Molecular Dynamics Simulations of Ether- and Ester-Linked

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Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipid Bilayers: A Comparative Study of Water Models Hujun Shen, Zhenhua Wu, Mingsen Deng, Shuiguo Wen, Chenggui Gao, Shixiong Li, and Xupu Wu J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.8b06726 • Publication Date (Web): 19 Sep 2018 Downloaded from http://pubs.acs.org on September 25, 2018

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The Journal of Physical Chemistry

Molecular Dynamics Simulations of Ether- and Ester-linked Phospholipid Bilayers: A Comparative Study of Water Models

Hujun Shen1,2*, Zhenhua Wu2, Mingsen Deng1,2, Shuiguo Wen1, Chenggui Gao1, Shixiong Li1, Xupu Wu1

1

Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University No.115, Gaoxin Road, Guiyang, Guizhou, 550018, P. R. China

2.

Guizhou University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou, 550025, P. R. China

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ABSTRACT Membrane Dipole potential influences a variety of important biological processes involving cell membranes. Since it is quite challenging to directly measure the membrane dipole potential in experiments, molecular dynamics (MD) simulation has emerged as a powerful tool for a reasonable prediction of the dipole potential. Although MD predictions agree well with experiment about the sign of dipole potential, the magnitude of dipole potential varies significantly with the force field parameters. It has been shown that the positive dipole potential of PC bilayer membranes would be overestimated by a non-polarizable model owing to the treatment of many-body polarization effects in a mean-field fashion. In this work, we carried out atomistic MD simulations of the diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers and made a comparative study of three different non-polarizable water models (TIP3P, TIP4P, and TIP5P). Interestingly, we discover that the calculated dipole potential by the TIP5P model show a nice agreement with the result obtained using the cryoelectron microscopy (cryo-EM) experiment, suggesting that a better description of electrostatic interactions in a non-polarizable water model can effectively ameliorate the overestimation in the calculation of dipole potential. In addition, our MD results show that the substitution of the ether linkage for the ester linkage of phospholipid would bring about a change in the orientation of the linkage group with respect to the bilayer normal, leading to the difference in the membrane dipole potential. Surprisingly, although water molecules provide a major contribution to the positive dipole potential, they have a limited impact on the difference of dipole potential between the ether-DPhPC and ester-DPhPC bilayer membranes.


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INTRODUCTION A lipid bilayer is a thin membrane, in which lipid molecules are arranged in such a way that the hydrophobic chains form the membrane interior and the hydrophilic headgroups are exposed to aqueous environment. Owing to the amphiphilic nature of lipid molecules, the alignment of the dipolar groups (such as the lipid headgroups and water molecules) produces the difference of electrostatic potential between the membrane interior (with low dielectric constant) and the aqueous medium (with high dielectric constant), and this difference in electrostatic potential is termed as “dipole potential”.1 It has been recognized that a large positive dipole potential within the membrane interior would substantially promote the permeation of anions or prevent the transport of cations into the membrane. For instance, when Liberman and Topaly 2 were studying the permeability of phospholipid membranes for fat-soluble ions, they were surprised to find that tetraphenylborate (TPB-) increases the membrane permeability at least 105 times larger as compared to triphenylmethylphosphonium (TMP+). It has been known that the dipole potential can generate the electric field of 108-109 V/m, which is at least 1 order of magnitude greater than the electric fields (106 -107 V/m) generated by the transmembrane and surface potentials.3.4 Thus, the studies on the effects of dipole potential have attracted much attentions of many cell biology researchers. For instance, Rokitskaya and coworkers5 revealed the effects of dipole potential on the association and dissociation of gramicidin channels in lipid bilayer membranes. In addition, Rokitskaya and coworkers6 measured the proton permeation through gramicidin A channels in experiment, finding that the proton conductance of gramicidin channels can be modulated by modifying the membrane dipole potential. When Cladera and O’Shea7 were investigating the relationship between the membrane dipole potential and the interaction of peptides with membranes, they discovered that the membrane dipole potential would influence the peptide conformation in the model membranes on the one hand and the insertion of peptide into the model membranes would affect the membrane dipole potential on the



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other hand. Recently, Kovács and coworkers8 have shown that the homo-association and hetero-association of ErbB proteins (receptor tyrosine kinases) can be regulated by modifying the membrane dipole potential, and they suggested that the signaling efficiency of ErbB proteins should be related to the membrane dipole potential. To measure the membrane dipole potential, there are a few commonly used experimental methods: planar lipid bilayer method,9 planar lipid monolayer method,3 and lipid vesicle method.10 Among them, the lipid bilayer method is an indirect measurement based on the kinetics of hydrophobic ion translocation through lipid bilayer while the lipid monolayer method requires air electrodes to measure the electrical potential difference across lipid monolayer. In the lipid vesicle method, the estimate of the dipole potential can be made either based on hydrophobic ion interaction or using voltage-sensitive dyes. In general, the values of the dipole potential (200-300 mV) determined from the lipid bilayer and vesicle methods are lower than those (300-400 mV) calculated from the lipid monolayer methods.10 The dipole potential can be determined by cryoelectron microscopy method (cryo-EM) proposed by Wang and coworkers11, who used point charge probes (electrons) instead of large hydrophobic ions or voltage-sensitive dyes. Nevertheless, the cryo-EM method heavily relies on the calculated atom density profile obtained from molecular dynamics (MD) simulation,4,11 the accuracy of which depends on the force field parameters employed. Thus, the dipole potential determined from the cryo-EM method shows a large difference from the results obtained from the lipid bilayer and monolayer

methods.

For

instance,

the

dipole

potential

of

diphytanyl

phosphatidylcholine (DPhPC) bilayer was estimated to be 228 mV by a lipid bilayer method12 and was determined to be 510 mV by the cryo-EM method.11 It has been shown that a variety of MD simulations can successfully reproduce the physical properties of lipid bilayers measured by the X-ray and NMR experiments.13-19 Meanwhile, MD simulations can provide a reasonable prediction of the membrane dipole potential as well as a valuable interpretation of experimental results on a microscopic level.20-25 For instance, Shinoda and coworkers20 carried out atomistic MD simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and ACS Paragon Plus Environment

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diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers under aqueous conditions, revealing that the dipole potential of the ether-linked phospholipid bilayer is about half of that of the ester-linked phospholipid bilayer. This observation is consistent with the cryo-EM experiment11 and the lipid bilayer experiments.12,26 It has been established that the membrane dipole potential is influenced by the orientation and magnitude of molecular dipoles, including the contributions from the water molecules,3 lipid headgroup,3 and ester (or ether) linkage.11,12,26 Based on various MD simulations, it has been clearly revealed that, in the case of phospholipidcholine (PC) lipid bilayers, the positive contribution of water molecules to total dipole potential can overcompensate the negative contribution of lipid molecules,27 leading to the positive dipole potential inside the PC lipid membranes. Although these simulation results agree with experiment about the positive sign of the dipole potential, the magnitude varies significantly with the force field parameters employed. In particular, the commonly used water models (such as SPC/E,28 TIP3P,29 TIP4P29) yield too positive values of the dipole potential as compared to experiment.30,31 It has been suggested that the overestimation is due to the mean-field treatment of many-body polarization effects in the fixed charge model.30-32 In this work, we discover for the first time that the overestimation could be significantly reduced by using the TIP5P water model,33 which has a better description of electrostatic interactions than other water models (such as TIP3P and TIP4P ). This is consistent with an earlier observation that a slight change in the molecular charge distribution would results in a significant change in the air-water surface potential.34,35 In the following work, we show a comparative study of the effect of water models (TIP3P, TIP4P, and TIP5P) on the dipole potential of the ether-DPhPC and ester-DPhPC bilayer membranes. Our results reveal that the TIP3P and TIP4P models allow water molecules to penetrate more deeply into the membrane interior than the TIP5P model, influencing the positive contributions of water molecules to the dipole potential. It is encouraging that the calculated values of the dipole potential using the TIP5P water model can effectively reduce the overestimation by the TIP3P and TIP4P models. Meanwhile, MD simulations based on the different water models can ACS Paragon Plus Environment


correctly predict the difference of the dipole potential between the ether-DPhPC and ester-DPhPC membranes. Our work shows that this difference mainly arises from the different orientation of the linkage groups (ether and ester) with respect to the bilayer normal.

METHODS Lennard Jones Modified General Amber Force Field for Lipids The General Amber Force Field (GAFF)36 was originally developed for MD simulations of biomolecular complexes with ligands (including small organic molecules, drugs, etc.). Jójárt et al.37 made a first attempt to simulate POPC bilayers using the GAFF parameters, finding that the GAFF/TIP3P combination shows a nice performance. Siu et al.38 presented the comparison between the GAFF and CHARMM27 simulations of DOPC lipid bilayers, demonstrating that the two approaches can offer consistent results. Rosso and Gould39 have demonstrated the reliability of GAFF in the simulations of DOPC and DMPC lipid bilayers, suggesting that the combination of the AMBER force field and RESP charge methodology can provide a promising way for theoretical studies of lipid-protein interactions. However, in the absence of a surface tension, the prediction of area per lipid by GAFF would underestimate the experimental results.39 To solve the limitation of GAFF, Dickson and coworkers16 suggested that the GAFF Lennard Jones (LJ) parameter should be adjusted to simulate lipid bilayers without applying surface tension.


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Figure 1. Stick representation for the ester-DPhPC and ether-DPhPC molecules.

In this work, we derived the Lennard Jones modified GAFF force field (LJ-GAFF) for the ether-DPhPC and ester-DPhPC lipids (presented respectively in Figure 1) by following the traditional procedure: 1) Initial structures for the ester-DPhPC and ether-DPhPC molecules were generated using the Gaussian viewer software and then optimized at the Hartree–Fock self-consistent field (HF-SCF) level with the 6-31G* basis set using the Gaussian 09 program.40 Then, the minimized structures were further optimized using the DFT-B3LYP/3-21g* method. 2) Single point calculations on the optimized structures were carried out at the HF/6-31G* level and then atomistic charges were derived based on the restrained electrostatic potential (RESP) method41. Please note that the initial partial charges for atoms will be updated in step 7. 3) The van der Waals (vdW) parameters were directly obtained from the GAFF force field. Meanwhile, the LJ parameters for GAFF “c3”and “hc” atom types were modified according to the Table 2 of reference 16. The conventional Lennard-Jones term was used to compute the vdW interactions. 4) The bonded parameters (in the bond stretching, angle bending, and torsional terms) were directly extracted from the GAFF force field. A simple harmonic functional form was adopted in the bond stretching and angle bending terms respectively while a cosine functional form was employed in the torsional term 5) The ACPYPE utility42 was used to generate the topology and coordinate files for MD simulations in the GROMACS simulation package.43 6) For each lipid type (ester-DPhPC or ether-DPhPC), 64 lipid molecules were randomly immerged in a cubic box containing 2500 water molecules and then 50 ns MD simulations of the lipid-water mixtures were carried out in order to generate different monomer conformations. 7) For each case, 100 different monomer conformations were randomly selected



from the 50 ns MD simulations and were respectively optimized using DFT-B3LYP/3-21g* and finally HF/6-31G*. Then, the RESP calculations of 100 different conformations were respectively carried out and the final partial charges for atoms were determined in an average way. The traditional coulombic potential was used to calculate the electrostatic interactions.

Atomistic MD Simulations Atomistic MD simulations of the ether-DPhPC and ester-DPhPC lipid bilayers were carried out with the LJ-GAFF force field in the simulation package GROMACS 4.6.7.43 For each lipid type, 256 lipids and 10400 water molecules (using the TIP3P , TIP4P, and TIP5P water models respectively) were mixed together using the PACKMOL program.44 The starting conformation was minimized by the conjugate gradient (CG) method45 and then by the steepest descent (SD) method.46 Subsequently, each system was equilibrated for 200 ps under NPT condition before a NPT production run was performed for 300 ns. Finally, the simulation data collected from last 200 ns were used for the analysis of physical properties of lipid bilayers. During the NPT simulations, the semi-isotropic pressure of 1 bar (in the z direction and x/y plane respectively) was maintained by using the Parrinello-Rahman algorithm47 while the velocity rescaling method48 was used to control the constant temperature of 323 K. All bonds involving hydrogen atoms were constrained with the LINC algorithm49 such that an integration time step of 2 fs could be adopted. Electrostatic interactions with a cutoff value of 1.5 nm were calculated based on the particle mesh Ewald (PME) algorithm50 while van der Waals (vdW) interactions were truncated at a cutoff value of 1.5 nm.

RESULTS and DISCUSSION 1. Lennard Jones Modified General Amber Force Field (LJ-GAFF) for the ester- and ether-DPhPC lipids In this work, we performed atomistic MD simulations of the ester-DPhPC and ether-DPhPC bilayers using the LJ-GAFF parameters. For each lipid type, a lipid


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bilayer membrane was respectively simulated using three different water models (TIP3P, TIP4P, and TIP5P). The number density profiles for the phosphate (PO4) and choline (CHOL) groups are shown in Figure 2. In the case of the ether-DPhPC bilayer, it seems that the water models have a slight influence on the peak sharpness in the density distribution of PO4 (shown in Figure 2A). However, the TIP5P water model noticeably increases the peak sharpness in the density distribution of CHOL in comparison with the TIP3P and TIP4P water models (presented in Figure 2C). Similarly, in the case of the ester-DPhPC bilayer, the TIP5P water model tends to sharpen the density distributions of PO4 and CHOL as compared to the TIP3P and TIP4P water models, shown in Figures 2B and 2D. These results suggest that, in comparison with the TIP3P and TIP4P models, the TIP5P water model would cause a denser distribution of the angle θ between the phosphorus-nitrogen (P-N) vector and the bilayer normal (z-axis), which is given in Figure S1 of Supporting Information. From the number density profiles for PO4, we can calculate the bilayer thickness, which is defined as the phosphate-to-phosphate distance (dPtP) in this work. Table 1 summarizes the calculated values for the bilayer thickness obtained from our MD simulations as well as the comparison to experiment and the CHARMm results calculated by Shinoda and coworkers,20 showing a nice agreement between them.

Table 1. Physical properties of the ether-DPhPC and ester-DPhPC bilayer membranes obtained from the MD simulations using the LJ-GAFF parameters, and the comparison is made between the LJ-GAFF and CHARMm results.18 The experimental (Exp.) values for the bilayer thickness (dPtP) and area per lipid (Ap) are respectively taken from Ref. 51. ether-DPhPC CHARMm

dPtP (nm) 2

Ap (nm )

Φd (mV)

3.83±0.06

0.74

567

ester-DPhPC

LJ-GAFF TIP3P

TIP4P

TIP5P

3.89

3.91

3.83

±0.06

±0.07

±0.05

Exp.

CHARMm

LJ-GAFF TIP3P

NA

0.73

0.74

0.71

±0.01

±0.01

±0.01

644

609

190

260 11

±58

±47

±31

114 12*

NA

3.71±0.04

0.78

1002

* the dipole potential of ether-linked DPPC (DHPC)


TIP4P

Exp.

TIP5P

3.81

3.76

3.79

±0.06

±0.05

±0.05

3.80

0.76

0.77

0.74

±0.01

±0.01

±0.01

0.76

1072

1001

515

510 11

±87

±81

±46

228 12


Figure 2. Number density profiles for (A) the phosphate group (PO4) of ether-DPhPC, (B) the phosphate group (PO4) of ester-DPhPC, (C) the choline group (CHOL) of ether-DPhPC, and (D) the choline group (CHOL) of ester-DPhPC, obtained from the LJ-GAFF simulations using three different water models: TIP3P (black), TIP4P (red) and TIP5P (blue).

The area per lipid for the ether-DPhPC and ester-DPhPC bilayers was respectively measured according to the following equation: 2 ∙ ∙ 1

where represents the number of lipids, and respectively denote the x- and

y-dimension of the simulation box, and the x-y plane defines the surface of lipid bilayer systems. From Table 1, one can see that the LJ-GAFF/TIP3P and LJ-GAFF/TIP4P simulations nicely reproduce the results for area per lipid obtained from the CHARMm simulations, consistently demonstrating that the area per lipid is


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slightly smaller for the ether-DPhPC bilayer than for the ester-DPhPC bilayer. However, the wide-angle X-ray scattering (WAXS) experiment52 revealed that the substitution of an ether-linkage for an ester linkage of DPPC would lead to a slight increase in area per lipid. This suggests that the force field parameters (in particular LJ parameters) for lipids need to be slightly refined to accurately reproduce the experimental trend, which is under work. As for the LJ-GAFF/TIP5P simulations, it appears that the bilayer membranes are slightly compressed along the x-y plane, leading to a noticeable decrease in area per lipid. The decrease in area per lipid would prevent a deeper water penetration into the lipid bilayers, shown in Figure 3.

Figure 3. Number density profiles for water in the (A) ether-DPhPC and (B) ester-DPhPC bilayers, obtained from the GAFF simulations with three different water models: TIP3P(black), TIP4P(red), and TIP5P(blue).

Figure 4 shows the radial distribution functions (RDFs) for the ether-DPhPC and ester-DPhPC bilayers. Although the water models have a limited impact on the peak position in the RDF profiles, the TIP3P and TIP4P models significantly enhance the intensity of the peaks (or the degree of hydration of lipid headgroups) as compared to the TIP5P model. The increase in the peak height agrees with the observation in Figure 3, showing that the TIP3P and TIP4P models would allow water molecules to penetrate more deeply into the membranes than the TIP5P model. When compared with the TIP3P and TIP4P models, the TIP5P model improves the description of electrostatic interactions, which has a significant effect on the calculations of the structural and thermodynamic properties of water.33,53 Actually, it has been well



recognized that the reliability of MD prediction of dipole potential should heavily rest on the accuracy of describing the ordering of water molecules at the lipid/water interface. One can see from Table 1 that the TIP5P model can significantly improve the prediction of the dipole potential as compared to the TIP3P and TIP4P models, suggesting that improving the description of electrostatic interactions is critical to the accurate estimation of dipole potential.

Figure 4. Radial distribution functions g(r) for lipid-water mixtures, obtained from the LJ-GAFF simulations with three different water models: TIP3P (black), TIP4P (red), and TIP5P (blue). (A) g(Nlipid-Owater) for the ether-DPhPC bilayer, (B) g(Plipid-Owater) for the ether-DPhPC bilayer, (C) g(Nlipid-Owater) for the ester-DPhPC bilayer, and (D) g(Plipid-Owater) for the ester-DPhPC bilayer.

2. Effect of Water Models on the Membrane Dipole Potential By setting z-axis as the bilayer normal, the electrostatic potential along the bilayer normal can be calculated from a double integration of local charge density ρz :


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1 z dz ρz dz 2 ε

where ε represents the vacuum permittivity. To investigate the effect of water models on the membrane dipole potential, we constructed the electrostatic potential profiles for the ether-DPhPC and ester-DPhPC bilayers with three different water models (TIP3P, TIP4P, and TIP5P), shown in Figure 5. In this work, the electrostatic potential in the aqueous region is set to 0, such that the dipole potential is actually equivalent to the electrostatic potential at the center of the lipid bilayers. Table 1 summarizes the calculations of the dipole potential, showing that the experimental values are significantly overestimated by the TIP3P and TIP4P models. However, the overestimation by the TIP3P and TIP4P models can be effectively reduced by using the TIP5P model, which has an improved description of the electrostatic interactions. In addition, one can see from Figure 5 that these electrostatic potential profiles share a similar pattern: the electrostatic potential rises from the aqueous region to the interior of lipid bilayers and then decrease moderately (0.1-0.2 V) at the center of the lipid bilayers. The moderate drop in the electrostatic potential at the center of lipid bilayers should be associated with the increased negative contribution of lipids at the center, shown in Figure 6.

Figure 5. Electrostatic potential profiles for the (A) ether-DPhPC and (B) ester-DPhPC bilayer membranes.



Figure 6. Electrostatic potential profiles for the positive contributions of water molecules from (A) the ether-DPhPC and (B) ester-DPhPC bilayer membranes, as well as for the negative contributions of lipids from (C) the ether-DPhPC and (D) ester-DPhPC bilayer membranes.

In Figure 6, we separately plotted the individual contributions of the water and lipid molecules to total electrostatic potential. These figures show the positive contribution of water molecules (in Figures 6A-B) and the negative contribution of lipids (in Figures 6C-D), in consistence with previous MD studies.20-25 The negative contribution from lipids can be overcompensated by the positive contribution of water molecules, leading to the positive dipole potential inside the membranes. However, these individual contribution profiles show the dependence of the electrostatic potential on the water model. When compared with the TIP5P model, it seems that the TIP3P and TIP4P models significantly enhance the positive contributions of water molecules as well as the negative contributions of lipid molecules. Meanwhile, the effect of water models influences the positive contributions of water more significantly than the negative contributions of lipid molecules. This emphasizes the importance of the better description of electrostatic interactions in a non-polarizable ACS Paragon Plus Environment

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water model.

Figure 7. Electrostatic potential profiles for the individual contributions of ether segments from the (A) ether-DPhPC bilayer membrane, and those of ester segments from the (B) ester-DPhPC bilayer membrane

Figure 7 demonstrates the individual contributions of the ester and ether segments to total electrostatic potential. Similarly, these figures show the dependence of the electrostatic potential on the water models as well as the positive contribution from the ether or ester linkage. Table 2 shows that the positive contribution of water molecules can overcompensate the negative contribution of lipid molecules, partly owing to the positive contribution of the ether or ester linkage. However, one can see from Table 2 that the water molecules play a major role in the positive dipole potential while the ether or ester linkage plays a minor role. Interestingly, Table 1 shows that the TIP5P water model influences the dipole potential of the ether-DPhPC bilayer more significantly than that of the ester-DPhPC bilayer as compared to the TIP3P and TIP4P models. This difference arises from the different influence of the water models on the water penetration into bilayer (see Figure S2 of Supporting Information), which affects the negative contribution of lipids and the positive contribution of water molecules, shown in Table 2 and Figure 6. For instance, in the case of the ether-DPhPC bilayer, the use of TIP5P decreased the negative contribution of lipids and the positive contribution of water similarly to about 1/2 of the values obtained from TIP3P and TIP4P. However, in the case of the ester-DPhPC bilayer, the use of TIP5P reduced the negative contribution of lipids to about 1/4 and the positive ACS Paragon Plus Environment


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contribution of water to about 1/3 as compared to the values obtained from TIP3P and TIP4P. Table 2. The dipole potential of the ether-DPhPC and ester-DPhPC bilayer membranes calculated from the LJ-GAFF simulations using three different water models (TIP3P, TIP4P, and TIP5P), including their individual contributions from water, lipid. and ether or ester.

ether-DPhPC Total Dipole Potential

ester-DPhPC

TIP3P

TIP4P

TIP5P

TIP3P

TIP4P

TIP5P

0.644

0.609

0.190

1.072

1.001

0.515

2.325

1.874

0.930

2.615

2.239

0.842

-1.681

-1.265

-0.740

-1.543

-1.238

-0.327

0.252

0.147

0.076

0.569

0.501

0.337

(V) Contribution of water (V) Contribution of lipid (V) Contribution of ether or ester (V)

3. Comparison of the Dipole Potential between the Ether-DPhPC and Ester-DPhPC Bilayer Membranes

Figure 8. (A) Electrostatic potential profiles for the ether-DPhPC and ester-DPhPC bilayer


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membranes, including the contributions from (B) water, (C) lipid, and (D) ether or ester. The calculated results were obtained from the LJ-GAFF/TIP5P simulations.

Figure 8 illustrates the comparison between the electrostatic potential profiles for the ether-DPhPC and ester-DPhPC membranes, including the individual contributions from water, lipid, and ether- or ester-linkage. Please note that the comparison is made based on the results obtained from the LJ-GAFF/TIP5P simulations. Meanwhile, Table 3 summarizes the difference of the dipole potential between the two different membranes, showing that the calculated result for the difference can reproduce the result obtained from the cry-EM experiment. It has been shown above that the positive contribution of water plays a dominant role in the positive dipole potential inside the bilayer membranes, given in Figure 6 and Table 2. One would expect that the decreased dipole potential arising from the substitution of the ester-linkage for the ether-linkage should be attributed to the decreased positive contribution of water. Surprisingly, our results show that this substitution slightly increases the positive contribution of water, presented in Figure 8B and Table 3. In contrast, one can see from Figure 8C and Table 3 that this substitution actually yields a significant decrease in the negative contribution of lipid, in particular the contribution of the linkage group (shown in Figure 8D and Table 3). Table 3. The difference (∆ ) of the dipole potential and individual contributions (from water, lipid, and linkage group), which was respectively obtained by subtracting the values of the ester-DPhPC membrane from those of the ether-DPhPC membrane. Difference of the dipole potential

Difference of the

Difference of the

Difference of the

(mV)

contribution of

contribution of

contribution of

water

lipid

linkage group

(mV)

(mV)

(mV)

88

-413

-425

LJ-GAFF

∆

-325

CHARMm

-435

Exp 11

-250 -12912*

* Difference between DHPC and DPPC

Based on the LJ-GAFF/TIP5P simulations, we plotted the number density profile for water with respect to the bilayer center, shown in Figure 9A. This figure shows



that water molecules penetrate into the interior of the ester-DPhPC bilayer more deeply than into that of the ether-DPhPC bilayer. This result is consistent with a previous observation by Shinoda and coworkers,20 revealing that the ester-linkage group is oriented to expose the carbonyl and ester oxygen atoms to water, leading to the deeper water penetration. Figure 9B shows the orientation of the dipole moment vector between the linkage group and the bilayer normal (Z-axis). In this figure, the dipole moment vector of the ether linkage is defined as the oxygen-carbon (O-C) vector and that of the ester linkage as the vector connecting the middle point of two oxygen atoms (the carbonyl and ester oxygen atoms) and the carbon atom, shown in the insets of Figure 9B respectively. Figure 9B demonstrates that the ester-linkage group is oriented more parallel to the membrane surface (x-y plane) than the ester-linkage group. Meanwhile, the orientation distribution of the ether linkage is wider than that of the ester linkage. These results provide a straightforward explanation of the change in the dipole potential owing to the substitution.

Figure 9. (A) Number density profile for water, obtained from the LJ-GAFF/TIP5P simulations of the ether-DPhPC and ester-DPhPC bilayers. (B) Probability distribution of the angles θether and θester. θether defines the orientation of the ether linkage with respect to the bilayer normal (Z-axis) while θester represents the orientation of the ester linkage with respect to the bilayer normal.

CONCLUSIONS In this work, we present a comparative study of the effect of water models (TIP3P, TIP4P, and TIP5P) on the dipole potential of the ether-DPhPC and ester-DPhPC ACS Paragon Plus Environment

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bilayer membranes. The calculated results for the dipole potential agree well with experiment about the positive sign of dipole potential inside the lipid bilayers. When the TIP3P and TIP4P models yield too positive dipole potential as compared to experiment, the TIP5P water model can effectively reduce the overestimation of the dipole potential. In comparison with the TIP5P model, the TIP3P and TIP4P models allow deeper water penetration into the interior of the lipid bilayers, increasing the positive contributions of water molecules to total dipole potential. This suggests that a better description of electrostatic interactions (in a non-polarizable water model) can effectively diminish the inaccuracy introduced by the mean-field treatment of many-body polarization effects. Second, our MD simulations correctly predict the difference of the dipole potential between the ether-DPhPC and ester-DPhPC membranes, showing that the membrane dipole potential is significantly reduced by replacing the ester linkage with the ether linkage. Our work reveals that this substitution would induce the alteration in the orientation of the linkage group with respect to the bilayer normal, leading to the difference in the membrane dipole potential. Surprisingly, this substitution has a limited influence on the positive contribution of water to the dipole potential but significantly affects the negative contribution of lipid.

AUTHOR INFORMATION Corresponding Authors *E-mail: [email protected],

Notes The authors declare no competing financial interest.

ACKNOWLEDGEMENTS This work is supported by the Plan Project for Guizhou Provincial Science and Technology (No. QKHJC[2016]1109), the construction project for Guizhou Provincial Key Disciplines (No. ZDXK[2015]10), the start-up fund from the Guizhou Education



University. We would like to thank Professor Luo Yi (Heifei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China) for helpful discussions.

Supporting Information for Publication Supporting Information contains the distributions of the angle θ between the phosphorus-nitrogen (P-N) vector and the bilayer normal and the number density profile for water. This information is available free of charge via the Internet at http://pubs.acs.org.

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Table of Content (TOC) Graphic


Molecular Dynamics Simulations of Ether- and Ester-Linked

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