101 |
|
\begin{figure} |
102 |
|
\centering |
103 |
|
\includegraphics[width=\linewidth]{./figures/mdLipidModels.pdf} |
104 |
< |
\caption{Three different representations of DPPC lipid molecules, |
104 |
> |
\caption[Three different representations of DPPC lipid |
105 |
> |
molecules]{Three different representations of DPPC lipid molecules, |
106 |
|
including the chemical structure, an atomistic model, and the |
107 |
|
head-body ellipsoidal coarse-grained model used in this |
108 |
|
work.\label{mdfig:lipidModels}} |
141 |
|
Pechukas.\cite{Berne72} The potential is constructed in the familiar |
142 |
|
form of the Lennard-Jones function using orientation-dependent |
143 |
|
$\sigma$ and $\epsilon$ parameters, |
144 |
< |
\begin{equation} |
144 |
< |
\begin{split} |
144 |
> |
\begin{multline} |
145 |
|
V_{ij}({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j}, {\mathbf{\hat |
146 |
< |
r}_{ij}}) = & 4\epsilon ({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j}, |
146 |
> |
r}_{ij}}) = 4\epsilon ({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j}, |
147 |
|
{\mathbf{\hat r}_{ij}})\left[ \left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i}, |
148 |
< |
{\mathbf{\hat u}_j}, {\mathbf{\hat r}_{ij}})+\sigma_0}\right)^{12} \right.\\ |
149 |
< |
&\left. -\left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i}, |
148 |
> |
{\mathbf{\hat u}_j}, {\mathbf{\hat r}_{ij}})+\sigma_0}\right)^{12} |
149 |
> |
\right. \\ |
150 |
> |
\left. - \left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i}, |
151 |
|
{\mathbf{\hat u}_j}, {\mathbf{\hat |
152 |
|
r}_{ij}})+\sigma_0}\right)^6\right] |
152 |
– |
\end{split} |
153 |
|
\label{mdeq:gb} |
154 |
< |
\end{equation} |
154 |
> |
\end{multline} |
155 |
|
|
156 |
|
The range $(\sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf |
157 |
|
\hat{r}}_{ij}))$, and strength $(\epsilon({\bf \hat{u}}_{i},{\bf |
172 |
|
where $l$ and $d$ describe the length and width of each uniaxial |
173 |
|
ellipsoid. These shape anisotropy parameters can then be used to |
174 |
|
calculate the range function, |
175 |
< |
\begin{equation} |
176 |
< |
\begin{split} |
177 |
< |
& \sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) = |
178 |
< |
\sigma_{0} \times \\ |
179 |
< |
& \left[ 1- \left\{ \frac{ \chi \alpha^2 ({\bf \hat{u}}_i \cdot {\bf |
175 |
> |
\begin{multline} |
176 |
> |
\sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) = \\ |
177 |
> |
\sigma_0 \left[ 1 - \left\{ \frac{ \chi \alpha^2 ({\bf \hat{u}}_i \cdot {\bf |
178 |
|
\hat{r}}_{ij} ) + \chi \alpha^{-2} ({\bf \hat{u}}_j \cdot {\bf |
179 |
|
\hat{r}}_{ij} ) - 2 \chi^2 ({\bf \hat{u}}_i \cdot {\bf |
180 |
|
\hat{r}}_{ij} )({\bf \hat{u}}_j \cdot {\bf |
181 |
|
\hat{r}}_{ij} ) ({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j)}{1 - \chi^2 |
182 |
|
\left({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j\right)^2} \right\} |
183 |
< |
\right]^{-1/2} |
184 |
< |
\end{split} |
187 |
< |
\end{equation} |
183 |
> |
\right]^{-1/2} |
184 |
> |
\end{multline} |
185 |
|
|
186 |
|
Gay-Berne ellipsoids also have an energy scaling parameter, |
187 |
|
$\epsilon^s$, which describes the well depth for two identical |
208 |
|
\left[1-\chi^{2}({\bf \hat{u}}_{i}.{\bf |
209 |
|
\hat{u}}_{j})^{2}\right]^{-1/2} |
210 |
|
\end{eqnarray*} |
211 |
< |
\begin{equation*} |
212 |
< |
\begin{split} |
213 |
< |
& \epsilon_{2}({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) |
214 |
< |
= 1 - \\ |
218 |
< |
& \left\{ \frac{ \chi' \alpha'^2 ({\bf \hat{u}}_i \cdot {\bf |
211 |
> |
\begin{multline*} |
212 |
> |
\epsilon_{2}({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) |
213 |
> |
= \\ |
214 |
> |
1 - \left\{ \frac{ \chi' \alpha'^2 ({\bf \hat{u}}_i \cdot {\bf |
215 |
|
\hat{r}}_{ij} ) + \chi' \alpha'^{-2} ({\bf \hat{u}}_j \cdot {\bf |
216 |
|
\hat{r}}_{ij} ) - 2 \chi'^2 ({\bf \hat{u}}_i \cdot {\bf |
217 |
|
\hat{r}}_{ij} )({\bf \hat{u}}_j \cdot {\bf |
218 |
|
\hat{r}}_{ij} ) ({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j)}{1 - \chi'^2 |
219 |
|
\left({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j\right)^2} \right\}, |
220 |
< |
\end{split} |
225 |
< |
\end{equation*} |
220 |
> |
\end{multline*} |
221 |
|
although many of the quantities and derivatives are identical with |
222 |
|
those obtained for the range parameter. Ref. \citen{Luckhurst90} |
223 |
|
has a particularly good explanation of the choice of the Gay-Berne |
244 |
|
\begin{figure} |
245 |
|
\centering |
246 |
|
\includegraphics[width=\linewidth]{./figures/md2LipidModel.pdf} |
247 |
< |
\caption{The parameters defining the behavior of the lipid |
248 |
< |
models. $\sigma_h / d$ is the ratio of the head group to body diameter. |
249 |
< |
Molecular bodies had a fixed aspect ratio of 3.0. The solvent model |
250 |
< |
was a simplified 4-water bead ($\sigma_w \approx d$) that has been |
251 |
< |
used in other coarse-grained simulations. The dipolar strength |
252 |
< |
(and the temperature and pressure) were the only other parameters that |
253 |
< |
were varied systematically.\label{mdfig:lipidModel}} |
247 |
> |
\caption[The parameters defining the behavior of the lipid |
248 |
> |
models]{The parameters defining the behavior of the lipid |
249 |
> |
models. $\sigma_h / d$ is the ratio of the head group to body |
250 |
> |
diameter. Molecular bodies had a fixed aspect ratio of 3.0. The |
251 |
> |
solvent model was a simplified 4-water bead ($\sigma_w \approx d$) |
252 |
> |
that has been used in other coarse-grained simulations. The dipolar |
253 |
> |
strength (and the temperature and pressure) were the only other |
254 |
> |
parameters that were varied systematically.\label{mdfig:lipidModel}} |
255 |
|
\end{figure} |
256 |
|
|
257 |
|
To take into account the permanent dipolar interactions of the |
323 |
|
\begin{table*} |
324 |
|
\begin{minipage}{\linewidth} |
325 |
|
\begin{center} |
326 |
< |
\caption{Potential parameters used for molecular-scale coarse-grained |
327 |
< |
lipid simulations} |
326 |
> |
\caption{POTENTIAL PARAMETERS USED FOR MOLECULAR SCALE COARSE-GRAINED |
327 |
> |
LIPID SIMULATIONS} |
328 |
|
\begin{tabular}{llccc} |
329 |
|
\hline |
330 |
|
& & Head & Chain & Solvent \\ |
345 |
|
\end{minipage} |
346 |
|
\end{table*} |
347 |
|
|
348 |
< |
\section{Experimental Methodology} |
349 |
< |
\label{mdsec:experiment} |
348 |
> |
\section{Simulation Methodology} |
349 |
> |
\label{mdsec:simulation} |
350 |
|
|
351 |
|
The parameters that were systematically varied in this study were the |
352 |
|
size of the head group ($\sigma_h$), the strength of the dipole moment |
441 |
|
\begin{figure} |
442 |
|
\centering |
443 |
|
\includegraphics[width=\linewidth]{./figures/mdPhaseCartoon.pdf} |
444 |
< |
\caption{The role of the ratio between the head group size and the |
445 |
< |
width of the molecular bodies is to increase the local membrane |
446 |
< |
curvature. With strong attractive interactions between the head |
447 |
< |
groups, this local curvature can be maintained in bilayer structures |
448 |
< |
through surface corrugation. Shown above are three phases observed in |
449 |
< |
these simulations. With $\sigma_h = 1.20 d$, the bilayer maintains a |
450 |
< |
flat topology. For larger heads ($\sigma_h = 1.35 d$) the local |
451 |
< |
curvature resolves into a symmetrically rippled phase with little or |
452 |
< |
no interdigitation between the upper and lower leaves of the membrane. |
453 |
< |
The largest heads studied ($\sigma_h = 1.41 d$) resolve into an |
454 |
< |
asymmetric rippled phases with interdigitation between the two |
455 |
< |
leaves.\label{mdfig:phaseCartoon}} |
444 |
> |
\caption[ three phases observed in the simulations]{The role of the |
445 |
> |
ratio between the head group size and the width of the molecular |
446 |
> |
bodies is to increase the local membrane curvature. With strong |
447 |
> |
attractive interactions between the head groups, this local curvature |
448 |
> |
can be maintained in bilayer structures through surface corrugation. |
449 |
> |
Shown above are three phases observed in these simulations. With |
450 |
> |
$\sigma_h = 1.20 d$, the bilayer maintains a flat topology. For |
451 |
> |
larger heads ($\sigma_h = 1.35 d$) the local curvature resolves into a |
452 |
> |
symmetrically rippled phase with little or no interdigitation between |
453 |
> |
the upper and lower leaves of the membrane. The largest heads studied |
454 |
> |
($\sigma_h = 1.41 d$) resolve into an asymmetric rippled phases with |
455 |
> |
interdigitation between the two leaves.\label{mdfig:phaseCartoon}} |
456 |
|
\end{figure} |
457 |
|
|
458 |
|
Sample structures for the flat ($\sigma_h = 1.20 d$), symmetric |
478 |
|
for PE head groups. |
479 |
|
|
480 |
|
\begin{table*} |
485 |
– |
\begin{minipage}{\linewidth} |
481 |
|
\begin{center} |
482 |
< |
\caption{Phase, bilayer spacing, area per lipid, ripple wavelength |
483 |
< |
and amplitude observed as a function of the ratio between the head |
484 |
< |
beads and the diameters of the tails. Ripple wavelengths and |
490 |
< |
amplitudes are normalized to the diameter of the tail ellipsoids.} |
482 |
> |
\caption{PHASE, BILAYER SPACING, AREA PER LIPID, RIPPLE WAVELENGTH AND |
483 |
> |
AMPLITUDE OBSERVED AS A FUNCTION OF THE RATIO BETWEEN THE HEAD BEADS |
484 |
> |
AND THE DIAMETERS OF THE TAILS} |
485 |
|
\begin{tabular}{lccccc} |
486 |
|
\hline |
487 |
|
$\sigma_h / d$ & type of phase & bilayer spacing (\AA) & area per |
492 |
|
1.35 & symmetric ripple & 42.9 & 51.7 & 17.2 & 2.2 \\ |
493 |
|
1.41 & asymmetric ripple & 37.1 & 63.1 & 15.4 & 1.5 \\ |
494 |
|
\end{tabular} |
495 |
+ |
\begin{minipage}{\linewidth} |
496 |
+ |
%\centering |
497 |
+ |
\vspace{2mm} |
498 |
+ |
Ripple wavelengths and amplitudes are normalized to the diameter of |
499 |
+ |
the tail ellipsoids. |
500 |
|
\label{mdtab:property} |
502 |
– |
\end{center} |
501 |
|
\end{minipage} |
502 |
+ |
\end{center} |
503 |
|
\end{table*} |
504 |
|
|
505 |
|
The membrane structures and the reduced wavelength $\lambda / d$, |
515 |
|
\begin{figure} |
516 |
|
\centering |
517 |
|
\includegraphics[width=\linewidth]{./figures/mdTopDown.pdf} |
518 |
< |
\caption{Top views of the flat (upper), symmetric ripple (middle), |
519 |
< |
and asymmetric ripple (lower) phases. Note that the head-group |
520 |
< |
dipoles have formed head-to-tail chains in all three of these phases, |
521 |
< |
but in the two rippled phases, the dipolar chains are all aligned {\it |
522 |
< |
perpendicular} to the direction of the ripple. Note that the flat |
523 |
< |
membrane has multiple vortex defects in the dipolar ordering, and the |
524 |
< |
ordering on the lower leaf of the bilayer can be in an entirely |
525 |
< |
different direction from the upper leaf.\label{mdfig:topView}} |
518 |
> |
\caption[Top views of the flat, symmetric ripple, and asymmetric |
519 |
> |
ripple phases]{Top views of the flat (upper), symmetric ripple |
520 |
> |
(middle), and asymmetric ripple (lower) phases. Note that the |
521 |
> |
head-group dipoles have formed head-to-tail chains in all three of |
522 |
> |
these phases, but in the two rippled phases, the dipolar chains are |
523 |
> |
all aligned {\it perpendicular} to the direction of the ripple. Note |
524 |
> |
that the flat membrane has multiple vortex defects in the dipolar |
525 |
> |
ordering, and the ordering on the lower leaf of the bilayer can be in |
526 |
> |
an entirely different direction from the upper |
527 |
> |
leaf.\label{mdfig:topView}} |
528 |
|
\end{figure} |
529 |
|
|
530 |
|
The orientational ordering in the system is observed by $P_2$ order |
589 |
|
\begin{figure} |
590 |
|
\centering |
591 |
|
\includegraphics[width=\linewidth]{./figures/mdRP2.pdf} |
592 |
< |
\caption{The $P_2$ order parameters for head groups (circles) and |
593 |
< |
molecular bodies (squares) as a function of the ratio of head group |
594 |
< |
size ($\sigma_h$) to the width of the molecular bodies ($d$). \label{mdfig:rP2}} |
592 |
> |
\caption[The $P_2$ order parameters as a function of the ratio of head group |
593 |
> |
size to the width of the molecular bodies]{The $P_2$ order parameters |
594 |
> |
for head groups (circles) and molecular bodies (squares) as a function |
595 |
> |
of the ratio of head group size ($\sigma_h$) to the width of the |
596 |
> |
molecular bodies ($d$). \label{mdfig:rP2}} |
597 |
|
\end{figure} |
598 |
|
|
599 |
|
In addition to varying the size of the head groups, we studied the |
642 |
|
\begin{figure} |
643 |
|
\centering |
644 |
|
\includegraphics[width=\linewidth]{./figures/mdSP2.pdf} |
645 |
< |
\caption{The $P_2$ order parameters for head group dipoles (a) and |
646 |
< |
molecular bodies (b) as a function of the strength of the dipoles. |
645 |
> |
\caption[The $P_2$ order parameters as a function of the strength of |
646 |
> |
the dipoles.]{The $P_2$ order parameters for head group dipoles (a) |
647 |
> |
and molecular bodies (b) as a function of the strength of the dipoles. |
648 |
|
These order parameters are shown for four values of the head group / |
649 |
|
molecular width ratio ($\sigma_h / d$). \label{mdfig:sP2}} |
650 |
|
\end{figure} |
675 |
|
\begin{figure} |
676 |
|
\centering |
677 |
|
\includegraphics[width=\linewidth]{./figures/mdTP2.pdf} |
678 |
< |
\caption{The $P_2$ order parameters for head group dipoles (a) and |
679 |
< |
molecular bodies (b) as a function of temperature. |
680 |
< |
These order parameters are shown for four values of the head group / |
681 |
< |
molecular width ratio ($\sigma_h / d$).\label{mdfig:tP2}} |
678 |
> |
\caption[The $P_2$ order parameters as a function of temperature]{The |
679 |
> |
$P_2$ order parameters for head group dipoles (a) and molecular bodies |
680 |
> |
(b) as a function of temperature. These order parameters are shown |
681 |
> |
for four values of the head group / molecular width ratio ($\sigma_h / |
682 |
> |
d$).\label{mdfig:tP2}} |
683 |
|
\end{figure} |
684 |
|
|
685 |
|
Fig. \ref{mdfig:phaseDiagram} shows a phase diagram for the model as a |
698 |
|
\begin{figure} |
699 |
|
\centering |
700 |
|
\includegraphics[width=\linewidth]{./figures/mdPhaseDiagram.pdf} |
701 |
< |
\caption{Phase diagram for the simple molecular model as a function |
702 |
< |
of the head group / molecular width ratio ($\sigma_h / d$) and the |
703 |
< |
strength of the head group dipole moment |
704 |
< |
($\mu$).\label{mdfig:phaseDiagram}} |
701 |
> |
\caption[Phase diagram for the simple molecular model]{Phase diagram |
702 |
> |
for the simple molecular model as a function of the head group / |
703 |
> |
molecular width ratio ($\sigma_h / d$) and the strength of the head |
704 |
> |
group dipole moment ($\mu$).\label{mdfig:phaseDiagram}} |
705 |
|
\end{figure} |
706 |
|
|
707 |
|
We have computed translational diffusion constants for lipid molecules |
708 |
|
from the mean-square displacement, |
709 |
|
\begin{equation} |
710 |
< |
D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle {|\left({\bf r}_{i}(t) - {\bf r}_{i}(0) \right)|}^2 \rangle, |
710 |
> |
D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle {|\left({\bf |
711 |
> |
r}_{i}(t) - {\bf r}_{i}(0) \right)|}^2 \rangle, |
712 |
> |
\label{mdeq:msdisplacement} |
713 |
|
\end{equation} |
714 |
|
of the lipid bodies. Translational diffusion constants for the |
715 |
|
different head-to-tail size ratios (all at 300 K) are shown in table |
750 |
|
times that are too fast when compared with experimental measurements. |
751 |
|
|
752 |
|
\begin{table*} |
746 |
– |
\begin{minipage}{\linewidth} |
753 |
|
\begin{center} |
754 |
< |
\caption{Fit values for the rotational correlation times for the head |
755 |
< |
groups ($\tau^h$) and molecular bodies ($\tau^b$) as well as the |
756 |
< |
translational diffusion constants for the molecule as a function of |
757 |
< |
the head-to-body width ratio. All correlation functions and transport |
752 |
< |
coefficients were computed from microcanonical simulations with an |
753 |
< |
average temperture of 300 K. In all of the phases, the head group |
754 |
< |
correlation functions decay with an fast librational contribution ($12 |
755 |
< |
\pm 1$ ps). There are additional moderate ($\tau^h_{\rm mid}$) and |
756 |
< |
slow $\tau^h_{\rm slow}$ contributions to orientational decay that |
757 |
< |
depend strongly on the phase exhibited by the lipids. The symmetric |
758 |
< |
ripple phase ($\sigma_h / d = 1.35$) appears to exhibit the slowest |
759 |
< |
molecular reorientation.} |
754 |
> |
\caption{FIT VALUES FOR THE ROTATIONAL CORRELATION TIMES FOR THE HEAD |
755 |
> |
GROUPS ($\tau^h$) AND MOLECULAR BODIES ($\tau^b$) AS WELL AS THE |
756 |
> |
TRANSLATIONAL DIFFUSION CONSTANTS FOR THE MOL\-E\-CULE AS A FUNCTION |
757 |
> |
OF THE HEAD-TO-BODY WIDTH RATIO} |
758 |
|
\begin{tabular}{lcccc} |
759 |
|
\hline |
760 |
|
$\sigma_h / d$ & $\tau^h_{\rm mid} (ns)$ & $\tau^h_{\rm |
765 |
|
1.35 & $3.2$ & $4.0$ & $0.9$ & $3.42(1)$ \\ |
766 |
|
1.41 & $0.3$ & $23.8$ & $6.9$ & $7.16(1)$ \\ |
767 |
|
\end{tabular} |
768 |
+ |
\begin{minipage}{\linewidth} |
769 |
+ |
%\centering |
770 |
+ |
\vspace{2mm} |
771 |
+ |
All correlation functions and transport coefficients were computed |
772 |
+ |
from microcanonical simulations with an average temperture of 300 K. |
773 |
+ |
In all of the phases, the head group correlation functions decay with |
774 |
+ |
an fast librational contribution ($12 \pm 1$ ps). There are |
775 |
+ |
additional moderate ($\tau^h_{\rm mid}$) and slow $\tau^h_{\rm slow}$ |
776 |
+ |
contributions to orientational decay that depend strongly on the phase |
777 |
+ |
exhibited by the lipids. The symmetric ripple phase ($\sigma_h / d = |
778 |
+ |
1.35$) appears to exhibit the slowest molecular reorientation. |
779 |
|
\label{mdtab:relaxation} |
771 |
– |
\end{center} |
780 |
|
\end{minipage} |
781 |
+ |
\end{center} |
782 |
|
\end{table*} |
783 |
|
|
784 |
|
\section{Discussion} |
852 |
|
orientations of the membrane dipoles may be available from |
853 |
|
fluorescence detected linear dichroism (LD). Benninger {\it et al.} |
854 |
|
have recently used axially-specific chromophores |
855 |
< |
2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3-phospocholine |
856 |
< |
($\beta$-BODIPY FL C5-HPC or BODIPY-PC) and 3,3' |
855 |
> |
2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3-\\ |
856 |
> |
phospocholine ($\beta$-BODIPY FL C5-HPC or BODIPY-PC) and 3,3' |
857 |
|
dioctadecyloxacarbocyanine perchlorate (DiO) in their |
858 |
|
fluorescence-detected linear dichroism (LD) studies of plasma |
859 |
|
membranes of living cells.\cite{Benninger:2005qy} The DiO dye aligns |