Computer Simulation of Membrane
Proteins: Membrane Deformation,
Signal Transduction and Cellular
Uptake of Nanoparticles
Tongtao Yue and Xianren Zhang
Division of Molecular and Materials Simulation, State Key Laboratory of
Organic-Inorganic Composites，Beijing University of Chemical Technology，
Beijing 100029, China
Lipid
membrane
Clustering of
membrane anchored
proteins and its role in
membrane deformation
and signal transduction
Receptor-mediated
interaction between
membrane and
nanoparticles with
different properties
Story 1:
The Relationship Between Membrane
Deformation and Clustering of Anchored Proteins
Membrane curvature is ubiquitous in
cell environment
How to deform a membrane?
Mcmahon et al, Nature, 438, 590 (2005)
What if the clustering of anchored proteins is
taken into account?
Mcmahon et al, Nature, 438, 590 (2005)
Protein Clustering:
The different protein hydrophobic lengths not only result in different
aggregation numbers, but also lead to different aggregation dynamics.
Membrane Deformation
Effect of Membrane Surface Tension:
Membrane deformation by the anchored proteins
of ntp =6, at different values of lipid density: (A)
1.47; (B) 1.67; (C) 1.69; and (D) 1.73. The figure
shows typical snapshots (left), the corresponding
best-fitted geometric surfaces (bottom right) and
curvature distribution (top right).
A negative membrane tension is a prerequisite
for the bending of a lipid bilayer, and the
deformation of the membrane is found to be
located mainly around the protein clusters.
T. Yue et al, Soft Matter, 2010, 6, 6109
Membrane Deformation
Effect of Protein Hydrophobic Length:
Membrane deformation by the different anchored proteins, (A) ntp =3; (B) ntp =4; (C) ntp =6;
and (D) ntp =7. (E) shows the the largest membrane curvature as a function of lipid density.
Deep penetration of proteins into membrane would result into their clustering,
which in turn produces positive curvature considerably exceeding that for
shallow inserting proteins
Membrane Deformation
Effect of Protein Hydrophobic Length:
curvature
0.12
0.09
no proteins anchored
ntp=4
a
b
0.12
ntp=6
ntp=7
0.06
0.03
0.00
1.4
0.15
curvature
0.15
0.09
0.06
0.03
1.5
1.6
BR
LNPA
1.7
0.00
3
4
5
6
7
hydrophobic tail length
(a) The largest membrane curvature as a function of LNPA, and (b) the largest
membrane curvature as a function of the hydrophobic length of anchored proteins.
Note that LNPA is set to 1.70 in (b).
T. Yue et al, Soft Matter, 2010, 6, 6109
Membrane Vesiculation:
Typical snapshots during
the formation of a vesicle.
Before observable membrane curvature appears, the clustering of proteins
occurs because of the strong effective attraction between proteins due to their
perturbations on the membrane
cluster number
Protein clustering Senses Membrane Curvature:
15
12
9
6
3
0
0
5
10
15
20
25
0
5
10
15
20
25
0.25
curvature
0.20
0.15
Distribution of the cluster size (top) and
corresponding local curvature (bottom) as a
function of cluster size
0.10
0.05
0.00
cluster size
Most protein clusters are located on membrane positions with positive
curvature. More importantly, larger protein clusters tend to be located at
membrane positions with higher positive curvature.
T. Yue et al, Soft Matter, 2010, 6, 6109
Summaries:
Curvature production is enhanced by the clustering of
1 anchored proteins, and the enhancement depends on the
protein hydrophobic length.
For the membrane proteins with deep insertion, the
2 clustering of proteins may induce membrane vesiculation
at negative membrane tensions.
The protein clustering can sense the membrane curvature,
3 although the way they respond to the local curvature again
depends on the protein hydrophobic length.
T. Yue et al, Soft Matter, 2010, 6, 6109
Story 2:
Signal Transduction Across Cellular Membrane can
be Mediated by Coupling of the Clustering of
Anchored Proteins in Both Leaflets
One of the key questions regarding signal transduction is how the signal
received by outer-leaflet is relayed to the inner-leaflet.
How is the coupling occurs
between anchored proteins
in different leaflet?
Kusumi et al, Traffic (2004)
Three Coupling Patterns of Protein Clustering:
(a-c) Snapshots for three coupling patterns of
protein clustering. (a) A face-to-face clustering
(top: n=3; bottom: n=6), (b) an interdigitated
clustering (top: n=6; bottom: n=6), and (c) a
weak-coupled clustering (top: n=4; bottom: n=4).
Blue represents proteins in the bottom leaflet and
pink represents proteins in the upper leaflet. (d)
shows two-dimensional radial distribution
function (RDF) of proteins in one leaflet with
respective to those in the opposite leaflet.
The coupling pattern are strongly dependent on the hydrophobic
length of proteins in both leaflets.
T. Yue and X. Zhang, Phys. Rev. E, 2012, 85, 011917
Movies:
Face-to-face clustering
Interdigitated clustering
T. Yue and X. Zhang, Phys. Rev. E, 2012, 85, 011917
Membrane Perturbation:
Z-coordinates for lipids adjacent to the
anchored protein cluster. The local
membrane thickness and lipid order
parameter are given in the left and right
insets. The hydrophobic length of the
anchored proteins is set to (a) n=3, (b)
n=4, (c) n=5, and (d) n=6.
Both upper and bottom leaflets are strongly perturbed by the clustering of
anchored proteins in one leaflet. The membrane perturbation induced by upper
protein cluster thus tends to cause the proteins in the bottom leaflet to redistribute.
Trajectories:
T. Yue and X. Zhang, Phys. Rev. E, 2012, 85, 011917
Protein Clustering and Phase Diagram:
▲: weak coupled clustering
□: face-to-face clustering
○: interdigitated clustering
The extent of protein clustering is found to be affected by the coupling patterns,
which depends on the hydrophobic length of proteins in both leaflets
Summaries:
The disturbance of the clustering of anchored proteins in one
1 leaflet can extend across the full thickness of a bilayer, thus
inducing proteins in the opposite leaflet to redistribute.
Depending on the hydrophobic length of anchored
2 membrane proteins, three coupling patterns are observed.
We proposed a new mechanism for signal transduction via
3 coupling of protein clustering in this work, this mechanism
shows particular selectivity in the downstream signaling.
T. Yue and X. Zhang, Phys. Rev. E, 2012, 85, 011917
Story 3:
Molecular Understanding of Receptor-mediated
Membrane Responses to Ligand-coated Nanoparticles
Nanotechnology Present a
Janus Face!
How to maximize the efficiency of drug
delivery while minimize their cytotoxicity?
Huajian Gao et al, PNAS (2005)
McNerny et al. Nanomed. and Nanobio. (2010)
Four Kinds of Membrane Responses:
Receptor mediated endocytosis
Nanoparticle adhesion
Nanoparticle penetration
Nanoparticle induced membrane
rupture
T. Yue and X. Zhang, Soft Matter, 2011, 7, 9104
Receptor Mediated Endocytosis:
the extent of wrapping
1.0
A
0.8
0.6
0.4
0.2
Dp=4.0nm
0.0
0
1000
2000
3000
4000
5000
simulation time (ns)
Time evolution of the extent of wrapping.
The endocytosis is controlled by the balance of receptor-ligand binding
energy and membrane bending energy.
Receptor Mediated Endocytosis
Effect of Ligand Density:
0.8
wrapping extent
0.7
A
NL=18
NL=40
0.6
Time evolution of the extent of endocytosis for
NPs with different ligand densities, NL=18
(black line), and NL=40 (red line).
0.5
0.4
0.3
0.2
0.1
0.0
0.5
1.0
1.5
2.0
2.5
3.0
simulation time (s)
NPs with more coated ligands are more easily wrapped by the membrane.
T. Yue and X. Zhang, Soft Matter, 2011, 7, 9104
Adhesion and Penetration:
0.7
6
0.5
0.4
0.3
0.2
adhesion
penetration
0.1
0.0
adhesion
penetration
B
5
Z-Z0 (nm)
percentage
0.6
7
A
0
1000
2000
3000
simulation time (ns)
4000
4
3
2
1
5000
0
0
1000
2000
3000
4000
simulation time (ns)
(A) The evolution of the percentage of surface beads of the NP
contacting with the membrane and (B) the evolution of the NPmembrane distance.
Adhesion and penetration of NPs are mainly determined by NPs size and
membrane surface tension. Larger NPs tend to adhere on the membrane
with larger membrane tension and vice versa.
5000
NP Induced Membrane Rupture:
8
surface tension
6
A
4
with NP
without NP
2
0
-2
-4
-6
0
1000
2000
3000
simulation time (ns)
12
surface tension
9
without NP
Dp=4.0 nm, NL=18
B
Dp=6.0 nm, NL=40
Dp=6.0 nm, NL=18
6
3
0
NPs with smaller size and larger ligand
density are found to induce the membrane
rupture more easily.
-3
-6
0.8
1.0
1.2
1.4
1.6
BR
LNPA
T. Yue and X. Zhang, Soft Matter, 2011, 7, 9104
Morphology Diagram:
1.7
A
endocytosis
1.6
1.4
penetration
adhesion
BR
LNPA
1.5
1.3
1.2
rupture
1.1
3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
diameter (nm)
Morphology diagram of the membrane responses to adsorption of NP with 18 ligands
coated in the plane of membrane tension and NP radius.
Membrane tension, NPs size, and Ligand density are
important factors that determine the membrane responses
Summaries:
There exist four kinds of membrane responses, including
1 receptor-mediated endocytosis, NP adhesion, NP penetration,
and membrane rupture.
NP size, ligand density on the NP surface, and membrane
2 surface tension are all crucial in the membrane responding
processes.
The phase diagrams presented here have the potential to
3 provide both qualitative and quantitative guidelines for the
designing of novel drug delivery biomaterials.
T. Yue and X. Zhang, Soft Matter, 2011, 7, 9104
Story 4:
Cooperative Effect in Receptor-Mediated
Endocytosis of Multiple Nanoparticles
Endocytosis of Single
NP
NP size
√
NP shape
√
How about the endocytosis of
multiple NPs?
Reynwar et al, Nature. (2007)
Chithrani et al, Nano Lett. (2007)
Internalization of Nine Identical NPs:
D=2.5nm: NPs generally cluster together
on the membrane
D=4.0nm: NPs aggregate into pearl-chainlike arrangements
D=6.0nm: Independent endocytosis
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Movies:
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Movies:
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Internalization of Two Identical NPs:
Internalization pathway of two identical NPs are strongly dependent on
the NPs size. Smaller NPs tend to internalize together, while larger NPs
tend to internalize independently.
Internalization of Two NPs with Different Size:
Asynchronous
internalization
Synchronous
internalization
One NP’s diameter is fixed to be 4.5nm, while the diameter of the other NP is (A)
2.5nm, (B) 3.3nm, (C) 4.0nm.
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Pinocytosis-like Internalization of Two NPs
with Different Size :
30
27
15
C
Distance (nm)
B
12
24
0.6
Z (nm)
wrapping extent
1.0
0.8
(A) Typical snapshots showing the
pinocytosis-like internalization of two
NPs with different size. (B) The
evolution of wrapping extent for two
NPs. (C) evolution of COMs along
membrane normal direction and that of
distance between two NPs (inset)
0.4
21
9
0
18
2
4
6
8
15
0.2
0.0
D=4.5nm
D=2.5nm
0
2
4
6
simulation time (s)
8
D=4.5nm
D=2.5nm
12
9
0
2
4
6
simulation time (s)
8
Pinocytosis-like internalization tends to occur for two NPs with large
size difference and intermediate initial distance.
Other Internalization pathway for Two NPs
with Different Size :
35
30
Distance (nm)
B
14
C
0.8
0.6
Z (nm)
wrapping extent
1.0
0.4
25
12
10
8
20
0
2
4
6
15
0.2
D=4.5nm
D=2.5nm
0.0
0
2
D=4.5nm
D=2.5nm
10
4
simulation time (s)
6
0
2
4
6
simulation time (s)
When two NPs with large size difference and longer initial
distance are placed on the membrane, only the larger NP is
wrapped while the smaller NP keep adhering on the membrane
Morphology Diagram:
Initial distance (nm)
9
8
▲: Independent internalization pathway
●: Pinocytosis-like internalization pathway
■: Asynchronous internalization
▼: Synchronous internalization.
7
6
Note that the diameter of the larger NP is
fixed to 4.5nm
5
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
Diameter (nm)
The internalization pathway for two NPs with different size is
mainly determined by their size difference and initial distance
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Summaries:
Smaller NPs tend to form clusters while internalization. this
1 cooperative effect is weakened by increase the NPs size.
The internalization of two identical NPs confirms the
2 importance of NPs size to their internalization pathway.
Four different internalization pathways for two NPs with
3 different size are observed which is mainly determined by
their size difference and initial distance.
T. Yue and X. Zhang, ACS Nano, 2012, 6, 3196
Story 5:
Molecular modeling of the pathways of
vesicle–membrane interaction
High solubility
Advantages
of soft NPs
High environmental
sensitivity
Low toxicity
Shillcock and Lipowsky, Nature Mater. 2005
Yi, Shi, and Gao, Phys. Rev. Lett. 2011
Membrane Fusion and Hemifusion:
Time sequence of snapshots corresponding to the vesicle hemi-fusion (A) and
fusion (B) respectively. The values of LNPA are fixed to 1.54 (A) and 1.16 (B),
respectively.
Vesicle Adhesion:
In this figure the receptor density is fixed to 50% under the condition of aRL
=4.0 and LNPA =1.1.
Vesicle Rupture:
In this figure the receptor density is fixed to 50% under the condition of aRL
=0.0 and LNPA =1.66.
Vesicle Endocytosis:
In this figure the receptor density is fixed to 50% under the condition of aRL
=4.0 and LNPA =1.68.
Effect of Vesicle Elasticity:
The self-adjustment of vesicle shape bypasses the high energy barrier of membrane
bending to wrap an oblate vesicle, thus facilitates the receptor-mediated
endocytosis.
Phase Diagram:
■: Vesicle Fusion
●: Vesicle Hemifusion
▲: Vesicle Adhesion,
Rupture, or Endocytosis
Effect of Vesicle-Membrane Adhesion Strength:
As the adhesion strength decreases, the pathways for the vesicle-membrane
interaction changes from vesicle rupture, vesicle endocytosis to vesicle adhesion.
Effect of Membrane Surface Tension:
Strong vesicle-membrane
adhesion strength
Weak vesicle-membrane
adhesion strength
Higher membrane tension would promote vesicle rupture, while lower membrane
tension would facilitate vesicle endocytosis.
Effect of Receptor Density:
Strong vesicle-membrane
adhesion strength
Weak vesicle-membrane
adhesion strength
Increase of receptor density can accelerate the vesicle rupture at strong vesiclemembrane adhesion strength, while at weak vesicle-membrane adhesion strength,
increase of receptor density can facilitate the endocytosis process.
Effect of Vesicle Tension:
The vesicle with a lower vesicle tension tends to be wrapped by the membrane
more efficiently because the vesicle can deform more easily.
Effect of Ligand Density:
Both wrapping rate and extent are determined by the ligand density, and vesicles
with lower ligand density can not be fully wrapped by the membrane.
Summaries:
1
Different vesicle responses to the vesicle-membrane adhesion,
including vesicle fusion, vesicle hemi-fusion, vesicle adhesion,
vesicle endocytosis and vesicle rupture, are observed from our
simulations.
2
We also investigate how the pathways of vesicle-membrane
interaction depend on the adhesion strength and the membrane and
vesicle properties..
Tongtao Yue and Xianren Zhang, Submitted
Thank you for your attention!
zhangxr@mail.buct.edu.cn
tt1202@126.com
http://www.ms.buct.edu.cn/