ATP-binding cassette (ABC) exporters are a class of molecular machines that transport substrates out of biological membranes by gating movements leading to transitions between outward-facing (OF) and inward-facing (IF) conformational states. Despite significant advances in structural and functional studies, the molecular mechanism underlying conformational gating in ABC exporters is not completely understood. A complete elucidation of the state transitions during the transport cycle is beyond the capability of the all-atom molecular dynamics (MD) method because of the limited time scale of MD. In the present work, a coarse-grained molecular dynamics (CG-MD) method with an improved sampling strategy is performed for the bacterial ABC exporter MsbA. The resultant potential of the mean force (PMF) along the center-of-mass (COM) distances, d1 and d2, between the two opposing subunits of the internal and external gates, respectively, are obtained, delicately showing the details of the
Nonequilibrium coarse-grained (CG) molecular dynamics (MD) simulations show that the ATP-binding cassette (ABC) exporter performs highly cooperative gating movements during the conformational transitions.
Figure 1. Three conformations of an ABC exporter. (a) Inward-facing (IF) conformation, in which the internal gate is open whereas the external gate is closed. (b) Occluded (OC) conformation, in which both the internal and external gates are closed. (c) Outward-facing (OF) conformation, in which the internal gate is closed whereas the external gate is open. The TMD helices, TM1−TM6 on one subunit and TM1′−TM6′ on the other, are colored red and blue, respectively. The intracellular coupling helices ICH1 (ICH1′), which links TM2 (TM2′) and TM3 (TM3′) at its N- and C-terminus, and ICH2 (ICH2′), which links TM4 (TM4′) and TM5 (TM5′), are colored green and yellow, respectively.
Figure 2. Potential of mean force (PMF) expressed as a function of the COM distances, d1, for the internal gate, and d2, for the external gate. (a) d1=2.48 nm and d2=2.83 nm, (b) d1=2.61 nm and d2=2.42 nm, (c) d1=3.21 nm and d2=2.39 nm, and (d) d1=3.48–3.82 nm and d2=2.34 nm represent the OF, OC, IF1, and IF2 states, respectively. The coarse-grained structures, which represent the (a) OF, (b) OC, (c) IF1, and (d) IF2 states, and their corresponding atomistic structures are also presented.
Figure
4.
(A) Coarse-grained structures from the CG-MD simulations for the (a) OF, (b) OC, (c) IF1, and (d) IF2 states and (B) a mechanistic model for conformational state transitions in response to NBD dissociation. For clarity, two NBDs are presented with two balls (red and blue), and only TM3 and TM4-TM5 (red) and TM3′ and TM4′-TM5′ (blue) are presented with rectangular sticks. The COM distances d1 and d2 are displayed in (A). In (B), the wider rectangular sticks represent TM4-TM5 (red, TM2′ not shown) and TM4′-TM5′ (blue, TM2 not shown), whereas the narrower rectangular sticks represent TM3 (red) and TM3′ (blue). In (B), symbols
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Stroke patients | Healthy subjects | |
Male/Female | 14/9 | 10/7 |
Age (years) | 62 ± 11 | 60 ± 9 |
Paresis side (L/R) | 5/18 | N/A |
Symbol | Description |
m | The number of columns in the pressure image, m=32 |
n | The number of rows, n=100 |
x | The column index, x∈[1,m] |
y | The row index, y∈[1,n] |
t | The frame index |
k | The step index |
p(x,y,t) | The pressure at point (x,y) in the tth frame |
M | The number of pixels in the pressure image, M=32×100 |
T | The number of frames in one gait cycle |
Test(s) | Selector | |||
C-DT | C-SVM | C-RF | C-LR | |
Str | 0.979 (RF) | 0.846 (KNN) | 0.936 (RF) | 0.880 (KNN) |
RT | 1.000 (SVM) | 0.875 (RF) | 0.957 (RF) | 0.917 (RF) |
LT | 0.979 (KNN) | 0.870 (LR) | 0.955 (SVM) | 0.917 (MLP) |
RT+LT | 0.979 (RF) | 0.958 (RF) | 0.909 (RF) | 0.936 (RF) |
All | 0.979 (KNN) | 0.936 (RF) | 0.936 (RF) | 0.898 (RF) |
Dataset | The best classifier | Accuracy | Precision | F1-score |
IMU | SVM | 0.975 | 1.000 | 0.978 |
Pressure | SVM | 1.000 | 1.000 | 1.000 |
IMU+Pressure | SVM | 1.000 | 1.000 | 1.000 |
All | SVM | 1.000 | 1.000 | 1.000 |
Test(s) | Selector | |||
R-DT | R-SVM | R-RF | R-SR | |
Str | 0.167 (GB) | 0.348 (KNN) | 0.253 (RF) | 0.353 (GB) |
RT | 0.143 (RF) | 0.360 (GB) | 0.201 (RF) | 0.391 (GB) |
LT | 0.214 (RF) | 0.211 (GB) | 0.211 (RF) | 0.324 (RF) |
RT+LT | 0.138 (RF) | 0.300 (GB) | 0.194 (KNN) | 0.327 (GB) |
All | 0.158 (RF) | 0.313 (GB) | 0.172 (SVM) | 0.360 (DT) |
Test(s) | Regressor | MAE | RMSE | ME |
Str | GB | 0.167 | 0.239 | 0.614 |
RT | RF | 0.143 | 0.178 | 0.395 |
LT | RF | 0.214 | 0.241 | 0.450 |
RT+LT | DT | 0.138 | 0.174 | 0.441 |
All | RF | 0.158 | 0.198 | 0.503 |
No. | Feature names | MAE | RMSE | ME |
1 | LBackGyroZ_MinTime_LForeGyroY_Range | 0.242 | 0.293 | 0.692 |
2 | LImageMax_MinTime_RBackGyroY_SD | 0.192 | 0.267 | 0.778 |
3 | LBackGyroXyz_MaxTime_LBackAccXyz_SD | 0.164 | 0.220 | 0.582 |
4 | LForeGyroXyz_MaxTime_LBackAccX_ | 0.133 | 0.169 | 0.410 |
Entropy_Symmetry | ||||
5 | RMatCentreSpeed_MinTime_RForeAccZ_ | 0.128 | 0.158 | 0.333 |
Median | ||||
6 | RImageCV_MaxTime_RForeGyroX_Max | 0.126 | 0.149 | 0.310 |
7 | RForeGyroY_MaxTime_RForeAccX_Median | 0.122 | 0.163 | 0.340 |
8 | RImageMean_MaxTime_LBackAccX_SD | 0.148 | 0.193 | 0.458 |
9 | RImageHu5_Skewness_Min | 0.142 | 0.179 | 0.365 |
10 | LImageSD_Skewness_Min | 0.168 | 0.200 | 0.420 |