A stochastic automaton model for simulating kinesin processivity

Khataee, H. R.; Liew, Alan Wee‐Chung

doi:10.1093/bioinformatics/btu664

Cited by 8 publications

(15 citation statements)

References 34 publications

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“…We recently simulated the processivity of single kinesin over resisting forces using the four‐state kinetic scheme . We showed that the mean run length of the motor under resisting forces can be determined by the number of ATP hydrolysis and ATP synthesis cycles taken by the motor before dissociating from MT.…”

Section: Resultsmentioning

confidence: 99%

“…To analyze the stepping kinetics of kinesin, we develop a stochastic timed automaton M kinesin model and use the model to simulate the mean run length of the motor, based on our previous study in . The details of M kinesin model are provided in the section of Methods.…”

Section: Resultsmentioning

confidence: 99%

“…[16] We recently simulated the processivity of single kinesin over resisting forces using the four-state kinetic scheme. [19] We showed that the mean run length of the motor under resisting forces can be determined by the number of ATP hydrolysis and ATP synthesis cycles taken by the motor before dissociating from MT. Therefore, to investigate the effects of force direction on the stepping kinetics of kinesin, we generalize our model in [19] by taking into account the asymmetry of k F off and extending the direction of applied force to both resisting and assisting.…”

Section: Full Papermentioning

confidence: 99%

“…In our previous studies, we developed a set of theoretical models for studying the mechanochemical kinetics underlying forward and backward steppings of a single kinesin ,,. On the basis of our findings in, and following the recent experiments in,, here we propose a theoretical model which takes into account the asymmetry of the force‐unbinding rate relation and describes how stepping kinetics of kinesin is affected by changing the direction of applied external force from resisting (negative) to assisting (positive); see Figure a. The model uses both analytical and computational methods.…”

Section: Introductionmentioning

confidence: 99%

“…the average distance that the motor travels before detaching from MT). [17][18][19][20] These studies [17,18,20] have assumed a symmetric unidirectional force-unbinding rate relation for the motor, i.e. the unbinding rate under assisting forces (applied in the direction of stepping) is equal to that under resisting forces (applied against the direction of stepping).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Unbinding of Kinesin from Microtubule in the Strongly Bound States Enhances under Assisting Forces

Khataee

Naseri

Zhong

et al. 2017

Molecular Informatics

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The ability to predict the cellular dynamics of intracellular transport has enormous potential to impact human health. A key transporter is kinesin-1, an ATP-driven molecular motor that shuttles cellular cargos along microtubules (MTs). The dynamics of kinesins depends critically on their unbinding rate from MT, which varies depending on the force direction applied on the motor, i.e. the force-unbinding rate relation is asymmetric. However, it remains unclear how changing the force direction from resisting (applied against the motion direction) to assisting (applied in the motion direction) alters the kinesin's unbinding and stepping. Here, we propose a theoretical model for the influence of the force direction on the stepping dynamics of a single kinesin. The model shows that the asymmetry of the force-unbinding rate relation is independent of ATP concentration. It also reveals that the synthesis of ATP from backward stepping under assisting forces is less likely than under resisting forces. It then finds that the unbinding of kinesin in the strongly MT-bound kinetic states enhances under assisting forces.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%