分支拓扑DNA链上分子马达的协调运动

鲁頔; 陈彬

doi:10.1007/s10409-021-09045-x

Coordinated motion of molecular motors on DNA chains with branch topology

doi: 10.1007/s10409-021-09045-x

Lu Di¹,
Chen Bin^{1, 2,*
, ,}

1.
Department of Engineering Mechanics, Zhejiang University, Hangzhou 310058, China
2.
Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Hangzhou 310027, China

Funds:

the National Natural Science Foundation of China Grant

More Information

Corresponding author: Chen Bin, E-mail address: chenb6@zju.edu.cn (Bin Chen)

摘要

摘要: 为理解整合了DNA马达的响应性DNA水凝胶的宏观力学行为, 文章在分子水平上构建了单个FtsK_C在单个DNA链上的易位过程状态图, 并进一步研究了具有不同分支拓扑的DNA链上单个或多个FtsK_C马达的运动. 研究表明, 多个FtsK_C马达可以协调运动, 这主要是由于单个FtsK_C马达的力响应行为. 文章进一步指出FtsK_C马达结合特定分支拓扑的DNA链作为水凝胶中的应变传感器的潜在应用.
Abstract: To understand the macroscopic mechanical behaviors of responsive DNA hydrogels integrated with DNA motors, we constructed a state map for the translocation process of a single FtsK_C on a single DNA chain at the molecular level and then investigated the movement of single or multiple FtsK_C motors on DNA chains with varied branch topologies. Our studies indicate that multiple FtsK_C motors can have coordinated motion, which is mainly due to the force-responsive behavior of individual FtsK_C motors. We further suggest the potential application of motors of FtsK_C, together with DNA chains of specific branch topology, to serve as strain sensors in hydrogels.
- DNA /
- Molecular motor /
- Coordinated motion /
- Branch topology /
- Strain sensor

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1. Kinetic model of FtsK_C translocation to a single DNA chain. a Illustration of five 1st level kinetic states (I-V) within a DNA-FtsK_C interaction cycle. b Five 1st level kinetic states (I-V) are assigned to a FtsK_C motor within a DNA-FtsK_C interaction cycle. c Five 2nd level states (1-5) exist between state I and state II. d When the motor is in state IV, it randomly switches the translocating direction, which can be either forward or backward.

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2. Schematic diagram of the measurement of FtsK_C translocation on a single DNA chain. a In the experiment, each end of a DNA chain was attached to a bead. One bead was held by suction through a micropipette. Shortening of a DNA chain caused by translocation of a motor results from the formation of an expanding DNA loop [31]. When the motor translocates in the forward direction, the loop expands, and when the motor translocates in the backward direction, the loop shrinks. b Evolution of the extension of a DNA chain with time caused by the translocation of a single FtsK_C. The black curve represents the experimental result [31], and curves of other colors are simulated results with the Monte Carlo method.

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3. DNA chains with varied branch topology. a DNA chains with a linear topology. b DNA chains with a Y-shaped topology. c DNA chains with an X-shaped topology. d Deformation of DNA chains with a Y-shaped topology after a period of time. e Force-extension curve of a DNA chain calculated with the tWLC model. DNA is able to overstretch at F_overstretch. In the calculation, L_c = 13.6 μm, S = 1500 pN, C = 440 pN nm², F_overstretch = 60 pN.

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4. Flow chart of the simulation.

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5. a-c DNA chains with a linear topology: a the variation of the contour length of two DNA chains with time, b the variation of force on two DNA chains with time, c the variation of X_O with time. d-f DNA chains with a Y-shaped topology: d the variation of the contour length of three DNA chains with time, e the variation of force on three DNA chains with time, f the variation of X_O and Y_O with time. g-i DNA chains with an X-shaped topology: g the variation of the contour length of four DNA chains with time, h the variation of force on three DNA chains with time, i the variation of X_O and Y_O with time.

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6. a The total displacement of the motor, X(∆t), is the sum of the displacement of the motor due to the change in the initial length when the contour length changes, X₁(∆t), and the displacement of the motor due to the change in the elastic stretch, X₂(∆t). b Illustration of DNA chains together with FtsK_C that can be built within a hydrogel to measure the local stretches when subjected to hydrostatic pressure.

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Table 1. Comparison of K_I,II between the simulation and the experiment

Experiment/Simulation	Concentration of motor monomer (nM)	Average time required for the formation of 10000 FtsK_C hexamer (s)	K_I,II (s⁻¹)
Experiment	75-150	5.5	0.182
Simulated	75	10.56	0.095
	100	3.76	0.266
	150	1.05	0.952

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Table 2. Correlation analysis of the experimental results and simulated results

Experiment/Simulation	Pearson correlation coefficient
Experiment [31]	−0.856
Simulation 1	−0.976
Simulation 2	−0.775
Simulation 3	−0.943
Simulation 4	−0.979

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