Simulating Interactions of Cholesterol-Containing Lipid Bilayer

Membranes with Solid Supports using Molecular Dynamics Holden T. Ranz, Roland Faller, Department of Chemical Engineering and Materials Science, University of California, Davis

RESULTS Lipid Bilayer Simulations:

REFERENCES C Xing and R Faller. J. Phys. Chem. B, 2008, 112, 7086–7094

SJ Marrink et al. J. Phys. Chem. B 2007, 111, 7812-7824

C Liu and R Faller. Langmuir, 2012, 28 (45), pp 15907–15915

INTRODUCTION Lipids represent one of the fundamental groups of biological macromolecules serving as critical

components of cellular and intracellular membranes due to their amphipathic nature. In aqueous environment,

fatty acid tails form hydrophobic interactions while polar head groups interact with water facilitating self-

assembly into bilayers. Ternary systems containing a lipid with saturated tails (high Tm), a lipid with

unsaturated tails (low Tm), and cholesterol can exhibit liquid crystalline phase coexistence below a critical

temperature, which can be seen experimentally by the presence of liquid-ordered (Lo) microdomains

dispersed within a liquid-disordered (Ld) matrix.

CONCLUSIONS AND

FUTURE WORK

• Free bilayer simulations for 1 μs of effective time maintained very stable

structures and equilibrated area per lipid for temperatures from 290 – 310 K

• Highly symmetric density profiles

• Cholesterol stays packed within membrane

• Supported bilayers maintained stable bilayer configuration, but with increased

area per lipid causing ripple structure in membrane

• Likely due to change in force field parameters for water

• Further simulation of free bilayer with reduced water interaction required

• Further analysis required to characterize changes to supported lipids

• Area per lipid (refined for DPPC vs DOPC)

• Diffusion coefficients of lipids in proximal vs distal leaflets (via RMS)

• Order parameter (phase present, Lo vs Ld vs coexisting phases)

ACKNOWLEDGEMENTS

Thanks to Dr. Roland Faller and Chenyue Xing for starting this project, and to the

rest of the Faller Research Group for all their help in addition to the UC Davis

CHMS Department for funding this work.

Free Bilayer vs Supported Bilayer

MOTIVATION / OBJECTIVE • Improve understanding about how a solid support alters structural and dynamic characteristics of multi-

component membranes with cholesterol

• Molecular Dynamics computer simulations of model biomembranes provide a unique look into

thermodynamic properties associated with complex biological systems on the nano to microscale

• Build phase diagram(s) with respect to system composition and temperature

• Free bilayer final configuration

(after 250 ns) imposed onto solid

support

• 3.5 nm water layer slab removed

from free bilayer system

• Force field for supported system

changed to use reduced W-W

interaction and simulated for

additional 250 ns

• Free lipid bilayers simulated containing equimolar ratio

• DPPC(170):DOPC(170):Cholesterol(170)

• 12180 CG waters evenly distributed on top and bottom

• 250 ns simulation time (1 μs effective time)

• Berendsen thermostat and barostat

• T-coupling to reference temperatures from 260-310 K

• P-coupling to reference pressure of 1 bar

• Separate coupling in XY plane and Z to achieve

constant area per lipid

Molecular Dynamics simulations

have been used to accurately model free

bilayers, single-component supported

lipid bilayer systems, and tethered

bilayer systems. These simulations can

be used to effectively analyze changes

to structural properties of model

membranes, which provides tremendous

insight for experimental work and

medical/technological applications such

as molecular sensing.

METHODS Molecular Dynamics (MD):

GROMACS 4.6.5 MD Software Package

1. NVE energy minimization – ensure valid starting configuration

2. NPT md run – freeze test with solid support

3. NAPzT md run – constant area and z pressure, free and supported

Coarse-Graining (CG):

MARTINI v2 Coarse-Grained (CG) Force Field

• Typical CG beads defined by 4-1 atom mapping scheme

• Ring CG beads, smaller and weaker interaction

• CG effectively 4x faster (compared to atomistic)

Force Field Development: Support Considerations

• Van der Waals bead interactions modeled via Lennard-Jones (LJ) potential:

• Charged bead interactions included via Coulombic potential:

• MARTINI has mapped LJ parameters for non-bonded VdW interactions between CG

beads ranging from supra attractive (0) to super repulsive (IX)

• Support (SUN0)-* interactions all intermediate (IV), except SUN0-C* repulsive (VIII)

• Water-Water interactions typically attractive (I), reduced to 76%attractive (Su(ww)) to

get correct freezing temperature of water with solid support

Hydrated Lipid Systems:

• Ternary systems containing the following components were

simulated under free and supported conditions for hundreds of

nanoseconds to 1 microsecond effective time

1. 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)

2. 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)

3. Cholesterol

Tm = 41°C

>

Tm = -17°C

Qa

Q0

Na Na

C2

C1 C1

C1 C1

C1

C1 C1

C1

C2

SP1

SC1

SC1

SC1

SC3

SC1

C1

SC1

P4

Bead Definitions:

H-Bonding:

i = a, d, 0

a = H-acceptor

d = H-donor

da = H-donor/acceptor

Types:

P1-P5 = Polar Bead

Ni = Non-Polar Bead

Ci = Hydrophobic Bead

Qi = Charged Bead

S* = Ring Bead

(where * is any of typical bead types)