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Model for Unidirectional Movement of Axonemal and Cytoplasmic Dynein Molecules

Acta Biochimica et Biophysica Sinica 2006年第10期38卷 711-724页

作者： ping xie* shuo-xing dou peng-ye wang laboratory of soft matter Physics,beijing national laboratory for condensed matter Physics,institute of Physics,chinese Academy of sciences,beijing 1.0080,china laboratory of soft {2. Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of SciencesBeijing 100080 China

A model for the unidirectional movement of dynein is presented based on the structuralobservations and biochemical experimental results *** this model,the binding affinity of dynein formicrotubule (MT) is independent of its nucleotide state and the change between strong and weak MT-bindingis determined naturally by the variation of relative orientation between the stalk and MT,as the stalk rotatesfollowing nucleotide-state *** the enigmatic communication from the adenosine triphosphate(ATP)-binding site in the globular domain to the far MT-binding site in the tip of the stalk,which is aprerequisite in conventional models,is not *** the present model,the previous experimentalresults such as the effect of ATP and adenosine diphosphate (ADP) bindings on dissociation of dynein fromMT,the movement of single-headed axonemal dyneins at saturating ATP concentration,the load dependenceof step-size for the movement of two-headed cytoplasmic dyneins and the dependence of stall force on ATPconcentration can be well explained.

关键词： dynein mechanism mechanochemistry molecular motor

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RecQ Helicase-catalyzed DNA Unwinding Detected by Fluorescence Resonance Energy Transfer

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Acta Biochimica et Biophysica Sinica 2005年第9期37卷 593-600页

作者： xing-Dong ZHANG shuo-xing dou ping xie peng-ye wang Xu Guang XI laboratory of soft matter Physics,beijing {12. laboratory for condensed matter Physics,institute of Physics,chinese Academy of sciences,beijing 1.0080,china Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée CNRS UMR 8113.Ecole Normale Supérieure de Cachan,61 Avenue du Président Wilson,94235 Cachan cedex,France laboratory of soft {2. Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of SciencesBeijing 100080 China Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée CNRS UMR 8113 Ecole Normale Supérieure de Cachan61 Avenue du Président Wilson 94235 Cachan cedex France

A fluorometric assay was used to study the DNA unwinding kinetics induced by Escherichiacoli RecQ *** assay was based on fluorescence resonance energy transfer and carried out onstopped-flow,in which DNA unwinding was monitored by fluorescence emission enhancement of fluoresceinresulting from helicase-catalyzed DNA *** this method,we determined the DNA unwinding rateof RecQ at different enzyme *** also studied the dependences of DNA unwinding magnitudeand rate on magnesium ion *** showed that this method could be used to determine thepolarity of DNA *** assay should greatly facilitate further study of the mechanism for RecQ-catalyzed DNA unwinding.

关键词： helicase DNA unwinding kinetics stopped-flow fluorescence resonance energy transfer (FRET)

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Effects of rebinding rate and asymmetry in unbinding rate on cargo transport by multiple kinesin motors

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Communications in Theoretical Physics 2021年第1期73卷 106-116页

作者： Yao wang Yu-Ying Liu Jian Liang peng-{2. wang ping xie College of Engineering and College of Science China Agricultural UniversityBeijing 100083China Key laboratory of soft {2. Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

Many intracellular transports are performed by multiple molecular motors in a cooperative ***,we use stochastic simulations to study the cooperative transport by multiple kinesin motors,focusing mainly on effects of the form of unbinding rate versus force and the rebinding rate of single motors on the cooperative *** consider two forms of the unbinding *** is the symmetric form with respect to the force direction,which is obtained according to Kramers *** other is the asymmetric form,which is obtained from the prior studies for the single kinesin *** the asymmetric form the simulated results of both velocity and run length of the cooperative transport by two identical motors and those by a kinesin-1 motor and a kinesin-2.motor are in quantitative agreement with the available experimental data,whereas with the symmetric form the simulated results are inconsistent with the experimental *** the cooperative transport by a faster motor and a much slower motor,the asymmetric form can give both larger velocity and longer run length than the symmetric form,giving an explanation for why kinesin adopts the asymmetric form of the unbinding rate rather than the symmetric *** the cooperative transport by two identical motors,while the velocity is nearly independent of the rebinding rate,the run length increases linearly with the rebinding *** the cooperative transport by two different motors,the increase of the rebinding rate of one motor also enhances the run length of the cooperative *** dynamics of transport by N(N=3,4,5,6,7 and 8)motors is also studied.

关键词： molecular motors collective transport kinesin

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Acceleration of DNA Replication of Klenow Fragment by Small Resisting Force

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chinese Physics Letters 2021年第11期38卷 91-95页

作者： Yu-Ru Liu peng-ye {2. Wei Li ping xie laboratory of soft {2. Physics and beijing national laboratory for condensed {2. Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical sciences University of Chinese Academy of SciencesBeijing 100049China Songshan Lake Materials laboratory Dongguan 523808China

DNA polymerases are an essential class of enzymes or molecular motors that catalyze processive DNA syntheses during DNA replications. A critical issue for DNA polymerases is their molecular mechanism of processive DNA replication. We have proposed a model for chemomechanical coupling of DNA polymerases before, based on which the predicted results have been provided about the dependence of DNA replication velocity upon the external force on Klenow fragment of DNA polymerase I. Here, we performed single molecule measurements of the replication velocity of Klenow fragment under the external force by using magnetic tweezers. The single molecule data verified quantitatively the previous theoretical predictions, which is critical to the chemomechanical coupling mechanism of DNA polymerases. A prominent characteristic for the Klenow fragment is that the replication velocity is independent of the assisting force whereas the velocity increases largely with the increase of the resisting force,attains the maximum velocity at about 3.8 pN and then decreases with the further increase of the resisting force.

关键词： DNA Acceleration of DNA Replication of Klenow Fragment by Small Resisting Force

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