Coarse-Grained Model for Mechanosensitive Ion Channels - The

Key Laboratory for Nanomaterials, Ministry of Education, Beijing University of ... (1-3) MS channels are also proposed to act as emergency safety ...
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J. Phys. Chem. B 2009, 113, 14431–14438

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Coarse-Grained Model for Mechanosensitive Ion Channels Shuangyang Li, Xianren Zhang,* and Wenchuan Wang* DiVision of Molecular and Materials Simulation, Key Laboratory for Nanomaterials, Ministry of Education, Beijing UniVersity of Chemical Technology, Beijing 100029, China ReceiVed: June 8, 2009; ReVised Manuscript ReceiVed: September 3, 2009

In this work, a coarse-grained model for a kind of membrane protein, the mechanosensitive channel of small conductance (MscS), is proposed. The basic structure of the MscS is preserved when the protein is coarsegrained. For the coarse-grained model, the channels show two different states, namely the open and closed states, depending on the model parameters. Under the same membrane tension, the state of the ion channel is found to be critically determined by the protein structure, especially the length of the transmembrane R-helix. It is also found that for the protein with certain size, the gating transition occurs when the membrane tension is applied, resembling in a real mechanosensitive channel. 1. Introduction In eukaryotic and prokaryotic cells, mechanosensitive (MS) channels, which can be opened or closed upon the change in membrane tension, are used to detect mechanical stimuli such as touch, hearing, vibration, or swelling.1-3 MS channels are also proposed to act as emergency safety valves preventing the cell from hypo-osmotic shock.4-7 Two mechanosensitive channels have been cloned and crystallized: the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis8 and the mechanosensitive channel of small conductance (MscS) from Escherichia coli.6,9 MscS and MscL were discovered with the development of a “giant spheroplast” preparation, which was essential for the examination of a bacterial cell membrane by the patch clamp technique.7,10 The 3D structures of both MscL and MscS channels have been solved by X-ray crystallography,8,9 and their structure dynamics and functions have recently been studied by using a whole array of structural methods and techniques, including 2D electron crystallography,11 electron paramagnetic resonance (EPR) spectroscopy,12-14 and fluorescence resonance energy transfer (FRET) spectroscopy.15 While the gating mechanism of MscL, which is found almost exclusively in bacterial cells, is well-understood and extensive experimental and theoretical studies have been performed,12,13,16-21 the gating mechanism of MscS, which plays an important role in cellular processes underlying osmoregulation and growth22 for bacteria, archaea, fungi, and plants, remains controversial. Computer simulation methods become increasingly valuable for understanding the structure and function of MscS, as they can reveal the internal dynamic behavior and the structural transition. For example, using a targeted molecular dynamics method, Kong et al.20 studied the pathway of the gating conformational transition of mechanosensitive channel in the switch process between open and closed states. Akitake et al.23,24 also explored the pathway for conformational transitions in MscS and provided evidence for a functional cycle of MscS that involves transitions of different states, in which the processes are controlled by the flexibility of the Tm3b near Gly113 and Gly121. Sotomayor and Schulten25 studied the * Corresponding authors. E-mail: [email protected] (X.Z.); [email protected] (W.W.).

stability of the channel conformation with molecular dynamics (MD) simulations. They found that the state of MscS varies with surface tension, and the interaction between the transmembrane domain and the cytoplasmic domain of MscS may be essential for the gating mechanism. Sotomayor et al.26 also reported the electrostatic properties of MscS in a palmitoyloleoylphosphatidylcholine (POPC) bilayer using a coarse-grained particle-based description based on the Boltzmann transport Monte Carlo method. Spronk and his co-workers applied electric fields in their MD simulations to model the transmembrane potential, which was proved to be important to determine whether the structure of MscS can conduct ions or not.27 In addition, it is found that the crystal structure of MscS is nonconductive at physiological voltages.25,27,28 Several researches reveal that the expanded crystal structure of MscS always displays a strong anionic selectivity in both MD27,29 and Brownian dynamics Monte Carlo (MC)26,30 simulations. Recently, Anishkin et al.31 made progress in the structure and stability of MscS, and they observed tilting and straightening of the kinked pore during the barrel expansion. Although these MD simulations provide deep insights into the gating mechanisms of ion channels, they are confronted with the problem of the simulation time scale (a few nanoseconds), being far from the biological one (milliseconds). Consequently, the time scale limitation generally prevents the mechanosensitive channels from large conformational changes and is only suitable for the earliest stages of the mechanism. To compensate for the limitation, different strategies, such as working at high temperatures, imposing some constraints as in steered MD, biasing the potential energy as in umbrella sampling, and using different protocols, were employed to accelerate the gating conformational changes. The main results obtained by these simulations tended to confirm the general features of the gating mechanism. However, the nature of the constraints and the approaches they adopted may influence the response of the system. It is noticed that a feasible method to resolve the problem above is to use the coarse-grained model.32,33 For example, Yefimov et al.34 recently presented a coarse-grained MD lipid-peptide model applied to the Tb-MscL. In the present paper, the dissipative particle dynamics (DPD) method, which can deal with larger length and time scales compared with the MD method, was applied to study MscS

10.1021/jp9053567 CCC: $40.75  2009 American Chemical Society Published on Web 09/25/2009

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TABLE 1: Parameters for Pair Interactions between Different Beads aij (kBT)

H (head)

T (tail)

E (link H and T)

W (solvent)

H T E W

86.7 104 79.3 75.8

104 78.0 86.7 104

79.3 86.7 78.0 79.3

75.8 104 79.3 78.0

within a coarse-grained framework. The aims of this work are to construct a coarse-grained model of MscS and verify its feasibility to address the gating mechanism of a mechanosensitive channel. The remainder of the paper is organized as follows. In section 2, we describe the simulation method and propose the model for mechanosensitive ion channels. The results and discussion are presented in section 3, which is followed by a brief summary of the main conclusions.

Figure 1. (a) Schematic drawings of the model of a lipid molecule. (b) Typical snapshot of the predefined vesicle in which the lipids are arranged around the center of the box. (c) Typical snapshot of the cross section of the vesicle. The red beads represent hydrophilic heads, the blue beads represent hydrophobic tails, the white beads represent particle E of the lipid molecules, and the yellow beads are water confined in the vesicle. Water beads outside the vesicle are not shown for clarity.

2. Model and Simulation Method 2.1. Dissipative Particle Dynamics Method. The dissipative particle dynamics (DPD) method was proposed initially to study the hydrodynamic behaviors of complex fluids.35-37 Recently, it has been applied to study a variety of amphiphilic systems.38-47 Similar to MD simulation, the time evolution of a DPD system is obtained by solving the equation of motion. The interparticle force exerted on a particle is composed of conservative, dissipative, and random forces. The conservative force between particles i and j is a soft repulsion acting along the line of the particle centers and is given by FCij ) aijrˆij max{1 - (rij/rc), 0}, where aij is the maximum repulsive force between particles i and j, rij ) rj - ri (ri and rj are the positions of particle i and particle j), rij ) |rij|, rˆij ) rij/|rij|, and rc is the interaction range. The parameters described the interactions between different beads are given in Table 1. This set of DPD parameters was derived from a molecular-specific mapping on phosphatidylethanolamine by Groot and Rabone.48 Although some atomistic details are sacrificed during this coarse-graining procedure, the essential thermodynamics of the system is reproduced by the simulation model and the parameter set. In our work, the interaction cutoff rc, all bead masses, and the thermostat temperature kBT were set to unity, i.e. rc ) m ) kBT ) 1. The interactions between the beads were set on the room temperature of 1.0. It is well-known that the translation of model parameter rc to the actual physical size depends on the coarse-grained level. To map rc to its actual physical size, we used the formula proposed by Groot and Rabone,48 rc ) 3.107(FNm)1/3 [Å]. In the formula, Nm is the number of water molecules represented by a DPD bead and F is the density, i.e., the number of DPD beads per cube of volume rc3. As usual, it is assumed that Nm ) 3, F ) 3.0, and a water molecule has approximately a volume of 30 Å3. Hence, we obtain that rc is 6.46 Å according to the formula. Besides these forces, there are also some other conservative forces exerted on lipid and protein molecules in this work. They are the forces constraining the bond length and the bond angle, respectively. The bond length can be constrained by a spring kij, where KS is the spring constant and force, FS ) KS(rij - req)r req is the equilibrium bond length. The numerical values of KS and req used for our simulations are 128kBT and 0.7rc, respectively.40 The force constraining the variation of the bond angle is given by Uφ ) Kφ(1 - cos(φ - φ0)), where φ0 is set to π46 and Kφ is the bond bending force constant. The time evolutions of the systems were obtained from a modified version of the Velocity-Verlet algorithm36 with a time step of ∆t ) 0.03. 2.2. Coarse-Grained Model for Lipid and MscS. In our work, the cell is modeled as a vesicle and the membrane of

vesicle is composed of lipid molecules (see Figure 1a). Note that the force constraining the variation of the bond angles is only added on two tail groups and the bond bending force constant is 10.0. To prepare the vesicle, 2000 lipid molecules were put in a simulation box with the size of 40 × 40 × 40, and arranged around the center of the box to form a spherical vesicle (shown in Figures 1b and c). 8000 water beads were randomly inserted inside of the vesicle, and the corresponding density of the whole system in the simulation box was set to 3.0. From the predefined initial configuration, a long DPD simulation of 100 000 time steps was performed at the temperature of 1.0 (T ) 1.0). The simulation results indicate that a stable elliptical vesicle can be formed without any observable pores. To eliminate the effects of the predefined initial configuration, the system was relaxed at the higher temperature of 2.0 for 30 000 time steps and then was annealed slowly to T ) 1.0 with another 50 000 time steps. Finally, a simulation run was performed for 20 000 time steps at T ) 1.0 again to obtain the stable configuration, which was used in the next step. A coarse-grained model of MscS is then developed in this work. The real protein of MscS is known to be composed of seven identical monomers which enclose a channel in cylindrical shape. Each monomer here consists of transmembrane and extramembrane regions (see Figure 2a): an N-terminal periplasmic region (a transmembrane region) and a C-terminal cytoplasmic region. In this study, the complicated extramembrane part inside the cell was simply reduced to hydrophilic chains, because it is not directly related to the gating mechanism of the ion channel and its function is not known yet.49 The part embedded inside the membrane was modeled by analyzing the structure and properties of MscS. As the gating mechanism of ion channel is directly related to its architecture, its basic structure was preserved when the MscS protein was coarsegrained. According to its hydrophobicity, every R-helix is modeled as an individual hydrophobic chain, and the parts which link the R-helices are modeled as hydrophilic chains. Consequently, for a monomer in the model, there are three transmembrane R-helix chains called Tm1, Tm2, and Tm3, respectively (see Figure 2b). The bond bending force constant for the R-helix was set to 15.0 to make the R-helix straight to mimic its rigidity, while the chains linking R-helices could be bent randomly. Seven monomers were then encircled to form a channel. Note that in our model the neighboring monomers are linked by a hydrophilic chain of two head beads, instead of the interaction inside the protein, such as hydrogen bonding or coulomb interaction, to maintain the protein configuration. The schematic drawing of the coarse-grained process and the final model is shown in Figure 2.

Coarse-Grained Model of MscS

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Figure 3. Initial configuration of a vesicle with the MscS protein embedded. The blue beads represent tail groups of the lipids, the orange ones are hydrophilic head chains of MscS, and the white ones are hydrophobic tail chains of MscS.

Figure 2. Schematic drawings of the MscS model. (a) Monomer of MscS from Escherichia coli.9 (b) Three R-helices (Tm1, Tm2, and Tm3) in this model represented by three tail chains and other parts of the monomer represented by the head chains. The tail beads and head beads are represented by yellow and red particles, respectively. (c) Model of the two monomers linked by a hydrophilic chain on Tm3. The red lines represent hydrophilic chains, and the blue poles represent hydrophobic chains. (d) Arrangements of R-helices of the seven monomers in the closed and open states in the model, viewed from the outside of a cell in the direction perpendicular to the MscS.

At last, a hole was dug in the membrane of prepared vesicle and the model of MscS (see Figure 2) was put inside the hole (see Figure 3). Starting from the initial configurations, simulations of 300 000 time steps were performed to investigate the gating transitions of different states. 3. Results and Discussion 3.1. Effects of Protein Structures. To investigate this gating mechanism of ion channels, two different states of MscS, namely the closed and open states, need to be differentiated from the morphologies of MscS. The modern integral-geometry morphological measures, i.e. the Minkowski functionals,50 were calculated to determine the state of MscS in this work. The functionals, including the surface area, volume, integral mean curvature, and Euler characteristic of the vesicle were computed here by using the algorithm described by Michielsen and De Raedt.51,52 This procedure described in the literature52 is valid only for the coexisting phases consisting of pure components. For the systems, in which the composition of the coexisting phases is not 1 and 0, one has to apply the procedure described by Aksimentiev et al.53 In order to adapt the simulated system to the procedure, in our work we divided the simulation box into small cubes with unit length. A lattice site corresponding to a small cube was translated into segments of type A (1) when

50% or more of beads in the unit volume were hydrophobic segments. Otherwise, the lattice site was translated into segment B (0). With this kind of treatment, we can also exclude the effects of small aggregates on the Euler characteristic. It is noticed that in all of Minkowski functionals the Euler characteristic, χ, is a more important variable,43,54-56 since it gives the topological information of the ion channels on the vesicle. Euler characteristic is an invariant of a surface for all graphs able to be appropriately embedded in the surface. As is wellknown, χ for the studied region is given by the number of isolated subregions minus the number of tunnels plus the number of cavities. When a vesicle forms and there is no pore appearing on its surface, the Euler characteristic, χ, equals two. In contrast, the Euler characteristic becomes one when a hole or a channel appears in the membrane of the vesicle. In this work, the vesicle is totally closed except the channel formed by the protein. Hence, when the Euler characteristic is two, the gate of the channel is closed. And for the same reason, the gate is open if the Euler characteristic is one. In this work we used a vesicle to model a cell rather than using a plane bilayer since a vesicle is more convenient to observe the behavior of MscS in response to the increase of transbilayer pressure. However, for a spherical vesicle, it is difficult to compute the exact value of the surface tension. Hence, we used the density of the lipids on the surface of the vesicle instead of the value of the surface tension. This is based on the fact that there is a monotonic relationship between the area density of the lipids and the surface tension, namely, the surface tension increases (decreases) with the decrease (increase) of the area density of the lipids on the vesicle surface. Four types of the MscS proteins with different lengths of R-helices were simulated in this study, and for each protein, three runs with different seeds of random numbers were performed. Our simulation results indicate that the structure of MscS, especially the length of the three R-helices plays an important role in its gating mechanism. The details and the results are shown in Table 2 and discussed below. The results in Table 2 show that there are two different states, i.e., open and closed states (see Figure 4) for the proteins with different lengths of the R-helices. The surface tensions of the

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Figure 4. (a and b) Snapshots showing a closed state of MscS. (c and d) Open state of MscS. Parts a and c show the cross section of the vesicle and MscS. Parts b and d show the R-helices of the protein, viewed from the outside of a cell in the direction perpendicular to the membrane surface. The blue beads represent tail groups of the lipids, the orange ones are hydrophilic head chains, and the white ones are hydrophobic tail chains of MscS.

TABLE 2: Results for Four Different Proteins at the Same Condition protein 1 2 3 4

Tm1 Tm1 Tm1 Tm1

) ) ) )

8 Tm2 ) 7 Tm3 ) 4 10 Tm2 ) 9 Tm3 ) 5 12 Tm2 ) 11 Tm3 ) 6 14 Tm2 ) 13 Tm3 ) 7

density

S1

S2

S3

0.3963 open open open 0.3947 open open open 0.3938 open/closed 0.3937 closed closed closed

membrane in all the simulations are nearly the same due to almost the same area densities of the lipids and the same densities of the enclosed water beads. The experimental researches demonstrated that the state of MscS is in direct response to the tension applied to the bilayer.57 When the surface tensions are the same, however, the structure of MscS is an important factor determining the state of the channel. In all simulations of our work, the gate of the channel is always open when the three R-helices are sufficiently short, for example, in the cases of proteins I and II, in which the lengths of the first R-helix are 8 and 10, respectively. When the length of the three R-helices increases, the state of the channel begins to be closed. For instance, among the three runs for the protein III (Tm1 ) 12), two initial configurations lead to the closed state of the channels and the other one results in the open state. When the length of Tm1 increases to 14, the channel formed by protein IV becomes closed in all the three different simulations. The states of the four kinds of MscS proteins can be confirmed by the time evolutions of the Euler characteristic (see Figure 5). It is found that for proteins I and II the channels are open nearly all the time, and the channels are only closed for a short time and then open again immediately. For protein IV, the Euler characteristic is almost of a fixed value of 2, which means that the channel never opens. However, protein III shows different trend, and the two states switch frequently during the process of the simulations.

The number of the water leaked (shown in Figure 6) is another variable to identify the state of the MscS protein. Different from the strong fluctuation of the Euler characteristics, the water leakage is not affected by the small change of a protein structure in a short time. The results in Figure 6a and b show that water leakages for protein I and protein II increase linearly, which indicate that the open state remains for a long time. The opposite situation happens for protein IV (see Figure 6d), namely, a negligible increase of the water leakage is found since the gate is always closed. In general, the state of MscS identified by the Euler characteristic is consistent with that by water leakage. When the Euler characteristic is kept fixed at two for the closed states of the channel, the increase of the water leakage is nearly negligible. In contrast, when the Euler characteristic is kept fixed at one for the open state, the number of water molecules leaked increases sharply and linearly with time. Furthermore, the switch between the open or closed states for protein III (see Figure 6c) can also be clearly identified by the rate of the increase of the water leakage. For example, in Figure 7, through comparing the time evolution of the Euler characteristic with the water leakage for protein III, it is obvious that the open states indicated by the Euler characteristic correspond well to the quick increase of the water leakage. The pore structures of protein III are shown in Figure 8. In general, our model gives almost the same pore structures in comparison with the result of Vasquez et al.58 It is found from the figure that in the center of MscS, the Tm3 helices form a hydrophobic pore in the open state,25 and the helical axes of them are nearly parallel to each other and align themselves with the normal of the membrane. In the close state, the Tm3 R-helices approach to each other to reduce the radius of the pore and become diagonal to the axis of the protein, which is in agreement with the study of Wang et al.59 The frequent switch of the different states for protein III is ascribed to the intermediate length of R-helix. For this protein, its morphology may be affected by the small fluctuation of surface tension, which induces the frequent switch of the states from open to closed in turn. In this work, a model of MscS is proposed, and within the model, the channels with different states can be observed depending on the different model parameters. In the case of the same surface tension, the state of the ion channel is found to be critically depended on the protein structure, especially the length of the transmembrane R-helix. Even if the proteins possess same morphologies, only the protein with a proper length of R-helix can perform its biological functions efficiently. These results suggest that the length of the transmembrane helix in real MscS is fine-tuned so that the protein performs its function efficiently. This observation may also be of importance in ion-channel engineering. The emerging field of ion-channel engineering aims not only to understand the molecular mechanisms of ion channel function, but also to prepare and control variants of these molecular devices for future technological applications.60 We attribute the dependence of ion channel function on its R-helix length to the hydrophobic mismatch between the protein and lipid bilayers, which could influence their interaction. Venturoli et al.61 correlated the lipid-induced protein tilt with the hydrophobic mismatch between the protein hydrophobic length and the pure lipid bilayer hydrophobic thickness. On the other hand, the helix tilting was found to play a critical role in the gating mechanism of MscS.58 Here the hydrophobic mismatch determines the interaction between the protein and

Coarse-Grained Model of MscS

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Figure 5. Time evolutions of the Euler characteristic of the vesicle with four kinds of proteins: (a) protein I (Tm1 ) 8 Tm2 ) 7 Tm3 ) 4), (b) protein II (Tm1 ) 10 Tm2 ) 9 Tm3 ) 5), (c) protein III (Tm1 ) 12 Tm2 ) 11 Tm3 ) 6), and (d) protein IV (Tm1 ) 14 Tm2 ) 13 Tm3 ) 7). There are three independent runs for every protein with different seeds of random number.

Figure 6. Time evolutions of the number of the water beads leaked from the vesicles, Nw, with the four kinds of proteins.

the membrane and hence the helix tilting. Therefore, the thickness of the lipid bilayer constrains the length of the transmembrane R-helix of MscS in order to perform its biological functions. Consistent with this discussion, the hydrophobic mismatch has been confirmed to play an important role in the gating mechanism of MscL.13 Experimental results show that the MscL opens with a significantly lower activation threshold as the bilayer thickness decreases,13 in which the

Figure 7. Time evolutions of the Euler characteristic and the number of water beads leaked from the vesicles, Nw, in S3 for protein III. The domains labeled show that the change of the Euler characteristic corresponds to the quick increase of water leakage.

hydrophobic mismatch was controlled experimentally by using phospholipids with different acyl chain lengths. 3.2. Influence of the Surface Tension. To investigate whether the change of the state of the model MscS is sensitive to the surface tension applied to the membrane, a series of

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Figure 8. Averaged cross-sectional area of the MscS pores (only the hydrophobic beads were taken into account) in the closed and open states.

simulations for the four kinds of proteins were preformed. To characterize different surface tensions of the membrane, the area density of the lipids on the membrane was altered by two different methods. In the first case, the water molecules were randomly inserted into the vesicle, and the same number of randomly chosen water molecules outside the vesicle is deleted correspondingly. As a result, the surface area of the vesicle gradually increases and the area density of the lipids decreases. The other method corresponds to inserting the lipids into the membrane to increase the area density of the lipids, under the condition of keeping the proportion of the lipids in the inner and outer layers fixed. At the same time, the randomly chosen water molecules outside the vesicle, which are equal to the number of the lipid beads inserted, were deleted to keep the overall density fixed. For protein II, when 100, 300, and 500 lipids were added into the membrane formed by 2000 lipids, the area densities of lipids increases from 0.3947 to 0.4050, 0.4142, and 0.4179. Obviously although the shape of the vesicle changes from sphere to ellipse with the insertion of several hundreds lipids into the membrane, the change of the area density of the lipids and hence that of the surface tension are nearly negligible. The simulation results (see Figure 9a) do show that the channels are still open in all the time. A similar situation is found for protein IV, in which even 7000 water molecules were put into the cell to decrease the area density of lipid molecules from 0.3937 to 0.3170, the channels are always kept closed (see Figure 9b). From the discussion above, it is confirmed that the gating of the protein critically depends on the length of R-helix. A too long or too short R-helix would make the state transition of the protein impossible, even though significant change of the surface tension of the membrane is applied. Thus, it is concluded that only the model MscS protein with the proper architecture can be used to perform its biological functions of gating transition. Protein III is proved to be a sensitive mechanosensitive ion channel, since small change of the area density applied may lead to state switch. In our simulations, two kinds of the initial configurations of protein III, for which one of the channels is closed and the other one is open, were prepared. Two independent simulations, denoted by S1 and S2, from the initial configuration of the closed state were performed for 300 000 time steps after 3000 water beads were inserted into the vesicle to make the area density decreasing from 0.393 76 to 0.361 77. Simulation results are shown in Figure 10a, from which it is

Figure 9. Time evolutions of the Euler characteristic of the vesicle for protein II (a) and protein IV (b).

found that at the beginning of both simulations the Euler characteristic is two, indicating the channel is closed. And after about 46 000 steps (or 25 000 steps) for S1 (or S2) the Euler characteristic reduces to one and fluctuates around the value, which means that the channel is open due to the increase of surface tension. To observe the response of protein III to the decrease of surface tension, another simulation (denoted by S3) of 300 000 time steps from an initial configuration in the open state was performed after 300 lipids were inserted. The insertion of lipids into the membrane makes the area density of lipids increase from 0.3938 to 0.42080. The results (see S3 in Figure 10a) show that at the beginning the Euler characteristic stays at one for a short time and then increases to two. This means that the channel is changed from the open state to the closed state due to the decrease of the surface tension. By comparing the numbers of the water leakage at different time, the state of the channel can also be identified and confirmed (shown in Figure 10b). When the channel is open after a short time in S1 and S2, the water leaks from the vesicle very quickly and continuously, but it increases very slowly when the channel is closed in S3. By changing the area density of lipids, the influence of surface tension on the state of the ions channel is studied. When the surface tension increases, the channel, especially for protein III, opens from a closed state and water molecules inside and outside the vesicle could move across the membrane to equilibrate the

Coarse-Grained Model of MscS

J. Phys. Chem. B, Vol. 113, No. 43, 2009 14437 the length of the transmembrane R-helix. A too long or too short R-helix would make the state switch of the protein impossible even though a significant change of the surface tension of the membrane is applied. This observation suggests that the length of the transmembrane helix in the real MscS is fine-tuned so that the protein performs its function efficiently. We attribute the dependence of ion channel function on its R-helix length to the hydrophobic mismatch between the protein and lipid bilayers, which could influence their interaction. For the model protein with a certain size, the state of the channel depends on the surface tension of the membrane, as in a real ion channel. When the surface tension increases, the channel can open from a closed state and water inside and outside the vesicle could move across the membrane to equilibrate the osmotic pressure. And, the channel can be directly closed as a result of the decrease of the surface tension. Acknowledgment. The work is supported by National Natural Science Foundation of China (No. 20736005 and No. 20876004). X.Z. acknowledges the support of the Research Foundation for Young Researchers of BUCT. Generous allocations of computer time by “Chemical Grid Project” of BUCT, and the Supercomputing Center, CNIC, CAS, are acknowledged. References and Notes

Figure 10. (a) Time evolutions of the Euler characteristic of the vesicle for protein III. (b) Number of water beads leaked from the vesicles, Nw, for protein III, correspondingly.

osmotic pressure of water. In contrast, when the surface tension decreases, the channel is directly closed and water is confined in the cell for keeping the state of MscS stable. 4. Conclusions In this work, a coarse-grained model of the mechanosensitive channel of small conductance (MscS) is constructed. The basic structure characteristics of MscS are preserved when the protein is coarse-grained. In this model, a model MscS consists of seven identical monomers. For every monomer, the complicated extramembrane part inside the cell is simply reduced to hydrophilic chains because it is not directly related to the gating mechanism of ion channel and its function is not known yet.49 The part embedded inside the membrane is modeled by analyzing the structure and properties of MscS. The three R-helices of every monomer are modeled as rigid hydrophobic chains, and the parts which link the R-helices are modeled as the hydrophilic chains. Then, seven identical monomers are encircled to form a channel. For the coarse-grained MscS model, dissipative particle dynamics simulations show that different states of the channel can be observed depending on the model parameters. The pores of MscS for both the open and closed state are qualitatively in agreement with the experimental and theoretical studies.25,58,59 At the same surface tension, the state of the ion channel is found to be critically dependent on the protein structure, especially

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