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Coarse-grain simulations of active molecular machines in lipid bilayers
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Figures

Image of FIG. 1.

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FIG. 1.

The cycle of the model machine. Depending on the absence or presence of a ligand (black ball), the machine tends to evolve to the open (A) or closed (B) conformations, respectively.

Image of FIG. 2.

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FIG. 2.

(a) The molecular machine has 64 beads and 361 interconnecting springs. There are 16 hydrophobic beads (orange), while other beads are hydrophilic (red). Three ligand-binding beads located at the flexible joint are colored purple. (b) The machine conformation is characterized by the hinge angle θ that represents the angle between the vectors connecting two yellow (i = 7 and 64) beads with the center of mass of the binding sites (black).

Image of FIG. 3.

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FIG. 3.

Membranes with the immersed ligand-free (a) and ligand-bound (b) machines. Each lipid is represented by a flexible rod. The blue beads are the hydrophilic head beads, the light blue beads are the last tail beads of the lipid chains, the gray rods represent the hydrophobic part of the lipid chains, and the ligand is shown as a black bead. The solvent is not displayed, and only half of membrane is shown for clear visualization (enhanced online). [URL: http://dx.doi.org/10.1063/1.4803507.1] [URL: http://dx.doi.org/10.1063/1.4803507.2]doi: 10.1063/1.4803507.1.

doi: 10.1063/1.4803507.2.

Image of FIG. 4.

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FIG. 4.

Thickness (upper row) and midplane height (lower row) of the membrane with the ligand-free (left column) and ligand-bound (right column) machines immersed in the upper membrane leaflet. Normalized values of the membrane thickness and midplane height are displayed by using the color codes shown in the bars. Filled orange circles mark average positions of the hydrophobic beads of the machine, whereas open circles correspond to the machine hydrophilic beads which are immersed in or are in contact with the membrane.

Image of FIG. 5.

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FIG. 5.

Heights of the upper (upper row) and the lower (lower row) leaflets with ligand-free (left column) and ligand-bound (right column) machines. Normalized heights are displayed by using the color codes shown in the bars. Solid orange circles mark average positions of the hydrophobic beads of the machine, whereas open circles correspond to the machine hydrophilic beads which are immersed into or are in contact with the membrane.

Image of FIG. 6.

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FIG. 6.

The cycle of a membrane machine: (A) The ligand binds to the machine; (B) the machine conformation changes from the open state to the closed state; (C) the reaction takes place and the ligand is released; (D) the machine returns to its open state (enhanced online). [URL: http://dx.doi.org/10.1063/1.4803507.3]doi: 10.1063/1.4803507.3.

Image of FIG. 7.

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FIG. 7.

Hinge angle of an active machine as a function of time. The label A marks a ligand-binding event, while C marks a ligand-releasing event as shown in Fig. 6 .

Image of FIG. 8.

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FIG. 8.

The power spectrum of the free membrane (black circles), of the membrane anchored with a passive closed machine (red solid diamonds), the membrane anchored with a passive open machine (yellow solid diamonds), and the membrane anchored with an active machine (blue solid triangles).

Image of FIG. 9.

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FIG. 9.

Time autocorrelation function of the height fluctuation for the membrane without a machine.

Image of FIG. 10.

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FIG. 10.

Average lipid velocity fields for (a) opening segments and (b) closing segments. The arrows indicate the direction of the velocity and the colors characterize the flow speed.

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/content/aip/journal/jcp/138/19/10.1063/1.4803507
2013-05-15
2014-04-24

Abstract

A coarse-grain method for simulations of the dynamics of active protein inclusions in lipid bilayers is described. It combines the previously proposed hybrid simulations of bilayers [M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys.137, 055101 (Year: 2012)]10.1063/1.4736414, based on molecular dynamics for the lipids and multi-particle collision dynamics for the solvent, with an elastic-network description of active proteins. The method is implemented for a model molecular machine which performs active conformational motions induced by ligand binding and its release after reaction. The situation characteristic for peripheral membrane proteins is considered. Statistical investigations of the effects of single active or passive inclusions on the shape of the membrane are carried out. The results show that the peripheral machine produces asymmetric perturbations of the thickness of two leaflets of the membrane. It also produces a local saddle in the midplane height of the bilayer. Analysis of the power spectrum of the fluctuations of the membrane midplane shows that the conformational motion of the machine perturbs these membrane fluctuations. The hydrodynamic lipid flows induced by cyclic conformational changes in the machine are analyzed. It is shown that such flows are long-ranged and should provide an additional important mechanism for interactions between active inclusions in biological membranes.

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Scitation: Coarse-grain simulations of active molecular machines in lipid bilayers
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/19/10.1063/1.4803507
10.1063/1.4803507
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