ACNS2010_lipidAreas - The Canadian Institute for Neutron ...

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Nov 15, 2013 (3 years and 8 months ago)

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Lipid areas





obtained from

the simultaneous analysis of
neutron and X
-
ray scattering


Norbert Ku
č
erka
, Mu
-
Ping Nieh
and John Katsaras

Canadian Neutron Beam Centre

Chalk River, Ontario

Outline


Lipid Bilayers as
Biomimetic

Systems


X
-
ray Scattering


Neutron Scattering


Reconciling X
-
ray and Neutron Scattering


Lipid Areas for Various Lipids


SIMulation

to
EXPeriment

Comparison

DPPC
bilayer simulations by S
.
J
.
M
arrink@rug.nl

Biomimetic

Systems


lipid matrix is a 2D liquid, where lipids and proteins diffuse almost freely


the complex structural dynamics of membranes involve a balance of forces


lipid structural parameters determine the specific biomembrane functions


knowledge of lateral lipid area is central to MD simulations

A

Quantitaive

results


Despite their central role in
membrane biophysics, values of
lateral areas for lipid molecules
had been very uncertain.

Literature Results for DPPC @ 50
o
C:

(Nagle and Tristram
-
Nagle, BBA 2000)

Chaos for theory/simulations


MD simulations, due to non
-
perfect
force fields, are carried out at a
fixed area per lipid.


What value should be used?

Neutron scattering

simple/advanced models


C
rho
H
rho
C
rho
H
MD simulation
model
Water
HEAD
Water
HEAD
rho
C
MD simulation
model


CH
2
Water
HEAD
CH
2
Water
HEAD
rho
C
MD simulation
model
0.01
0.1
10
-5
10
-3
10
-1
10
1
10
3


I(q) [cm
-1
]
q [Å
-1
]
vesicle size and

size distribution

bilayer thickness

bilayer inner

structure

N. Ku
č
erka, J.F. Nagle, S.E. Feller and P. Balgav
ý
, Phys Rev E 69, 051903 (2004)

rho
MD simulation
model



The neutron scattering length density profiles of fluid
bilayers in solution are inherently quite featureless
(compared to X
-
ray scattering profiles)


Nevertheless, the mid
-
q

region provides high quality
information, reflecting the large scattering contrast
between the lipid bilayer (a lot of H) and solvent (D
2
O)

X
-
ray scattering

advanced models

DLPC, DMPC: N. Ku
č
erka, Y. Liu, N. Chu, H. I. Petrache, S. Tristram
-
Nagle, and J.F. Nagle, Biophys. J (2005)

DOPC, POPC, DEPC: N. Ku
č
erka, S. Tristram
-
Nagle, and J.F. Nagle, J Mem Biol (2005)

DPPC: N. Ku
č
erka, S. Tristram
-
Nagle, and J.F. Nagle, Biophys J Lett (2006)





D'
B
2
D
C


Total


Methyl
CG


P

CH
2


Water +

Choline
-30
-20
-10
0
10
20
30
0.0
0.1
0.2
0.3
0.4
electron density [e/Å
3
]
z [Å]
A combined global analysis approach takes
advantage of the complementarity of
ULVs and oriented samples, enhancing the
spatial resolution of the bilayer structure.

X
-
ray vs. Neutrons

Significant differences remain when comparing lipid areas


determined from X
-
ray and neutron scattering experiments!



e.g., DOPC @ 30
o
C:


A
X
-
ray

~ 72 Å
2


A
neutrons

~ 67 Å
2

X
-
ray vs. Neutrons

0.0
0.1
0.2
0
1x10
-4
2x10
-4
Area = 72.4 Å
2
Area = 67.4 Å
2


q
z

-1
]
|F(q
z
)|
0.0
0.2
0.4
0.6
0.8
0.0
0.5
1.0
1.5
2.0
Area = 72.4 Å
2
Area = 67.4 Å
2


q
z

-1
]
|F(q
z
)| [e/Å
2
]
-30
-20
-10
0
10
20
30
0.25
0.30
0.35
0.40
0.45

electron density [e/Å
3
]
Area = 72.4 Å
2
Area = 67.4 Å
2
z [Å]
-30
-20
-10
0
10
20
30
0
2x10
-6
4x10
-6
6x10
-6
neutron scattering length density
Area = 72.4 Å
2
Area = 67.4 Å
2
z [Å]

X
-
ray scattering is most
sensitive to the electron dense
headgroup peaks


But not to the lipid area


Neutron scattering, especially from
fully protonated lipid in D
2
O, is most
sensitive to the bilayer thickness which
directly relates to the area

Simultaneous analysis of x
-
ray and neutron
scattering data should allow for the inclusion
of fine details, and better determination of
the overall bilayer parameters.


Universal model of

Scattering Density Profile

0.0
0.1
0.2
PCN_d4
PCN
CholCD3
CG
glycerol
carbonyl
phosphate
choline_d9
choline_d13
CH
NSLD [10
-5
Å
-2
]


-30
-25
-20
-15
-10
-5
0
5
10
15
20
25
30
0.0
0.1
0.2
CholCH3
CG
PCN
CholCH3
carbonyl
glycerol
phosphate
choline
choline
CH
3
CH
CH
2
CH
3

ED [e/Å
3
]
z [Å]
-30
-25
-20
-15
-10
-5
0
5
10
15
20
25
30
0.0
0.2
0.4
0.6
0.8
1.0
CH
C
water
CH3
CH2
CholCH3
PCN
CG

Volume Probability
z [Å]
0.0
0.2
0.4
0.6
0.8
0.0
0.5
1.0
1.5
2.0
|F(q)| [e/Å
2
]
q [Å
-1
]
-5
0
5
10
15
20
25
30
0.20
0.25
0.30
0.35
0.40
0.45
A
D
HH
2


ED [e/Å
3
]
z [Å]
0.0
0.1
0.2
0.3
0.0
0.5
1.0
1.5
2.0
2.5
DOPC 50% D
2
O
DOPC 100% D
2
O
|F(q)| [10
-4
Å
-1
]
q [Å
-1
]
-5
0
5
10
15
20
25
30
0.0
0.2
0.4
0.6
B


NSLD [10
-5
Å
-2
]
z [Å]

Each of the component groups
has nearly the same functional
form for all of the different
contrast conditions


Volume distributions satisfy a
spatial conservation principle


N.Ku
č
erka, J.F.Nagle, J.N.Sachs, S.E.Feller, J.Pencer A.J.Jackson, and J.Katsaras, Biophys. J (2008)

The SDP model was fit (with only one
set of parameters) simultaneously to
the set of scattering data obtained
at different contrast conditions (X
-
rays and neutron contrast variation).

-
non
-
linearly in the case of lipids
with di
-
monounsaturated chains

-
non
-
linearly in the case of lipids
with di
-
monounsaturated chains

when the double bond is fixed
relative to the bilayer centre

12
14
16
18
20
22
24
56
58
60
62
64
66
68
70
72
74
diCn:mPC
m=1
m=0
A
L

2
]
n

6

8

10

10

10

10


SOPC (m=0.5)
POPC (m=0.5)
Areas

for Various Lipids

N. Ku
č
erka, S. Tristram
-
Nagle, and J.F. Nagle, J Mem Biol (2005)

N.Ku
č
erka, J. Gallová, D. Uhríková, P. Balgavý, M. Bulacu, S.
-
J. Marrink, and J.Katsaras, Biophys. J (2009)

-

chain length n (carbons)

-

unsaturation m

(0
-

fully saturated, 1


di
-
monounsaturated, 0.5


mixed chains)

1.) Lipid area increases with the
increasing chain length:

-
linearly in a case of saturated
chain lipids and

2.) Lipid area increases with the
introduction of first double bond
much more significantly than
with the addition of double bond
to the second chain

Concluding remarks


Neutron scattering techniques are proving more and more
their importance in the fields of structural biology and
biophysics.


Recent development has reconciled the differences
between small

angle X
-
ray and Neutron scattering
experimental results.


MD simulations complement experimental results and
experimental results provide guides for MD simulations.

N.
Kučerka
, J. Katsaras and J. Nagle, J
Mem

Biol

(2009)

Comparing Membrane Simulations to Scattering Experiments: Introducing the
SIMtoEXP

Software

The

comparison of
SIMulation

to
EXPeriment

www.norbbi.com/public/public.html

direct

Acknowledgement
and
Collaborators


SDP

model

development


John

Nagle

(CMU,

Pittsburgh,

PA)


Small
-
Angle

Neutron

Scattering


Andrew

Jackson

(NIST,

Giathersburg,

MD)


William

Heller

(ORNL,

Oak

Ridge,

TN)


Low
-
Angle

X
-
ray

Scattering


Arthur

Woll

(CHESS,

Ithaca,

NY)


Stephanie

Tristram
-
Nagle

(CMU,

Pittsburgh,

PA)


Molecular

Dynamics

simulations


Jonathan

Sachs

(U

of

Minnesota,

Minneapolis,

MN)


Scott

Feller

(Wabash

College,

Crawfordsville
,

IN)


Siewert
-
Jan

Marrink

(U

of

Groningen,

Netherlands)