Processivity of dimeric kinesin-1 molecular motors

ATP Concentration-Dependent Fractions of One-Head-Bound and Two-Head-Bound States of the Kinesin Motor during Its Chemomechanical Coupling Cycle

Kinesin is a typical motor protein that can use the chemical energy of ATP hydrolysis to step processively on microtubules, alternating between one-head-bound and two-head-bound states. Some published experimental results showed that the duration of the one-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the two-head-bound state is independent of ATP concentration, indicating that ATP binding occurs in the one-head-bound state. On the contrary, other experimental results showed that the duration of the two-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the one-head-bound state increases slightly with a decrease in ATP concentration, indicating that ATP binding occurs mainly in the two-head-bound state. Here, we explain consistently and quantitatively these contradictory experimental results, resolving the controversy that is critical to the chemomechanical coupling mechanism of the kinesin motor.

A Model for Chemomechanical Coupling of Kinesin-3 Motor

Introduction

Kinesin-3 motor, which is in the monomeric and inactive form in solution, after cargo-induced dimerization can step on microtubules towards the plus end with a high velocity and a supperprocessivity, which is responsible for transporting the cargo in axons and dendrites. The kinesin-3 motor has a large initial landing rate to microtubules and spends the majority of its stepping cycle in a one-head-bound state. Under the load the kinesin-3 motor can dissociate more readily than the kinesin-1 motor.

Methods

To understand the physical origin of the peculiar features for the kinesin-3 motor, a model is presented here for its chemomechanical coupling. Based on the model the dynamics of the motor under no load, under the ramping load and under the constant load is studied analytically.

Results

The theoretical results explain well the available experimental data under no load and under the ramping load. For comparison, the corresponding available experimental data for the kinesin-1 motor under the ramping load are also explained. The predicted results of the velocity, dissociation rate and run length versus the constant load for the kinesin-3 motor are provided.

Conclusions

The study has strong implications for the chemomechanical coupling mechanism of the kinesin-3 dimer. The origin of the kinesin-3 dimer in the predominant one-head-bound state is due to the fact that the rate of ATP transition to ADP in the trailing head is much larger than that of ADP release from the MT-bound head. The study shows that the kinesin-3 ADP-head has an evidently longer interaction distance with microtubule than the kinesin-1 ADP-head, explaining why in the initial ADP state the kinesin-3 motor has the much larger landing rate than the kinesin-1 motor and why under the load the kinesin-3 motor can dissociate more readily than the kinesin-1 motor.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12195-024-00795-1.

Effect of small molecular crowders on dynamics of kinesin molecular motors

Kinesin is a motor protein that can convert chemical energy of ATP hydrolysis into mechanical energy of moving processively on microtubules. Apart from the load and ATP concentration affecting the dynamics of the motor such as velocity, run length, dissociation rate, etc., the increase of solution viscosity by supplementing crowding agents of low molecular weight into the buffer can also affect the dynamics. Here, based on our proposed model for the chemomechanical coupling of the kinesin motor, a systematically theoretical study of the motor dynamics under the variation of the viscosity and load is presented. Both the load on the motor's stalk and that on one of the two heads are considered. The theoretical results provide a consistent explanation of the available contradictory experimental results, with some showing that increasing viscosity decreases sensitively the velocity whereas others showing that increasing viscosity has little effect on the velocity. The theoretical results reproduce quantitatively the puzzling experimental data showing that under different directions of the load on the stalk, increasing viscosity has very different effects on the change of run length or dissociation rate. The theoretical results predict that in both the pure and crowded buffers the dependence of the run length on the load acting one of the two heads has very different feature from that on the load acting on the stalk.

Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation

Microtubules (MTs) and their associated proteins play essential roles in maintaining cell structure, organelle transport, cell motility, and cell division. Two motors, kinesin and cytoplasmic dynein link the MT network to transported cargos using ATP for force generation. Here, we report an all-atom NMR structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The structure reveals the position and orientation of the functionally important neck linker and how ADP induces structural and dynamic changes that ensue in the neck linker. These results demonstrate that the neck linker is in the undocked conformation and oriented in the direction opposite to the KIF5B movement. Chemical shift perturbations and intensity changes indicate that a significant portion of ADP-KIF5B is in the neck linker docked state. This study also highlights the unique capability of MAS NMR to provide atomic-level information on dynamic regions of biological assemblies.

Modeling Study of the Dynamics of Kinesin-14 Molecular Motors

Kinesin-14s constitute a subfamily of the large superfamily of adenosine triphosphate-dependent microtubule-based motor proteins. Kinesin-14s have the motor domain at the C-terminal end of the peptide, playing key roles during spindle assembly and maintenance. Some of them are nonprocessive motors, whereas others can move processively on microtubules. Here, we take budding yeast Cik1-Kar3 and human HSET as examples to study theoretically the dynamics of the processive kinesin-14 motor moving on the single microtubule under load, the dynamics of the motor coupled with an Ndc80 protein moving on the single microtubule, the dynamics of the motor moving in microtubule arrays, and so on. The dynamics of the nonprocessive Drosophila Ncd motor is also discussed. The studies explain well the available experimental data and, moreover, provide predicted results. We show that the processive kinesin-14 motors can move efficiently in microtubule arrays toward the minus ends, and after reaching the minus ends, they can stay there stably, thus performing the function of organizing the microtubules in the bipolar spindle into polar arrays at the spindle poles.

Effect of Binding-Affinity and ATPase Activity on the Velocities of Kinesins Using Ratchet Models

We use two-state ratchet models containing single and coupled Brownian motors to understand the role of motor-microtubule binding, ATPase reaction rate and dimerisation on the translational velocities of Kinesin motors. We use model parameters derived from the experimental measurements on KIF1A, KIF13A, KIF13B, and KIF16B motors to compute velocities in μm/s. We observe that both the models show the same trend in velocities (KIF1A > KIF13A > KIF13B > KIF16B) as the experimental results. However, the models significantly underpredict the velocities when compared with the experiments. The predictions of the coupled-motor model are closer to the experiments than those of the single-motor model. Our results indicate that the variation of ATPase reaction rate governs the trend in velocities for the above four motors. The variation of motor-microtubule binding affinity and the coupling strength between the motor domains may only have a secondary effect. More rigorous models that incorporate the power-stroke mechanism are necessary for better quantitative compliance with the experiments.

Dynamics of kinesin motor proteins under longitudinal and sideways loads

The available single-molecule data showed that different species of N-terminal kinesin molecular motors have very different features on dependences of run length and dissociation rate upon longitudinal load acting on stalks of the motors. The prior single-molecule data for Loligo pealei kinesin-1 indicated that the sideways load has only a weak effect on the velocity, but even a small sideways load can cause a large reduction in the run length. However, these puzzling experimental data remain to be explained and the underlying physical mechanisms are unclear. Here, based on our proposed model we study analytically the dynamics of the N-terminal kinesin motors such as Loligo pealei kinesin-1, Drosophila kinesin-1, truncated kinesin-5/Eg5, truncated kinesin-12/Kif15, kinesin-2/Kif17 and kinesin-2/Kif3AB dimers under both longitudinal and sideways loads. The theoretical results explain quantitatively the available experimental data and provide predictions. The physical mechanism of different kinesin species showing very different features on the load-dependent dynamics and the physical mechanism of the effect of the sideways load on the dynamics are revealed.

Modeling processive motion of kinesin-13 MCAK and kinesin-14 Cik1-Kar3 molecular motors

Kinesin-13 MCAK, which is composed of two identical motor domains, can undergo unbiased one-dimensional diffusion on microtubules. Kinesin-14 Cik1-Kar3, which is composed of a Kar3 motor domain and a Cik1 motor homology domain with no ATPase activity, can move processively toward the minus end of microtubules. Here, we present a model for the diffusion of MCAK homodimer and a model for the processive motion of Cik1-Kar3 heterodimer. Although the two dimeric motors show different domain composition, in the models it is proposed that the two motors use the similar physical mechanism to move processively. With the models, the dynamics of the two dimers is studied analytically. The theoretical results for MCAK reproduce quantitatively the available experimental data about diffusion constant and lifetime of the motor bound to microtubule in different nucleotide states. The theoretical results for Cik1-Kar3 reproduce quantitatively the available experimental data about load dependence of velocity and explain consistently the available experimental data about effects of the exchange and mutation of the motor homology domain on the velocity of the heterodimer. Moreover, predicted results for other aspects of the dynamics of the two dimers are provided.

Effect of Kinesin-5 Tail Domain on Motor Dynamics for Antiparallel Microtubule Sliding

Kinesin-5 motor consists of two pairs of heads and tail domains, which are situated at the opposite ends of a common stalk. The two pairs of heads can bind to two antiparallel microtubules (MTs) and move on the two MTs independently towards the plus ends, sliding apart the two MTs, which is responsible for chromosome segregation during mitosis. Prior experimental data showed that the tails of kinesin-5 Eg5 can modulate the dynamics of single motors and are critical for multiple motors to generate high steady forces to slide apart two antiparallel MTs. To understand the molecular mechanism of the tails modulating the ability of Eg5 motors, based on our proposed model the dynamics of the single Eg5 with the tails and that without the tails moving on single MTs is studied analytically and compared. Furthermore, the dynamics of antiparallel MT sliding by multiple Eg5 motors with the tails and that without the tails is studied numerically and compared. Both the analytical results for single motors and the numerical results for multiple motors are consistent with the available experimental data.

Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

A model of processive walking and slipping of kinesin-8 molecular motors

Kinesin-8 molecular motor can move with superprocessivity on microtubules towards the plus end by hydrolyzing ATP molecules, depolymerizing microtubules. The available single molecule data for yeast kinesin-8 (Kip3) motor showed that its superprocessive movement is frequently interrupted by brief stick-slip motion. Here, a model is presented for the chemomechanical coupling of the kinesin-8 motor. On the basis of the model, the dynamics of Kip3 motor is studied analytically. The analytical results reproduce quantitatively the available single molecule data on velocity without including the slip and that with including the slip versus external load at saturating ATP as well as slipping velocity versus external load at saturating ADP and no ATP. Predicted results on load dependence of stepping ratio at saturating ATP and load dependence of velocity at non-saturating ATP are provided. Similarities and differences between dynamics of kinesin-8 and that of kinesin-1 are discussed.

A common ATP-dependent stepping model for kinesin-5 and kinesin-1: Mechanism of bi-directionality of kinesin-5

Kinesin-5 and kinesin-1 proteins are two families of kinesin superfamily molecular motors that can move processively on microtubules powered by ATP hydrolysis. Kinesin-1 is a unidirectional motor. By contrast, some yeast kinesin-5 motors are bidirectional and the directionality can be switched by changing the experimental conditions. Here, on the basis of a common chemomechanical coupling model, the dynamics of kinesin-1 and in particular the dynamics of kinesin-5 is studied theoretically, explaining the available experimental data. For example, the experimental data about different movement directions under different experimental conditions for kinesin-5 are explained well. The origin of why kinesin-1 can only make unidirectional movement and kinesin-5 can make bidirectional movements is revealed. The origin of mutations or deletions of several structural elements affecting the directionality of kinesin-5 is revealed. Moreover, some predicted results for kinesin-5 are provided.

A common chemomechanical coupling model for orphan and conventional kinesin molecular motors

Orphan and conventional kinesin dimers represent two families of the kinesin superfamily molecular motors. Conventional kinesin, having a 14-residue neck linker (NL) in each head, can step processively on microtubule (MT), with an ATP hydrolysis being coupled with a mechanical stepping under no load. Orphan kinesin phragmoplast-associated kinesin-related protein 2 (PAKRP2) dimer, despite having a NL of 32 residues in each head, can also step processively on MT and exhibits tight chemomechanical coupling under no load. However, the dynamic properties of the wild type PAKRP2 and the mutant one with each NL truncated to 14 residues are very different from those of the wild type conventional kinesin and the mutant one with each NL being replaced by the 32-residue NL from PAKRP2. Here, based on a common chemomechanical coupling model we study computationally the dynamics of the two families of the kinesin dimers, with the simulated results explaining quantitatively the available experimental data. The large differences in the dynamics between the two families of kinesin dimers arise mainly from different rate constants of NL docking and ATPase activity and different weak affinities of the head in ADP state for MT. The studies indicate that both the orphan kinesin PAKRP2 and conventional kinesin use the same mechanism for processive motility.

Theoretical Analysis of Dynamics of Kinesin Molecular Motors

Kinesin is a typical molecular motor that can step processively on microtubules powered by hydrolysis of adenosine triphosphate (ATP) molecules, playing a critical role in intracellular transports. Its dynamical properties such as its velocity, stepping ratio, run length, dissociation rate, etc. as well as the load dependencies of these quantities have been well documented through single-molecule experimental methods. In particular, the run length shows a dramatic asymmetry with respect to the direction of the load, and the dissociation rate exhibits a slip-catch-slip bond behavior under the backward load. Here, an analytic theory was provided for the dynamics of kinesin motors under both forward and backward loads, explaining consistently and quantitatively the diverse available experimental results.

Non-tight and tight chemomechanical couplings of biomolecular motors under hindering loads

Biomolecular motors make use of free energy released from chemical reaction (typically ATP hydrolysis) to perform mechanical motion or work. An important issue is whether a molecular motor exhibits tight or non-tight chemomechanical (CM) coupling. The tight CM coupling refers to that each ATPase activity is coupled with a mechanical step, while the non-tight CM coupling refers to that an ATPase activity is not necessarily coupled with a mechanical step. Here, we take kinesin, monomeric DNA helicase, ring-shaped hexameric DNA helicase and ribosome as examples to study this issue. Our studies indicate that some motors such as kinesin, monomeric helicase and ribosome exhibit non-tight CM coupling under hindering forces, while others such as the ring-shaped hexameric helicase exhibit tight or nearly tight CM coupling under any force. For the former, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the CM coupling efficiency, while the ATPase rate is independent or nearly independent of the force. For the latter, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the ATPase rate, while the CM coupling efficiency is independent or nearly independent of the force.

Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1

Kinesin-3 and kinesin-1 molecular motors are two families of the kinesin superfamily. It has been experimentally revealed that in monomeric state kinesin-3 is inactive in motility and cargo-mediated dimerization results in superprocessive motion, with an average run length being more than 10-fold longer than that of kinesin-1. In contrast to kinesin-1 showing normally single-exponential distribution of run lengths, dimerized kinesin-3 shows puzzlingly Gaussian distribution of run lengths. Here, based on our proposed model, we studied computationally the dynamics of kinesin-3 and compared with that of kinesin-1, explaining quantitatively the available experimental data and revealing the origin of superprocessivity and Gaussian run length distribution of kinesin-3. Moreover, predicted results are provided on ATP-concentration dependence of run length distribution and force dependence of mean run length and dissociation rate of kinesin-3.

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

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.

Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization

Multisubunit members of the CATCHR family: COG and NRZ complexes, mediate intra-Golgi and Golgi to ER vesicle tethering, respectively. We systematically addressed the genetic and functional interrelationships between Rabs, Kifs, and the retrograde CATCHR family proteins: COG3 and ZW10, which are necessary to maintain the organization of the Golgi complex. We scored the ability of siRNAs targeting 19 Golgi-associated Rab proteins and all 44 human Kifs, microtubule-dependent motor proteins, to suppress CATCHR-dependent Golgi fragmentation in an epistatic fluorescent microscopy-based assay. We found that co-depletion of Rab6A, Rab6A’, Rab27A, Rab39A and two minus-end Kifs, namely KIFC3 and KIF25, suppressed both COG3- and ZW10-depletion-induced Golgi fragmentation. ZW10-dependent Golgi fragmentation was suppressed selectively by a separate set of Rabs: Rab11A, Rab33B and the little characterized Rab29. 10 Kifs were identified as hits in ZW10-depletion-induced Golgi fragmentation, and, in contrast to the double suppressive Kifs, these were predominantly plus-end motors. No Rabs or Kifs selectively suppressed COG3-depletion-induced Golgi fragmentation. Protein-protein interaction network analysis indicated putative direct and indirect links between suppressive Rabs and tether function. Validation of the suppressive hits by EM confirmed a restored organization of the Golgi cisternal stack. Based on these outcomes, we propose a three-way competitive model of Golgi organization in which Rabs, Kifs and tethers modulate sequentially the balance between Golgi-derived vesicle formation, consumption, and off-Golgi transport.

Force dependence of unbinding rate of kinesin motor during its processive movement on microtubule

Kinesin is a biological molecular motor that can move continuously on microtubule until it unbinds. Here, we studied computationally the force dependence of the unbinding rate of the motor. Our results showed that while the unbinding rate under the forward load has the expected characteristic of "slip bond", with the unbinding rate increasing monotonically with the increase of the forward load, the unbinding rate under the backward load shows counterintuitive characteristic of "slip-catch-slip bond": as the backward load increases, the unbinding rate increases exponentially firstly, then drops rapidly and then increases again. Our calculated data are in agreement with the available single-molecule data from different research groups. The mechanism of the slip-catch-slip bond was revealed.

Dynamics of cooperative cargo transport by two elastically coupled kinesin motors

Intracellular transport is performed often by multiple motor proteins bound to the same cargo. Here, we study theoretically collective transport of the cargo by two kinesin motors. We propose that the motor has only the elastic interaction with the cargo via the linker connecting them and has no interaction with another motor. With parameters values for single motors from the available single-molecule data, we show that at linker's elastic strength [Formula: see text] pN/nm the theoretical data of both velocity and run length of the two-motor assembly under no load are identical to the available experimental data. The run length distribution is single exponential. The single-motor-bound state of the assembly dominates the transport. Both the force dependence of the velocity of the cargo driven by single load-bearing motor and that by two load-bearing motors in the assembly are consistent with the experimental data. The stall force of the assembly is larger than the sum of stall forces of two uncoupled motors. Moreover, we predict that the stall force increases with the increase of K and becomes saturated at large K, with the saturated value being 1.5-fold larger than the sum of stall forces of the two uncoupled motors.

Force Dependence of Velocity and Run Length of Kinesin-1, Kinesin-2 and Kinesin-5 Family Molecular Motors

Kinesin-1, kinesin-2 and kinesin-5 are three families of a superfamily of motor proteins; which can walk processively on microtubule filaments by hydrolyzing ATP. It was experimentally shown that while the three kinesin dimers show similar feature on the force dependence of velocity, they show rather different features on the force dependence of run length. However, why the three families of kinesins show these rather different features is unclear. Here, we computationally studied the movement dynamics of the three dimers based on our proposed model. The simulated results reproduce well the available experimental data on the force dependence of velocity and run length. Moreover, the simulated results on the velocity and run length for the three dimers with altered neck linker lengths are also in quantitative agreement with the available experimental data. The studies indicate that the three families of kinesins show much similar movement mechanism and the rather different features on the force dependence of run length arise mainly from the difference in rate constants of the ATPase activity and neck linker docking. Additionally, the asymmetric (limping) movement dynamics of the three families of homodimers with and without altered neck linker lengths are studied, providing predicted results.

Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all-atom molecular dynamics simulation

Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all-atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule-tubulin heterodimers induced by strong interaction with the head in strongly binding state are also indispensable to regulate the affinity of the head to the tubulin. In strongly binding state the high affinity of the head to microtubule arises largely from mutual conformational changes of the microtubule and head induced by the specific interaction between them via an induced-fit mechanism. Moreover, the ADP-head has a much weaker affinity to the local microtubule-tubulin, whose conformation is largely altered by the interaction with the head in strongly binding state, than to other unperturbed tubulins. This indicates that upon Pi release the ADP-head temporarily has a much weaker affinity to the local tubulin than to other tubulins.