A model of processive movement of dimeric kinesin

Guo, Si-Kao; Wang, Peng‐Ye; Xie, Ping

doi:10.1016/j.jtbi.2016.11.023

Cited by 40 publications

(91 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the model presented previously , it was assumed that when the MT‐bound head is in the ATP or ADP.P i state, once the detached head is near the intermediate position, the NL of the MT‐bound head is docked into its motor domain immediately, implying that the NL docking occurs with a rate of k NL →

\infty

. With this model, diverse experimental data on the dynamics of kinesin‐1 except the processivity were explained quantitatively . In this work, to be consistent with the available fluorescence polarization microscopy data , we improve the model by assuming that in the intermediate state, k NL has a small value when the MT‐bound head is in the ATP state and has a finite and large value when the MT‐bound head is in the ADP.P i state to study the processivity of kinesin‐1.…”

Section: Discussionmentioning

confidence: 67%

“…In the intermediate state, when the NL of the MT‐bound head is stretched forward by a length of l NL > 2.8 nm, it is considered to point forwards, and thus, the rate constant of P i release is equal to k c , while in other cases, the rate constant of P i release is equal to

k_{normalc}^{false(normallead false)}

. In the calculation, we take

k_{normalc}^{false(normallead false)}

= k c /40 (Table ), as done before , and take k c = 185 s −1 for both types of the kinesin (Table ). This value of k c is close to the biochemical data .…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Processivity of dimeric kinesin‐1 molecular motors

et al. 2018

Self Cite

View full text Add to dashboard Cite

Kinesin‐1 is a homodimeric motor protein that can move along microtubule filaments by hydrolyzing ATP with a high processivity. How the two motor domains are coordinated to achieve such high processivity is not clear. To address this issue, we computationally studied the run length of the dimer with our proposed model. The computational data quantitatively reproduced the puzzling experimental data, including the dramatically asymmetric character of the run length with respect to the direction of external load acting on the coiled‐coil stalk, the enhancement of the run length by addition of phosphate, and the contrary features of the run length for different types of kinesin‐1 with extensions of their neck linkers compared with those without extension of the neck linker. The computational data on other aspects of the movement dynamics such as velocity and durations of one‐head‐bound and two‐head‐bound states in a mechanochemical coupling cycle were also in quantitative agreement with the available experimental data. Moreover, predicted results are provided on dependence of the run length upon external load acting on one head of the dimer, which can be easily tested in the future using single‐molecule optical trapping assays.

show abstract

\infty

Section: Discussionmentioning

confidence: 67%

k_{normalc}^{false(normallead false)}

. In the calculation, we take

k_{normalc}^{false(normallead false)}

= k c /40 (Table ), as done before , and take k c = 185 s −1 for both types of the kinesin (Table ). This value of k c is close to the biochemical data .…”

Section: Methodsmentioning

confidence: 99%

Processivity of dimeric kinesin‐1 molecular motors

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…From Figure A‐C, a forward step was made by hydrolyzing an ATP. As shown elsewhere, based on this model the available single‐molecule experimental data on diverse aspects of movement dynamics of kinesin dimers can be reproduced quantitatively.…”

Section: Discussionmentioning

confidence: 67%

“…Although the binding energy between one head in ADP or nucleotide‐free state and the other ADP‐head is high (27‐28.5 k B T ), the two heads can still frequently dissociate from each other, as showed using Brownian dynamics simulations with considerations of 3‐dimensional (3D) translations and 3D rotations. As previous all‐atom MD simulations showed, for the dimer with the two heads being connected by NLs of 14 residues, when the two heads are bound to two adjacent MT‐tubulins of about 8.2 nm apart the NLs are stretched with a large elastic force of about 30 pN. Thus, if one head in ADP or nucleotide‐free state is bound to MT, before the other ADP‐head binds to the neighboring tubulin, driven by the large elastic force the detached ADP‐head returns and rebinds to the MT‐bound head due to the high affinity of 27‐28.5 k B T .…”

Section: Discussionmentioning

confidence: 75%

“…As done in Isojima et al, consider that the particle is positioned leftward when the labeled head is bound to MT (Figure S6A). Upon unbinding from MT the labeled head moves rapidly (with a timescale of the order of μs that is smaller than the temporal resolution of 55 μs in the experiments) to the intermediate position, where due to the linker that connects the head and particle having a certain persistent length the particle becomes positioned above the labeled ADP‐head (Figure S6B). Comparing Figure S6A with Figure S6B, it is seen that due to the large size of the particle and the linker having a certain length, when the labeled head is in the intermediate state the particle is biased rightward relative to the position of the particle when the labeled head is in the MT‐bound state.…”

Section: Discussionmentioning

confidence: 95%

See 1 more Smart Citation

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

et al. 2019

Self Cite

View full text Add to dashboard Cite

Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand‐over‐hand manner, transiting alternately between one‐head‐bound (1HB) and two‐heads‐bound (2HB) states. In 1HB state, one head bound by adenosine diphosphate (ADP) is detached from MT and the other head is bound to MT. Here, using all‐atom molecular dynamics simulations we determined the position and orientation of the detached ADP‐head relative to the MT‐bound head in 1HB state. We showed that in 1HB state when the MT‐bound head is in ADP or nucleotide‐free state, with its neck linker being undocked, the detached ADP‐head and the MT‐bound head have the high binding energy, and after adenosine triphosphate (ATP) binds to the MT‐bound head, with its neck linker being docked, the binding energy between the two heads is reduced greatly. These results reveal how the kinesin dimer retains 1HB state before ATP binding and how the dimer transits from 1HB to 2HB state after ATP binding. Key residues involved in the head‐head interaction in 1HB state were identified.

show abstract

A revised worm‐like chain model for elasticity of polypeptide chains

Liu

Wang

et al. 2017

J Polym Sci B Polym Phys

Self Cite

View full text Add to dashboard Cite

The elasticity of polypeptide chains is usually characterized by the worm‐like chain model that was proposed first to describe the elasticity of double‐stranded DNA. However, the molecular dynamics simulation data on the elasticity of the polypeptide chains are deviated significantly away from the theoretical data obtained based on the worm‐like chain model. Here, we provide a revised worm‐like chain model by considering entropic, enthalpic, and hydrophobic effects and the effect of the compressing force applied to the polypeptide chains. The theoretical data obtained based on the revised model are in good agreement with the molecular dynamics simulation data. Additionally, we reveal that, besides the positive‐force regime in the elasticity of polypeptide chains, the negative‐force regime also plays important roles in the biological functions of proteins. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 297–307

show abstract

A model of processive movement of dimeric kinesin

Cited by 40 publications

References 49 publications

Processivity of dimeric kinesin‐1 molecular motors

Processivity of dimeric kinesin‐1 molecular motors

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

A revised worm‐like chain model for elasticity of polypeptide chains

Contact Info

Product

Resources

About