 1.4 20 40 20 40 2 4 10 20

k / T

A /Nσ 2

K σ / T Γσ / T κ / T

area of tensionless membrane area compress modulus line tension bending rigidity 2d kα/T=10 ε /T=4

κ and Γ can be independently varied.

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Vesicle formation Very large membrane Rdis/σ >> 8kα/ε Buckling into two vesicles is also possible.

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rupture

ε/T= 1.5 -> 1.3

100 1000 10000 1.2 1.3 1.4

<t >D /σ 2

rup

ε /k T

B BD MPC

Noguchi and Gompper J. Chem. Phys. 125, 164908 (2006).

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curved surface molecular model

1 particle or segment > 100 lipid molecules 1 coarse-grained molecule

= 1~4 lipid molecules σ > thickness ~

length scale > 10 times ~

~

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atomistic models

0.1nm 0.4 nm 1nm

coarse-grained models

without explicit solvent ・Coarse-graining of lipids with explicit solvent

?

Klein et al.

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H. Noguchi, M. Takasu (2001)
O. Farago (2003)
G. Brannigan, F.L.H. Brown (2004)
G. Brannigan, P.F. Philips, F.L.H. Brown (2005)

I.R. Cooke, K. Kremer, M. Deserno (2005) Z.J. Wang, D. Frenkel (2005) J.D. Revalee, M. Laradji, P.B.S.Kumar (2008).

M. Hoemberg, M. Mueller (2010).

modifications solvent-free molecular model for bilayer membrane Only narrow parameter range Aim 1: make a model for wide parameter range

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3 spheres 1 sphere Aim 2: Coarse graining more to simulate larger scale

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Fournier, EPL 43, 725 (1998).

Continuum theory for bilayer membrane Membrane bending, area dilation, molecular tilt, chain stretching.

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Tilt + bending of membrane tilt + bending tilt only bending only

Kozlovsky and Kozlov, Biophys. J. 2002

u = n u n n u

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local density

Our new model

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Self-assembly

Vesicle formation

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surface tension tensionless membrane bilayer structure

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bending rigidity κ linear dependence

n ktilt and kbend

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line tension line tension

l i n e t e n s i

m e m b r a n e e d g e

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rupture

Cʼ0 = 0 -> 0.85

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droplet-vesicle transition

Bilayer is metastable at ktilt = 0.

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Preliminary simulation: Membrane fusion

Dai et al., J. Neurosci. 18, 6681 (1998). 2.5mm

Optical tweezers External force

Fusion!

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Experimental studies

Quick-freezing Electron microscopy images Bars, 100 nm.

Kanaseki et al. J. Cell Biol. 137, 1041 (1997).

Electric resistance measurement

V.A. Frolov et al. Biophys. J. 85, 1725 (2003).

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fusion pathways found by simulations

Solvent-free models Noguchi et al. 2001 Lattice MC Mueller, et al. 2002 LJ model Marrink et al. 2003 Stevens et al. 2003 Smeijers, et al. 2006 Kasson et al. 2007 DPD model Li and Liu 2005 Shillcock et al. 2005 Atomistic model Knecht and Marrink 2007

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Membrane fusion by mechanical force Pathway of modified stalk model

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10 20 30 5000 10000

Time step t

ns nm

My previous simulation

Distance between nanoparticles Xnp

Stochastically

Noguchi J. Chem. Phys. 117, 8130 (2002).

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Summary ○ A new CG model is proposed. ・ Minimum molecular size: a sphere and orientation ・ Membrane properties can be varied in wide range (including metastable bilayer). ・ Application: membrane fusion etc.

T h a n k y

f

y

r a t t e n t i

!

Supported by KAKENHI (Grant-in-Aid for Scientific Research)

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