Purified MscL mutants (Figure 3—figure supplement 1) were labeled with Alexa Fluor 488 (AF488) and Alexa Fluor 568 (AF568) and reconstituted into ∼50 nm liposomes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) with 2% 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-biotinyl (BPE) (Figure 1D). The liposomes were then immobilized on a glass coverslip, via biotin-avidin interaction, for smFRET measurements (Figure 1D). To access the open state of the channels, 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine or lysophosphatidylcholine (LPC) of 25% molar ratio was added (Perozo et al., 2002b, 2002a; Corry et al., 2005b, 2010; Figure 1E) and incubated for >10 min before immobilization. Just before performing smFRET experiments, the fluorescence spectra of the samples (±LPC) were recorded with excitation at 488 nm to confirm that the channels open up with LPC by observing the shift in the FRET peaks. (The channel activity is also determined by observing the opening of the channels upon application of negative pressure [suction] to the patch pipette. The labeled proteins for patch-clamp experiments are from a different aliquot, although the same batch, of the labeled proteins for smFRET experiments). We emphasize that, although smFRET has been applied to study the conformational changes of channels and transporters (Choi et al., 2010; Zhao et al., 2010, 2011; Akyuz et al., 2013), to our knowledge, it is the first time that smFRET has been used with channels reconstituted to liposomes.

Via smFRET measurements, we observed fluorescence intensity traces with one or two photobleaching steps (Figure 3—figure supplement 2A,B). This is the expected result because MscL is a homo-pentamer and the labeling of fluorophores is stochastic. The number of photobleaching steps tells the number of fluorophores attached to a channel. Only the traces showing a single photobleaching step in both the donor and acceptor channels, ensuring that only a single donor and/or acceptor fluorophore, were included in the analysis (Figure 3—figure supplement 2A). Donors were, in most cases, photobleached first, resulting in simultaneous dropping of the fluorescence intensities in both donor and acceptor channels (Figure 3—figure supplement 2A,B). Subtraction of the intensities before and after photobleaching gives the intensities of donor (I_D) and acceptor (I_A), which are used for the calculation of FRET efficiency. Note that the intensities, I_D and I_A, automatically remove the direct excitation of acceptor (i.e., the leakage of acceptor emission in the donor channel). However, the leakage of donor emission in the acceptor channel is still present. To measure this leakage, MscL channels were labeled with donors-only and the leakage coefficient (ℓ) was measured experimentally: ℓ = I_D^A/I_D^D ≈ 0.09, where I_D^A is the intensity of donor emission in the acceptor channel and I_D^D is the intensity of donor emission in the donor channel. Furthermore, to determine the actual FRET efficiency, another instrumental correction was made through the correction factor γ, which accounts for the differences in quantum yield and detection efficiency between the donor and the acceptor. It was calculated as the ratio of change in the acceptor intensity, ΔI_A, to the change in the donor intensity, ΔI_D, upon acceptor photobleaching: from the traces where the acceptor photobleached first (Roy et al., 2008), we estimated the value γ = ΔI_A/ΔI_D ≈ 0.89 ± 0.06 (Figure 3—figure supplement 2C).

We analyzed a few hundred traces (varying between 134 and 577 traces) with single photobleaching steps in the absence and presence of LPC for each mutant (Figure 1C, Figure 3). Here we focus on the mutant M42C for the sake of illustration. For the single photobleaching steps of M42C, 428 and 577 traces, in the absence and presence of LPC, respectively, were analyzed. The corrected FRET efficiencies were calculated and their distribution was then plotted and fitted with Gaussians via maximum likelihood estimates, shown in Figure 3A,B, while the number of Gaussians was determined according to the corrected Akaike information criterion (AICc) and the Bayesian information criterion (BIC) (Table 1; Akaike, 1974; Schwarz, 1978; Sugiura, 1978). In the absence of LPC, we observed three peaks at E = 0.1, 0.28 and 0.63, respectively (Figure 3A). In the presence of LPC, the third peak showing the highest FRET efficiency diminishes, leaving mainly two Gaussians (E = 0.1 and 0.23, Figure 3B). This transition (i.e., the highest peak decreases and the lowest peak increases) is more obvious when we plotted the difference between the normalized FRET distributions ( ${{\displaystyle \sum }}^{\text{}}{\text{P}}^{\text{X}}=1$, where X = + for in the presence of LPC and X = − for in the absence of LPC) under the two conditions, as shown in Figure 3C: after adding 25% LPC, the peak at E ∼0.6 went away but the fraction of the peak at E ∼0.1 built up. Note that the highest peak at E ∼0.6 does not completely disappear in the presence of 25% LPC, which is consistent with (Perozo et al., 2002b).

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In the absence of LPC, the existence of three peaks, rather than two peaks, can be explained by considering the effect of tethering on the liposome. As the MscL channel is a homo-pentamer, we initially expected two distances between donor and acceptor in each state (R_n and R_f in Figure 4A) and thus two peaks for the distribution of FRET efficiency, assuming that all the channels are closed in the absence of LPC. However, this assumption is not necessarily true, especially in our situation where liposomes are immobilized and the proteins are responsive to membrane tension. It had been predicted by theories and observed in experiments that immobilization of liposomes (or vesicles) results in significant membrane tension and possibly rupture (Zhdanov et al., 2006; Chung et al., 2009; Serro et al., 2012). In our experiments, the membrane tension is expected to be high, ∼30–40 k_BT, due to the strong interaction between BPE and the surface via biotin-neutravidin (Miyamoto and Kollman, 1993; Rico and Moy, 2007). With such strong interaction, giant unilamellar vesicles ruptured spontaneously, as has been observed experimentally (Chung et al., 2009). The consequence is that some of the MscL channels switch to the open conformation upon the immobilization of the liposomes. (However, the fraction of open channels might be different for different mutants even if the membrane tension is similar). Therefore, the FRET histogram for the no-LPC sample includes a mixture of closed and open MscL channels. To test this hypothesis, control experiments were performed by increasing the fraction of BPE in the liposomes, guided by a theoretical prediction (Zhdanov et al., 2006): if the hypothesis was true, the membrane tension in the liposomes due to immobilization would be higher, more channels would open in the absence of LPC, and therefore the difference between the FRET histograms with and without LPC would be smaller. We varied the fractions of BPE in the liposomes from 2% to 16% and, indeed, observed that the difference between the samples with and without LPC decreases (Figure 3D). We quantified the difference by the (unscaled) variance, $\text{Δ}{P}^2={\displaystyle \sum }_{i=1}^N{\left(P_i^{+}-P_i^{-}\right)}^2$, where $P_i^X$ is the probability distribution of FRET efficiency, ${\displaystyle \sum }_{i=1}^N{P}_i^X=1$. We observed that the variance ΔP² decreased by 98%, from 0.084 to 0.002, when the fraction of BPE in the liposomes increased from 2% to 16%, supporting the hypothesis that the sample without LPC is a mixture of closed and open channels.

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A simple estimation based on the crystal structure of MscL in the closed state (Chang et al., 1998) and previously predicted/estimated open pore-size (Cruickshank et al., 1997; Perozo et al., 2002a; Corry et al., 2010) indicates that it is likely that, due to limited resolution of FRET, the middle peak (E = 0.28) is an overlap of two peaks corresponding to R_n of the open state (R_no) and R_f of the closed state (R_fc) (for R_n and R_f, Figure 4A,B). The geometry of the protein (i.e., fivefold symmetry) gives $R_n=D\cdot \sin \left(\frac{\pi }{5}\right)$ and $R_f=D\cdot \sin \left(\frac{2\pi }{5}\right)$ where D is the protein diameter. Take M42C as an example: the crystal structure gives the diameter of the protein in the closed state (using the C_α atoms), D_c = 4.4 nm, resulting in $R_{fc}=D_c\cdot \sin \left(\frac{2\pi }{5}\right)=4.2$ nm. The expected change in the protein size (ΔD) is from 2.5 to 4 nm (Cruickshank et al., 1997; Perozo et al., 2002a; Corry et al., 2010), with the most recent report of 2.8 nm from ensemble FRET measurements (Corry et al., 2010). Then the expected D_o = D_c + ΔD is 7.2 nm, which gives $R_{no}=D_o\cdot \sin \left(\frac{\pi }{5}\right)=4.2$ nm, exactly the same as R_fc (The expected R_no is 4.1–4.9 nm when taking into account the expected range from the literature). In the simple calculation above, the positions of C_α atoms for the estimations were used. However, the side chains of the residues and the attached fluorescent probes will add an additional length on the order of 2 nm, resulting in that the chance for R_fc and R_no to overlap is even higher. Furthermore, it has been observed that ≤30% of MscL are hexamers, instead of pentamers, in detergents such as n-Dodecyl-β-D-maltopyranoside (DDM) used in the current study (Gandhi et al., 2011). This would tend to ‘smear’ the middle peaks of FRET in the absence of LPC. Therefore, to be consistent and accurate, we always use the highest FRET efficiency (E_nc and E_no) for the calculation of distance changes (ΔR_n). On the other hand, we did find that all mutants give E_fo measurements compatible (i.e., within error) with the final model (except that M42C is slightly off), as shown in Figure 3—figure supplement 3.

FRET between neighboring MscL channels on the same liposome had been a problem in previous ensemble FRET experiments. To decrease the likelihood of its happening, and to effectively solve the problem, we applied two strategies. First, we used 5% labeled channels together with 95% unlabeled ones for reconstitution in liposomes. As a result, we had 16x lower molar ratio of labeled proteins (pentamers) to lipids than that in the ensemble FRET experiments: 1:4000 vs 1:250 (Corry et al., 2005b, 2010), greatly reducing the likelihood of inter-molecular FRET. We found that adding a mixture of labeled and unlabeled protein helps to obtain no more than one fluorescent channel per liposome while ensuring efficient incorporation of channels into liposomes. In addition, only traces showing a single photobleaching step in both donor and acceptor channels were included in analysis, which helps further removing the FRET between neighboring MscL channels in the analysis. These strategies reduce significantly the likelihood that energy transfer happens between two adjacent channels even in the presence of MscL clustering, simplifying the interpretation of FRET results.

Another note is that we used maximum-likelihood estimation (MLE) (In Jae, 2003) for peak fitting. This method was chosen particularly because it does not require binning the data before fitting. Although there are mathematical ways for selection of ‘good’ bin sizes (Shimazaki and Shinomoto, 2007), the selection of bin size is, in practice, subjective, and the peaks derived can be affected with different bin sizes. After MLE fitting, we then bin the data and plot the histograms for the sake of presentation purpose. How the data is binned does not change the fitting parameters.

The Förster radius (R₀) for AF488 and AF568 is calculated by means of R₀ ∝ (κ² Q_D)^1/6 (Förster, 1948; Iqbal et al., 2008). Because κ² and Q_D, can be environmentally sensitive, we measured the quantum yield and orientation factor for the fluorophores conjugated to each and every channel mutant (Fery-Forgues and Lavabre, 1999; Lakowicz, 1999; Figure 5). The quantum yields of AF488 conjugated to various MscL mutants are summarized in Table 2; Figure 5A, corrected for polarization effects (Fery-Forgues and Lavabre, 1999; Lakowicz, 1999). It is noted that the fluorophores used in the current study are mixtures of 5′ and 6′ isomers. However, it was expected that this will not affect the results because (1) they have successfully been used in many smFRET studies (Marras et al., 2002; Yin et al., 2005; Jäger et al., 2006; Granier et al., 2007; Majumdar et al., 2007); (2) the chromophores of the isomers are exactly the same while the only difference between the isomers lies in where the linker of carbon-chain [(CH₂)₅NHCO] is attached; (3) we examined the molecular structures of the probe-isomers and confirmed that the difference in molecular size is <5% between isomers (Figure 4—figure supplement 1).

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The orientation factor κ², was determined by measuring the anisotropy of the conjugated fluorophores (Table 2; Figure 5B, Figure 5—figure supplement 1). The anisotropy of both donor and acceptor for most residues is <0.2 and therefore κ², in fact, is close to 2/3 (Clegg, 1992; Andrews and Demidov, 1999; Roy et al., 2008). Nonetheless, we calculated the maximum possible errors in R₀ due to anisotropic orientation of the dyes (Table 2; Figure 5B, Figure 5—figure supplement 1); the actual errors in R₀ should be much smaller. Another source of error in R₀ lies in the measurements of Q_D, which were performed for AF488-MscL in detergent (PBS + 1 mM DDM), which was not exactly the same environment for fluorophore-MscL conjugates in smFRET experiments (incorporated in liposomes in PBS), although the buffer was kept the same. Furthermore, it is possible that the addition of LPC and the conformational change of MscL changes Q_D as well, resulting in additional errors in R₀ and in the distances calculated below.

It is noticed that the anisotropy of the acceptor is consistently lower than that of the donor although the acceptor is larger. This could be attributed to many factors, as stated by the Perrin equation (Perrin, 1926): A₀/A = 1 + 6Dτ, including the rotational diffusion coefficient (D), fluorescence lifetime (τ) and, more significantly, the fundamental anisotropy (A₀) which varies according to wavelength (Weber and Shinitzky, 1970; Lakowicz, 1999). The anisotropies given in Table 2 were measured at the wavelengths where smFRET experiments were performed.

We note that the finite size and length of the fluorescent probes brings additional difficulty to converting FRET measurements to the estimation of distances and therefore to structural modeling. To overcome this difficulty, our strategy is to focus on the movement of residues, instead of the absolute distances, and then to develop the structural model based on the changes of distances.

For illustration purpose, we set up the general scene in Figure 4—figure supplement 2. The pentameric MscL channel (light blue), centered at point O, is labeled with two probes (dark blue) on two cysteine residues (specified by residue #), while the other three residues (with the same residue # but on different subunits) remain empty/unlabeled (dashed green). (Here the breaking of symmetry is taken into account in this general case). To emphasize the size and length of the probes, filled green and red circles are used to indicate the actual chromophores. Then the actual chromophores of the labeled probes (green and red circles) and the center of the protein (O) define a pentagon (dotted orange pentagon, with a side length of R) and a circumcircle (black circle, with a diameter of D, or a radius of r = D/2). We call R, D and r apparent distance/diameter/radius because they could be measured/calculated from FRET experiments (with corrections) and they gave the apparent size of the protein (i.e., the protein appears to have a radius of r based on FRET experiments). There is another set of distances, which are more relevant to the protein and to the MD simulations for the structural model. We call this set of distances true values. For example, the true radius of the protein (r_t) (referring to a specific residue) is defined as the distance between the Ca atom of the residue and the center of protein (O). We note that the exact atom chosen for the definition of the true radius (r_t) does not matter.

Generally r = r_t + r_p ≠ r_t due to the finite size of the probes (r_p ≠ 0). As a result, converting the FRET measurements into a structural model is not straightforward. However, if the size of the probes does not change (i.e., Δr_p = 0) upon channel activation, we then have Δr = Δr_p + Δr_t = Δr_t (similarly ΔD = ΔD_t). We believe Δr_p = 0 is a reasonable assumption for the following reasons: (1) no chemical reactions are happening for the probes and thus the structures of the probes do not change before and after channel opening; (2) anisotropy measurements show that the orientation of probes are not constrained significantly. As a result, the change in the apparent distances is the same as the change in the true distances. In other words, the movement of residues (in the radical direction, Δr_t) can be obtained from the FRET measurements, even if the sizes and lengths of probes are nonzero.

A note to make is that we have assumed that donors and acceptors have similar sizes in the argument above. This assumption could be justified by the molecular structures of the probes (shown in Figure 4—figure supplement 1), which shows that the difference between the donor-size and acceptor-size is <2%. On the other hand, a caveat is that, although not likely, there are possible situations where the size of the probe can change (i.e., Δr_p ≠ 0) upon channel opening, due to, for example, steric hindrance.

To conclude, the finite size of probes (r_p ∼1.7 nm) brings additional difficulties to converting FRET measurements to estimation of distances: FRET results gave the distances between the chromophores of donors and acceptors, which is different from the distances between the C_α atoms of residues of interest. However, on the other hand, the movement of the residues (or the movement of the C_α atoms of the residues) in the radial direction is the same as the movement of the chromophores assuming that the size of the probes does not change (i.e., Δr_p = 0) upon channel opening. We also note that, although the fivefold symmetry is broken due to the binding of one donor and one acceptor per pentamer, the geometric construction will not be affected. From here on, we use Δr (and ΔD) for the movement of residues (and the change of the protein diameter) without any subscript.

We measured the change of FRET efficiency of MscL before and after channel activation using smFRET. For example, for M42C, the FRET efficiency changed from 0.63 (closed state) to 0.23 (open state). We also determined experimentally the Förster radii (R₀ = 5.5^+0.4_−0.3 nm for M42C). This permitted us to estimate the change in the distance between donors and acceptors from the closed to open states (Figure 4), ΔR_n = R_no–R_nc = R₀ (E_no⁻¹–1)⁻¹–R₀ (E_nc⁻¹–1)⁻¹ (≈1.7 nm for M42C). We emphasize that some of the distances between fluorophores (R_no and R_nc in Table 3) are indeed out of the sensitive range of EPR measurements, making FRET a more suitable technique in this context.

As illustrated in the previous section, we focus on the more relevant distance of interest: the movement of the residue away from the pore center, Δr (Figure 4B), or the change of protein diameter measured from the residue, ΔD. Because of the fivefold symmetry of the MscL channel, ΔD and Δr can be calculated readily according to ΔD = ΔR_n/sin( π /5 ) ≈ 2.8 nm, which yields Δr = ΔD/2 ≈ 1.4 nm (for M42C). The Δr values of the residues are summarized in Table 2. This value is above 2.5 nm, a lower bound predicted by EPR experiments (Perozo et al., 2002a), but larger than ΔD obtained from the previous ensemble FRET measurement: ΔD_M42C = 2.8 nm (smFRET) vs ΔD_M42C = 1.6 nm (ensemble FRET) (Corry et al., 2005b, 2010). We emphasize that the measurements of two more residues (I25C and A27C) in the current study were also reported previously (Corry et al., 2010). Our results are close to the values in their simulations (ΔD_I25C = 2.4 vs 2.5 nm; ΔD_A27C = 2.5 vs 2.6 nm) but differ significantly from the values measured directly from ensemble FRET experiments (ΔD_I25C = 2.4 vs 0.2 nm). It should be noted that ensemble experiments gave inconsistent measurements for ΔD_I25C = 0.2 nm and ΔD_A27C = 2.9 nm, although the two residues are close. In contrast, smFRET results show that ΔD_I25C = 2.4 nm is similar to ΔD_A27C = 2.5 nm. This clearly demonstrates the advantage of smFRET.

We note that fluorophores/linkers at different residues are likely to be constrained differently. Furthermore, how they are constrained differently is not clear, partly due to the unavailability of the crystal structure of EcoMscL. However, certain residues are in agreement between the EcoMscL and the MtMscL (Perozo et al., 2001). Nevertheless, the distances between donors and acceptors are not good to compare for different residues of EcoMscL. A more reasonable way is to compare the changes of distances, that is, the movements of residues.

The calculations above were performed with the assumption that EcoMscL are pentamers. However, it is noted that a mixture of hexamers and pentamers were observed in certain detergents for EcoMscL (Gandhi et al., 2011) (≤30% hexamers in DDM). In our experiments, we ran FPLC (Superdex 200 10/300 GL column) for our MscL proteins and used the proteins from a single peak and checked with SDS-PAGE (Figure 3—figure supplement 1). In addition, in the smFRET experiments, we reconstituted the channels into liposomes, different from proteins in detergents where a mixture of hexameric channels and pentameric channels were observed (Gandhi et al., 2011). Third, as the conductance of the mutants (from electrophysiological recordings) used in this study agrees with that of MscL pentamers (Figure 4—figure supplement 3C), it is likely that we are reconstituting MscL pentamers into liposomes. Nonetheless, the possibility of having a (small) portion of hexamers in the sample in smFRET experiments could not be excluded completely. To estimate the introduced uncertainties, we investigated quantitatively the effect of the presence of hexamers via numerical simulations and found that the main effect of the presence of hexamers is not the shift of the peak center but the broadening of peak width (Figure 4—figure supplement 3A-B). If the sample was 100% hexamers, the diameters of the protein, as well as the pore size, will be greater by a factor of sin(π/5)/sin(π/6)−1 ≈ 17.6%. In the presence of 30% hexamers, as observed in (Gandhi et al., 2011), the calculations would be off by about 7.5%.

Because the size of both Alexa fluorophores is significant (∼1.7 nm), it is possible that the attachment of the fluorophores to MscL channel results in various effects on the protein and on the FRET measurements. For example, the presence of the fluorophores might sterically hinder the conformational change of the proteins and prevent them from opening or closing. On the other hand, the steric hindrance might constrain the orientation of fluorophores, affect the relative orientation between the fluorophores and therefore add more errors on the distances converted from FRET efficiencies. In addition, the insertion of fluorophores to the protein might force the channel to be in a state different from the fully closed state, resulting in the distance change measurement is underestimated. However, we would like to emphasize that the expected effect is insignificant for the following reasons. First, if the insertion of fluorophore would result in significant steric hindrance on the protein, it is expected that the labeling is difficult (i.e., it takes much more effort for the fluorophores to be attached due to the steric hindrance). In other words, it is expected that steric hindrance is not significant on the mutants that are labeled well. More importantly, the channels after being labeled with AF488 and AF568 were confirmed to be functional by both ensemble FRET experiments (by observing the shift in the FRET peak) and patch-clamp measurements (by observing the opening of the channels upon application of negative pressure to the patch pipette) as shown in Figure 6 and previous publications with the same fluorophores (Corry et al., 2010).

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With smFRET, we measured the movements of three residues on TM1 (M42C, A27C, and I25C) and three on TM2 (Y75C, Q80C and V82C) summarized in Table 2 and Figure 4C,D. We observed directly and reliably for the first time, that both TM1 and TM2 swing away from the pore, supporting the helix-tilt model. Note that, among the three residues on each helix, two sites were very close to each other (A27C and I25C on TM1, Q80C and V82C on TM2). They were chosen purposefully to be close; they served as consistency checks and confirmed that our smFRET measurements are accurate (Table 2). In addition, the top of both helices (periplasmic side, Figure 1B,C; residues 42 on TM1 and 75 on TM2) moves further than the bottom (1.4 nm vs 1.2 nm for TM1 and 2.0 nm vs 1.4 nm for TM2), indicating that rotational tilting of the helices (toward the membrane plane) is involved. We emphasize that it is the first direct (model-free) observation of both TM1 and TM2 swinging away from the pore center and of the tilting of the transmembrane helices. Therefore it is the first direct observation in favor of the helix-tilt model.

To quantitatively investigate in detail how the MscL channel opens (i.e., how the helices move and rotate upon opening), we developed a computational model for the open structure of the MscL, starting from the crystal structure of MscL in the closed state (PDB: 2OAR) (Chang et al., 1998; Steinbacher et al., 2007) and employing the measured residue movements. For this purpose, we performed MD simulation with distance constraints (Brünger et al., 1986; Trabuco et al., 2009) (i.e., a virtual spring, Figure 7—figure supplement 1) using NAMD 2.9 (Phillips et al., 2005). Although similar modeling attempts have been made by Corry et al. (2010) and Deplazes et al. (2012) by using distance changes measured from ensemble FRET, we would like to emphasize that all smFRET measurements were used for the simulation while previously only a selected subset of ensemble data were used (as other data were not consistent with the resultant model) (Corry et al., 2010). For each measured residue, ten virtual springs were placed, five springs between the central carbon atom C_α of identical residues (highlighted green in Figure 7—figure supplement 1) from adjacent monomers (red springs in Figure 7—figure supplement 1) and five springs between the C_α of identical residues from non-adjacent monomers (yellow springs in Figure 7—figure supplement 1). The virtual springs were not applied to side chains because the flexibility of side chains likely introduces errors under large forces in the modeling process. The equilibrium lengths of the springs were chosen by adding the distance changes measured from smFRET to the equilibrium distances seen in the closed state, thereby, opening the crystal structure of M. tuberculosis MscL (PDB: 2OAR) (Chang et al., 1998; Perozo et al., 2001; Steinbacher et al., 2007). In the simulation, the virtual springs pushed corresponding residues from the distance in the closed state to the equilibrium length in the open state. We note that the uncertainty due to the size of the FRET probes was minimized by focusing on the change of the distances between the closed and open state, rather than absolute distances as discussed in previous section.

We note several limitations in the modeling: as the spring constant was kept constant through the simulations, resulting in a large force at beginning of the simulation, we applied both secondary structure restraints (Trabuco et al., 2009) and symmetry restraints (Chan et al., 2011) to prevent structural distortion. The secondary structure restraints prevents some subtle changes in the structure, such as kinks observed previously in the upper part of TM1 in the open model of MscL (Deplazes et al., 2012). Therefore, we limit our discussion of the open model to pore size and helix tilting. The membrane tension, which causes membrane thinning, plays an important role in the MscL opening process (Corry et al., 2010; Louhivuori et al., 2010; Deplazes et al., 2012). However, the restraint MD simulation cannot address the question of how the channel is activated. For the simplicity of the modeling, membrane tension is not considered here. We did observe that the membrane near the MscL becomes thinner during the channel opening process to match with the flattening MscL (Figure 7—figure supplement 2), confirming that a thinning membrane, likely caused by tension, matches the open channel better.

The resulting open state structure of MscL is shown in Figure 7B,D, and compared with the crystal structure of MscL in the closed state (Figure 7A,C). The open structure satisfies all the distance constraints measured in our smFRET experiments. In contrast, previous models based on ensemble FRET measurements failed to be consistent with all experimental measurements (Corry et al., 2010). In the open conformation, the pore is mainly lined by helices TM1 (indicated by blue arrows), consistent with the helix-tilt model. In addition, it is observed that both TM1 and TM2 indeed tilt toward the membrane plane (horizontal) upon channel activation. For example, the orientation of TM1 tilts from the green arrow orientation (Figure 7C, closed state) to the yellow arrow orientation (Figure 7D, open state). The change in tiling angle of the TM1 and TM2 helices is ∆θ₁≈27° and ∆θ₂≈19°, respectively, where θ is the angle between helix and the fivefold symmetry axis. The all-atom model and backbone model of the open state resulting from the current study are provided in PDB format in SI.

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We used two independent methods to measure the pore size of MscL in the open state. The first method is to measure the movements of the residues forming the narrowest pore constriction of the channel, that is residues around I25 for E. coli MscL (Chang et al., 1998; Perozo et al., 2001, 2002a; Corry et al., 2010). However, this method, although straightforward, has its limitations. It is likely that the function of the channel is affected by mutation and labeling of (some of) the residues at the pore region. For example, the activation thresholds (P_a, defined as the pressure at which the first channel opening was observed [Nomura et al., 2012]) of mutants G22C and I24C are more than double the wild-type thresholds (Figure 6) and both ensemble and single molecule FRET measurements of these mutants showed no change in the FRET efficiency after adding 25% LPC. The effect of the point mutations near the pore on the electro-physiological properties of the channel can be quantitatively explained by the closed and open structure of MscL as shown in Figure 6—figure supplement 1, the residue G22 (A20 in M. tuberculosis MscL) is very close to the pore and is facing the pore. The residue V22 (V22 in M. tuberculosis MscL) is also close to the pore and sandwiched between helix 1 and neighboring helix 1. Mutating these two residues is likely to perturb the channel function. On the other hand, the residue I25 is further from the pore than G22 and I24. The mutation I25C is less likely effect the channel properties. Indeed the I25C mutation does not affect the channel’s gating parameters (Figure 6C,D). I25 is still close enough to the pore, making it a perfect candidate for measuring pore size. Furthermore, among the three mutated residues shown in Figures 6, I25 (green) is the only one facing outward from the channel axis and accessible from the periphery of the protein (Figure 6—figure supplement 1B,D). We were able to determine the movement of residue I25C (Corry et al., 2010); and measured that the residue I25 moves away from the pore center by Δr = 1.2 nm, indicating that the pore opens up by ΔD = 2.4 nm in diameter. Taking into account that the pore diameter in the closed state (Φ_close) is 0.4 nm (Chang et al., 1998), we conclude that the pore size in the open state (Φ_open) is Φ_open = Φ_close + ΔD = 2.8 nm, which agrees with previously reported values (Perozo et al., 2002a; Corry et al., 2010).

The second method is based on the open state model of MscL constructed by means of molecular dynamics. The surfaces of water molecules inside the channel were rendered (Figure 7E,F) using VMD (Humphrey et al., 1996) and the narrowest constriction seen provided an estimate of the pore size. This estimate accounts for all residues of the transmembrane domain and therefore is expected to be more accurate than the estimate of the first method. Using this method we estimate that the pore size of the MscL channel in the fully open state is 2.7–2.8 nm, which is consistent with the value from the first method, 2.8 nm.

The E. coli MscL gene (EcoMscL) was cloned into plasmid pQE-32 (Qiagen, Hilden, Germany) as the BamHI-SalI fragment, which also added a hexa-histidine tag (his-tag) to the protein at the N-terminus. The protein was expressed in E. coli (M15 strain) (Qiagen) that were lysed by sonication and purified from DDM solubilized membranes using TALON Metal affinity chromatography (Clontech Laboratories, Inc, Mountain View, CA), followed by a further purification step using fast protein liquid chromatography (FPLC; Superdex 200 10/300 GL column, GE Healthcare, Pittsburgh, PA). Purification was performed in the presence of 1 mM DDM.

The wild type of MscL protein does not contain any cysteine. To label the proteins with fluorescent probes, MscL was mutated using site-directed mutagenesis such that a residue at the desired position was replaced by a cysteine. Because the MscL protein is a homo-pentamer (Chang et al., 1998), this mutation introduced five identical cysteine sites.

The protein with his-tag was then labeled with Alexa Fluor 488 (AF488) and/or Alexa Fluor 568 (AF568) maleimide, which specifically reacted with the introduced cysteines (Kim et al., 2008). Right before labeling, proteins were reduced with 10 mM DTT for 30 min, followed by purification using PD-10 desalting columns (GE Healthcare). We titrated the pentameric protein-to-fluorophore molar ratio from 1:1 to 1:5 and used the molar ratio of 1:5 for labeling in all the experiments. Under our labeling conditions, this ratio gave satisfying results such that most of the proteins are labeled (averagely ∼1.7 donors and ∼1.3 acceptors per pentamer) and that many of proteins are attached by a single donor and a single acceptor (∼30% of good traces show multiple donors and/or acceptors). Excess fluorophores were then removed using PD-10 desalting columns. The sample was reduced with 10 mM DTT before this purification step. A note to make is that the fluorophores (Alexa Fluor 488 maleimide and Alexa Fluor 568 maleimide) come as mixtures of 5′ and 6′ isomers, which would potentially complicate interpretation of smFRET data. However, we expect that the results would not be affected because the exactly same fluorophores have been successfully used in many single molecule FRET studies (Marras et al., 2002; Yin et al., 2005; Jäger et al., 2006; Granier et al., 2007; Majumdar et al., 2007).

MscL channels were reconstituted into artificial liposomes (∼50 nm diameter), following the protocol described in Perozo et al. (2002a, 2002b). Liposomes were prepared by drying, rehydrating and extruding lipids through filters with ∼50 nm pores. The lipids used in all the measurements were a mixture of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC, Avanti Polar Lipids, Inc, Alabaster, AL) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-biotinyl (BPE, Avanti Polar Lipids, Inc.) dissolved in chloroform at a molar ratio of POPC:BPE = 1000:20. BPE was used for immobilization. To incorporate MscL channels into the liposomes, a mixture of unlabeled and labeled MscL proteins (5% labeled) was then reconstituted into the liposomes, at a final volume of 1 ml, with a protein/lipid (molar) ratio of 1:200, resulting in a molar ratio of 1:4000 for the labeled proteins to lipids. The liposomes were immobilized onto a glass coverslip. This immobilization was achieved by biotin-avidin linkages between biotinylated-PEG molecules on the surface to a neutravidin molecule, and then biotinylated lipids (BPE) in the liposomes (Roy et al., 2008).

To open the MscL channels in the liposomes, a conical lipid, 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine or lysophosphatidylcholine (LPC, Avanti Polar Lipids, Inc), was added to the liposomes, at a molar fraction of 25%. As LPC incorporates itself into the outer leaflet of a lipid bilayer, it introduces membrane tension, changes the lipid pressure profile, and triggers the MscL to open (Perozo et al., 2002a, 2002b).

MscL protein purification and reconstitution into soybean azolectin liposomes were described previously (Nomura et al., 2012). All results were obtained with proteoliposomes at the protein: lipid ratio of 1:200 (wt/wt). Channel activities of the wild-type and mutant MscL were examined in inside-out liposome patches using patch-clamp technique. Borosilicate glass pipettes (Drammond Scientific Co, Broomall, PA) were pulled using a Narishige micropipette puller (PP-83; Narishige, Tokyo, Japan). Pipettes with resistance of 2.5–4.9 MΩ were used for the patch-clamp experiments. Pipette and bath solution contained 200 mM KCl, 40 mM MgCl2, and 5 mM HEPES (pH 7.2 adjusted with KOH). The current was amplified with an Axopatch 200B amplifier (Molecular Devices, Sunnyvale, CA), filtered at 2 kHz and data acquired at 5 kHz with a Digidata 1440A interface using pCLAMP 10 acquisition software (Molecular Devices, Sunnyvale, CA) and stored for analysis. Negative pressure (suction) was applied to the patch pipettes using a syringe and was monitored with a pressure gauge (PM 015R, World Precision Instruments, Sarasota, FL).

Since the MscL channel is a homo-pentamer (Chang et al., 1998) (or possibly homo-hexamer [Gandhi et al., 2011]), there is always a distribution of various donor/acceptor combinations. To exclude signal from those channels having multiple donors or multiple acceptors, the fluorescence intensity of single channels (and hence the step-wise photobleaching) was monitored. Because multiple donors or acceptors have multiple ‘staircase’ photobleaching, these channels were simply not used. Only the traces with a clear single-step photobleaching in both donor and acceptor channels were included in the analysis. Subtraction of the intensities (averaged) before and after photobleaching gives the intensities of donor (I_D) and acceptor (I_A), which are then used for FRET efficiency calculation as described below.

Single molecule FRET experiments were performed using total internal reflection fluorescence microscopy (TIRFM) with a 1.45 NA 100X oil immersion objective (Selvin and Taekjip, 2007; Roy et al., 2008). The fluorescence intensities were used to calculate the energy transfer efficiency by the corrected FRET equation: E = (I_A − ℓI_D)/(I_A + γI_D): where E is the FRET efficiency, ℓ represents leakage of donor signals in the acceptor channel, γ is the correction factor which accounts for the differences in quantum yield and detection efficiency between the donor and the acceptor, I_A and I_D represent the acceptor and donor intensities, respectively (Roy et al., 2008). Note that the direct excitation of the acceptor by the donor excitation has been corrected automatically when getting the acceptor intensity from the fluorescence traces. The distance between the donor and acceptor is given by R = R₀(E⁻¹−1)^1/6, where R₀ is the Förster radius (Förster, 1948). The Förster radius, R₀, given by ${\mathrm{R}}_{\mathrm{0}}={\left(\frac{0.529 {\kappa }^2 Q_D J\left(\lambda \right)}{N_A n^4}\right)}^{1/6}\propto {\left({\mathrm{\kappa }}^{\mathrm{2}}{\mathrm{Q}}_{\mathrm{D}}\right)}^{1/6}$, and its error were measured experimentally by measuring the absorbance and fluorescence spectra, quantum yield of the donor, AF488, (Q_D = Q_AF488) and anisotropy (A_a and A_d which give the maximum possible error in κ²) of the fluorescent probes conjugated to proteins.

The quantum yield of AF488 conjugated to MscL was measured using fluorescein in 0.1 M NaOH as a standard (Fery-Forgues and Lavabre, 1999; Lakowicz, 1999) using the equation $Q_{\text{X}}=\frac{A_S}{A_X}\times \frac{F_X}{F_S}\times {\left(\frac{n_X}{n_S}\right)}^2\times Q_S$, where Q is the quantum yield, A is the absorbance at the excitation wavelength (470 nm); F is the area under the corrected emission curve, and n is the refractive index of the solvent. Subscripts S and X refer to the standard (fluorescein) and to the unknown (AF488), respectively. The spectra of absorbance and fluorescence of AF488-MscL in PBS + DDM (1 mM DDM) were measured using Agilent 8453 UV-Vis absorbance spectrophotometer (Agilent Technologies, Santa Clara, CA) and PC1 spectrofluorimeter (ISS, Inc., Champaign, IL), respectively.

In order to determine the maximum error in the orientation factor, κ², and therefore the error in R₀, the anisotropy of the fluorophores conjugated to MscL was measured. The fluorophores-protein conjugates were immobilized on a glass coverslip which was covered with PEG (5% biotinylated), then a layer of neutravidin (Thermo Scientific, Waltham, MA), followed by a layer of penta-his biotin conjugate (Qiagen). The emission of the fluorophores-protein conjugates were split into two channels of polarization and used to calculate the anisotropy, $A=\frac{I_{\parallel }-I_{\perp }}{I_{\parallel }+2 I_{\perp }}$, where $I_{\parallel }$ is the fluorescence emission with polarization parallel to the excitation polarization and $I_{\perp }$ is the fluorescence emission with polarization perpendicular to the excitation polarization (Lakowicz, 1999). Anisotropies were corrected for the intrinsic polarization properties of the microscope by calibrating to known freely diffusing fluorophores. Anisotropies were also corrected for the high numerical aperture of the objective. Then the maximum range of κ² was given by κ²_max = 2/3(1 + 2.5A_d+2.5A_a) and κ²_min = 2/3(1−1.25A_d−1.25A_a) where A_d and A_a are the anisotropy of AF488 (donor) and AF568 (acceptor), respectively (Dale et al., 1979; Cha et al., 1999).

To evaluate directly the sizes of the fluorescent probes used in our FRET experiments, the molecular structures of the AF488-C5-Maleimide and AF568-C5-Maleimide were constructed using Avogadro (Hanwell et al., 2012). Both the 5′- and 6′-isomers were constructed. These structures were then optimized in Avogadro with molecular dynamics using the universal force field (UFF) (Rappe et al., 1992). From the optimized molecular structures (shown in Figure 4—figure supplement 1), we estimated the probe sizes which were defined as the distance between the oxygen atom of the fluorophore (indicated by the magenta arrows in Figure 4—figure supplement 1B,F) and the nitrogen atom of the maleimide group (indicated by the cyan arrows in Figure 4—figure supplement 1A–E). We found that the donor is 17.1 Å (5′-isomer) or 16.3 Å (6′-isomer) while the acceptor is 17.4 Å (5′-isomer) or 17.4 Å (6′-isomer). The difference in the molecular size between donor-isomers or between acceptor-isomers is small, <5%.

Due to lack of an E. coli MscL (EcoMscL) crystal structure, the simulation were performed using the structure of MscL from M. tuberculosis (MtMscL, PDB: 2OAR) (Chang et al., 1998; Steinbacher et al., 2007). The CP domain was truncated in the simulation because the complete deletion of the CP does not change the gating parameters substantially (Anishkin et al., 2003). The residues to which the distance constraints were applied, were shifted according to the sequence alignment in Chang et al. (1998). A spring constant of 0.2 kcal mol⁻¹Å⁻² was used for the virtual spring in the distance constrained simulation. Both secondary structure restraints (Trabuco et al., 2009) and symmetry restraints (Chan et al., 2011) were applied to prevent structural distortion under large force in the distance constrained simulation. Total simulation time is 5 ns. A model of MscL in the open state was obtained at the end of the distance constrained simulation, when the simulation satisfied all the distance constraints measured by means of smFRET experiment. The restraint MD simulation procedure is similar to the one used previously (Corry et al., 2010; Deplazes et al., 2012).

The simulation system was prepared by first imbedding the crystal structure of MscL (PDB: 2OAR) (Chang et al., 1998; Steinbacher et al., 2007) into a membrane patch with 1727 POPC lipids. Solvent was then added to both sides of the membrane, and the system was neutralized with 200 mM NaCl using VMD (Humphrey et al., 1996). The final simulation system contained 1,137,413 atoms. The all-atom MD simulations were performed using NAMD 2.9 (Phillips et al., 2005) with the TIP3P model (Jorgensen et al., 1983) for explicit water and the CHARMM36 force field (Best et al., 2012). The simulation was conducted in the NPT ensemble (constant pressure and temperature) with periodic boundary condition. Constant temperature of 300 K was maintained using a Langevin thermostat with a damping coefficient of 1 ps⁻¹. A Nosé–Hoover Langevin piston barostat was used to maintain a constant pressure of 1 atm with a period of 200.0 fs and damping timescale of 100.0 fs. The multiple time-stepping algorithm was employed, with an integration time step of 2 fs, the short-range force being evaluated every time step, and the long-range electrostatics every second time step. Non-bonded energies were calculated using particle mesh Ewald full electrostatics and a smooth (10–12 Å) cutoff of the van der Waals energy.

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

The authors acknowledge supercomputer time on Stampede provided by the Texas Advanced Computing Center (TACC) at The University of Texas at Austin through Extreme Science and Engineering Discovery Environment (XSEDE) Grant MCA93S028, supported by National Science Foundation Grant OCI-1053575. We thank Kai Wen Tseng for assistance with the quantum yield measurements. We also thank Eduardo Perozo (U of Chicago) for early work and for some MscL plasmids.

© 2014, Wang et al.

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