Wang Peng-Ye

Mechanism for unidirectional movement of kinesin

Kinesin motors have been studied extensively both experimentally and theoretically. However, the microscopic mechanism of the processive movement of kinesin is still an open question. In this paper, we propose a hand-over-hand model for the processivity of kinesin, which is based on chemical, mechanical and electrical couplings. In the model the ATPase rates of the two kinesin heads are regulated by forces, both from internal elasticity and external load, exerted on their necks. At a low external load, the ATPase rate of the trailing head is much higher than the leading head and the two heads are coordinated in their ATP hydrolysis and mechanical cycles. The motor walks processively with one ATP being hydrolyzed per step. At a higher forward external load, the ATPase rates of the two heads become comparable and thus the two heads are no longer well coordinated in their ATP hydrolysis and mechanical cycles. The model is consistent with the structural study of kinesin and the measured pathway of the kinesin ATPase. Using the model we have estimated the driving force to be ~5.8pN, which is in agreement with the experimental results (5–7.5pN). The estimated time for moving one step (~10μs) is also consistent with the measured values of 0–50μs. The previous observation of substeps within the 8nm step is explained. The shapes of velocity versus load (both positive and negative) curves show close resemblance to previous experimental results.In the calibration of the optical trap stiffness, it is found that there appears an attenuating oscillation as an oscillatory disturbance added to the trapped bead movement, when the scanner is driven by a triangular wave input.An equivalent oscillator model is put forward to explain the mechanism of the oscillatory disturbance. Both the measurements and calculations show that the attenuating oscillation comes from the oscillation of the scanner and the triangular wave drive causes this additional oscillation of the scanner. Furthermore, the analysis indicates that the oscillatory disturbance will become stronger, when the stiffness of the trap increases or the natural frequency of the scanner decreases. We adopt another driving way, i.e. a sinusoidal wave input is used instead of the triangular wave input. Our experiment has verified that in this case the oscillatory disturbance is eliminated completely.

Control of spiral waves and turbulent states in a cardiac model by travelling-wave perturbations

We propose a travelling-wave perturbation method to control the spatiotemporal dynamics in a cardiac model. It is numerically demonstrated that the method can successfully suppress the wave instability (alternans in action potential duration) in the one-dimensional case and convert spiral waves and turbulent states to the normal travelling wave states in the two-dimensional case. An experimental scheme is suggested which may provide a new design for a cardiac de brillator.We propose a travelling-wave perturbation method to control the spatiotemporal dynamics in a cardiac model. It is numerically demonstrated that the method can successfully suppress the wave instability (alternans in action potential duration) in the one-dimensional case and convert spiral waves and turbulent states to the normal travelling wave states in the two-dimensional case. An experimental scheme is suggested which may provide a new design for a cardiac defibrillator.

Effect of Cisplatin on the Flexibility of Linear DNA

With the aid of an atomic force microscope (AFM), we study the interaction between linear DNA fragment and cisplatin. For different cisplatin concentrations, the AFM used to observe the conformation of DNA has a gradual change. The contour length, the end-to-end distance and the local bend angles of the linear DNA fragment can be accurately measured. The persistence length of DNA interacting with cisplatin is decreased with the increasing cisplatin concentration. Furthermore, it is demonstrated that the local bend angles of DNA chains are increased by the binding interaction of cisplatin.

Interactions between DNA and histones- a dynamic process of nucleosome formation

We have studied the dynamic process of interactions between a DNA chain and a histone octamer by numerical simulations. It is found that DNA indeed may wrap around the histone octamer about two turns as in the actual situations. The simulation shows that the interaction potential between DNA and histone is a key factor for the wrapping of DNA and the temperature is also an important parameter in the process.

Model for processive movement of myosin V and myosin VI

Kinesin motors have been studied extensively both experimentally and theoretically. However, the microscopic mechanism of the processive movement of kinesin is still an open question. In this paper, we propose a hand-over-hand model for the processivity of kinesin, which is based on chemical, mechanical, and electrical couplings. In the model the ATPase rates of the two kinesin heads are regulated by forces, both from internal elasticity and external load, exerted on their necks. At a low external load, the ATPase rate of the trailing head is much higher than the leading head and the two heads are coordinated in their ATP hydrolysis and mechanical cycles. The motor walks processively with one ATP being hydrolyzed per step. At a higher forward external load, the ATPase rates of the two heads become comparable and thus the two heads are no longer well coordinated in their ATP hydrolysis and mechanical cycles. The model is consistent with the structural study of kinesin and the measured pathway of the kinesin ATPase. Using the model we have estimated the driving force to be -5.8pN, which is in agreement with the experimental results (5 7.5pN).The estimated time for moving one step (-10μs) is also consistent with the measured values of 50μs. The previous observation of substeps within the 8nm step is explained. The shapes of velocity versus load (both positive and negative)curves show close resemblance to previous experimental results.Myosin V and myosin VI are two classes of two-headed molecular motors of the myosin superfamily that move processively along helical actin filaments in opposite directions. Here we present a hand-over-hand model for their processive movements. In the model, the moving direction of a dimeric molecular motor is automatically determined by the relative orientation between its two heads at free state and its heads binding orientation on track filament. This determines that myosin V moves toward the barbed end and myosin VI moves toward the pointed end of actin. During the moving period in one step, one head remains bound to actin for myosin V whereas two heads are detached for myosin VI: the moving manner is determined by the length of neck domain. This naturally explains the similar dynamic behaviours but opposite moving directions of myosin VI and mutant myosin V (the neck of which is truncated to only one-sixth of the native length). Because of different moving manners, myosin VI and mutant myosin V exhibit significantly broader step-size distribution than native myosin V. However, all the three motors give the same mean step size of ~36nm (the pseudo-repeat of actin helix). All these theoretical results are in agreement with previous experimental ones.Myosin V and myosin VI are two classes of two-headed molecular motors of the myosin superfamily that move processively along helical actin filaments in opposite directions. Here we present a hand-over-hand model for their processive movements. In the model, the moving direction of a dimeric molecular motor is automatically determined by the relative orientation between its two heads at free state and its heads binding orientation on track filament. This determines that myosin V moves toward the barbed end and myosin VI moves toward the pointed end of actin. During the moving period in one step, one head remains bound to actin for myosin V whereas two heads are detached for myosin VI: the moving manner is determined by the length of neck domain. This naturally explains the similar dynamic behaviours but opposite moving directions of myosin VI and mutant myosin V (the neck of which is truncated to only one-sixth of the native length). Because of different moving manners, myosin VI and mutant myosin V exhibit significantly broader step-size distribution than native myosin V. However, all the three motors give the same mean step size of similar to 36nm (the pseudo-repeat of actin helix). All these theoretical results are in agreement with previous experimental ones.

Spiking Regularity and Coherence in Complex Hodgkin–Huxley Neuron Networks

We study the effects of the strength of coupling between neurons on the spiking regularity and coherence in a complex network with randomly connected Hodgkin–Huxley neurons driven by colored noise. It is found that for the given topology realization and colored noise correlation time, there exists an optimal strength of coupling, at which the spiking regularity of the network reaches the best level. Moreover, when the temporal regularity reaches the best level, the spatial coherence of the system has already increased to a relatively high level. In addition, for the given number of neurons and noise correlation time, the values of average regularity and spatial coherence at the optimal strength of coupling are nearly independent of the topology realization. Furthermore, there exists an optimal value of colored noise correlation time at which the spiking regularity can reach its best level. These results may be helpful for understanding of the real neuron world.

Modelling of a DNA packaging motor

During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage 29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the 29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.

A non-Markov ratchet model of molecular motors: processive movement of single-headed kinesin KIF1A

A fluctuating ratchet model of non-Markov process is presented to describe the processive movement of molecular motors of single-headed kinesin KIF1A, where the fluctuation perturbation to the local potential is introduced and the detailed ATPase pathway of the motor is included. The theoretical results show good quantitative agreement with the previous experimental ones.

Monte Carlo Simulation of Kinesin Movement with a Lattice Model

Kinesin is a processive double-headed molecular motor that moves along a microtubule by taking about 8 nm steps. It generally hydrolyzes one ATP molecule for taking each forward step. The processive movement of the kinesin molecular motors is numerically simulated with a lattice model. The motors are considered as Brownian particles and the ATPase processes of both heads are taken into account. The Monte Carlo simulation results agree well with recent experimental observations, especially on the relation of velocity versus ATP and ADP concentrations.

Light-Gradient-Induced Spiral Wave Drifts in a Belousov–Zhabotinsky Reaction

The dynamic behaviour of spiral tip in the light-sensitive Belousov–Zhabotinsky reaction under the influence of an externally applied light gradient was experimentally studied. The gradient causes different drifts for different spiral patterns. The centre of the spiral wave moved toward the region of lower light intensity. The direction of an additional perpendicular drift depended on the chirality of the spiral wave. The dependences of the drifting angle and the drifting velocity on light gradient have been measured.