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Abstract
Kinesins are a diverse superfamily of microtubule-based motors that perform fundamental roles in intracellular transport, cytoskeletal dynamics and cell division. These motors share a characteristic motor domain that powers unidirectional motility and force generation along microtubules, and they possess unique tail domains that recruit accessory proteins and facilitate oligomerization, regulation and cargo recognition. The location, direction and timing of kinesin-driven processes are tightly regulated by various cofactors, adaptors, microtubule tracks and microtubule-associated proteins. This Review focuses on recent structural and functional studies that reveal how members of the kinesin superfamily use the energy of ATP hydrolysis to transport cargoes, depolymerize microtubules and regulate microtubule dynamics. I also survey how accessory proteins and post-translational modifications regulate the autoinhibition, cargo binding and motility of some of the best-studied kinesins. Despite much progress, the mechanism and regulation of kinesins are still emerging, and unresolved questions can now be tackled using newly developed approaches in biophysics and structural biology.
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Affiliation(s)
- Ahmet Yildiz
- Physics Department, University of California at Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, USA.
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2
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Rao L, Wirth JO, Matthias J, Gennerich A. A Two-Heads-Bound State Drives KIF1A Superprocessivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.14.632505. [PMID: 39868206 PMCID: PMC11761605 DOI: 10.1101/2025.01.14.632505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
KIF1A, a neuron-specific Kinesin-3 motor, is indispensable for long-distance axonal transport and nuclear migration, processes vital for neuronal function. Using MINFLUX tracking, we reveal that KIF1A predominantly adopts a two-heads-bound state, even under ATP-limiting conditions, challenging prior models proposing a one-head-bound rate-limiting step. This two-heads-bound conformation, stabilized by interactions between the positively charged K-loop and negatively charged tubulin tails, enhances microtubule affinity and minimizes detachment. The shorter neck linker facilitates inter-head tension, keeping the heads out of phase and enabling highly coordinated stepping. In contrast, Kinesin-1 (KIF5B) transitions to a one-head-bound state under similar conditions, limiting its processivity. Perturbing KIF1A's mechanochemical cycle by prolonging its one-head-bound state significantly reduces processivity, underscoring the critical role of the two-heads-bound state in motility. These findings establish a mechanistic framework for understanding KIF1A's adaptations for neuronal transport and dysfunction in neurological diseases.
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3
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Baig F, Bakdaleyeh M, Bazzi HM, Cao L, Tripathy SK. Dissecting the pH Sensitivity of Kinesin-Driven Transport. J Phys Chem B 2024; 128:11855-11864. [PMID: 39575923 PMCID: PMC11627161 DOI: 10.1021/acs.jpcb.4c03850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 10/11/2024] [Accepted: 10/23/2024] [Indexed: 12/06/2024]
Abstract
Kinesin-1 is a crucial motor protein that drives the microtubule-based movement of organelles, vital for cellular function and health. Mostly studied at pH 6.9, it moves at approximately 800 nm/s, covers about 1 μm before detaching, and hydrolyzes one ATP per 8 nm step. Given that cellular pH is dynamic and alterations in pH have significant implications for disease, understanding how kinesin-1 functions across different pH levels is crucial. To explore this, we executed single-molecule motility assays paired with precise optical trapping techniques over a pH range of 5.5-9.8. Our results show a consistent positive relationship between increasing pH and the enhanced detachment (off rate) and speed of kinesin-1. Measurements of the nucleotide-dependent off rate show that kinesin-1 exhibits the highest rate of ATPase activity at alkaline pH, while it demonstrates the optimal number of ATP turnover and cargo translocation efficiency at the acidic pH. Physiological pH of 6.9 optimally balances the biophysical activity of kinesin-1, potentially allowing it to function effectively across a range of pH levels. These insights emphasize the crucial role of pH homeostasis in cellular function, highlighting its importance for the precise regulation of motor proteins and efficient intracellular transport.
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Affiliation(s)
- Fawaz Baig
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128, United States
| | - Michael Bakdaleyeh
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128, United States
| | - Hassan M. Bazzi
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128, United States
| | - Lanqin Cao
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128, United States
| | - Suvranta K. Tripathy
- Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128, United States
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4
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Benoit MPMH, Rao L, Asenjo AB, Gennerich A, Sosa H. Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Nat Commun 2024; 15:5530. [PMID: 38956021 PMCID: PMC11219953 DOI: 10.1038/s41467-024-48720-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Mutations in the microtubule-associated motor protein KIF1A lead to severe neurological conditions known as KIF1A-associated neurological disorders (KAND). Despite insights into its molecular mechanism, high-resolution structures of KIF1A-microtubule complexes remain undefined. Here, we present 2.7-3.5 Å resolution structures of dimeric microtubule-bound KIF1A, including the pathogenic P305L mutant, across various nucleotide states. Our structures reveal that KIF1A binds microtubules in one- and two-heads-bound configurations, with both heads exhibiting distinct conformations with tight inter-head connection. Notably, KIF1A's class-specific loop 12 (K-loop) forms electrostatic interactions with the C-terminal tails of both α- and β-tubulin. The P305L mutation does not disrupt these interactions but alters loop-12's conformation, impairing strong microtubule-binding. Structure-function analysis reveals the K-loop and head-head coordination as major determinants of KIF1A's superprocessive motility. Our findings advance the understanding of KIF1A's molecular mechanism and provide a basis for developing structure-guided therapeutics against KAND.
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Affiliation(s)
- Matthieu P M H Benoit
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Lu Rao
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ana B Asenjo
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Hernando Sosa
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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5
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Xie P. Effect of small molecular crowders on dynamics of kinesin molecular motors. J Theor Biol 2024; 578:111685. [PMID: 38061488 DOI: 10.1016/j.jtbi.2023.111685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 10/15/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
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.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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6
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Kita T, Sasaki K, Niwa S. Modeling the motion of disease-associated KIF1A heterodimers. Biophys J 2023; 122:4348-4359. [PMID: 37853694 PMCID: PMC10698283 DOI: 10.1016/j.bpj.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
KIF1A is a member of the kinesin-3 motor protein family that transports synaptic vesicle precursors in axons. Mutations in the Kif1a gene cause neuronal diseases. Most patients are heterozygous and have both mutated and intact KIF1A alleles, suggesting that heterodimers composed of wild-type KIF1A and mutant KIF1A are likely involved in pathogenesis. In this study, we propose mathematical models to describe the motility of KIF1A heterodimers composed of wild-type KIF1A and mutant KIF1A. Our models precisely describe run length, run time, and velocity of KIF1A heterodimers using a few parameters obtained from two homodimers. The first model is a simple hand-over-hand model in which stepping and detachment rates from a microtubule of each head are identical to those in the respective homodimers. Although the velocities of heterodimers expected from this model were in good agreement with the experimental results, this model underestimated the run lengths and run times of some heterodimeric motors. To address this discrepancy, we propose the tethered-head affinity model, in which we hypothesize a tethered head, in addition to a microtubule-binding head, contributes to microtubule binding in a vulnerable one-head-bound state. The run lengths and run times of the KIF1A heterodimers predicted by the tethered-head affinity model matched well with experimental results, suggesting a possibility that the tethered head affects the microtubule binding of KIF1A. Our models provide insights into how each head contributes to the processive movement of KIF1A and can be used to estimate motile parameters of KIF1A heterodimers.
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Affiliation(s)
- Tomoki Kita
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
| | - Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Shinsuke Niwa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, Miyagi, Japan.
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7
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Nguyen T, Narayanareddy BJ, Gross SP, Miles CE. ADP release can explain spatially-dependent kinesin binding times. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.563482. [PMID: 37986962 PMCID: PMC10659338 DOI: 10.1101/2023.11.08.563482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that most but not every motor binding event is limited by their ADP state. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and spatial distances.
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Affiliation(s)
- Trini Nguyen
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
| | | | - Steven P. Gross
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697
| | - Christopher E. Miles
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697
- Center for Multiscale Cell Fate, University of California, Irvine, Irvine, CA 92697
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8
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Chang C, Zheng T, Nettesheim G, Song H, Cho C, Crespi S, Shubeita G. On the use of thermal forces to probe kinesin's response to force. Front Mol Biosci 2023; 10:1260914. [PMID: 38028555 PMCID: PMC10644364 DOI: 10.3389/fmolb.2023.1260914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023] Open
Abstract
The stepping dynamics of cytoskeletal motor proteins determines the dynamics of cargo transport. In its native cellular environment, a molecular motor is subject to forces from several sources including thermal forces and forces ensuing from the interaction with other motors bound to the same cargo. Understanding how the individual motors respond to these forces can allow us to predict how they move their cargo when part of a team. Here, using simulation, we show that details of how the kinesin motor responds to small assisting forces-which, at the moment, are not experimentally constrained-can lead to significant changes in cargo dynamics. Using different models of the force-dependent detachment probability of the kinesin motor leads to different predictions on the run-length of the cargo they carry. These differences emerge from the thermal forces acting on the cargo and transmitted to the motor through the motor tail that tethers the motor head to the microtubule. We show that these differences appear for cargo carried by individual motors or motor teams, and use our findings to propose the use of thermal forces as a probe of kinesin's response to force in this otherwise inaccessible force regime.
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Affiliation(s)
- Chuan Chang
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tiantian Zheng
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Guilherme Nettesheim
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Hayoung Song
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Changhyun Cho
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuele Crespi
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Shubeita
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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9
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Kondo Y, Sasaki K, Higuchi H. Fast backward steps and detachment of single kinesin molecules measured under a wide range of loads. Traffic 2023; 24:463-474. [PMID: 37679870 DOI: 10.1111/tra.12909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 09/09/2023]
Abstract
To understand force generation under a wide range of loads, the stepping of single kinesin molecules was measured at loads from -20 to 42 pN by optical tweezers with high temporal resolution. The optical trap has been improved to halve positional noise and increase bandwidth by using 200-nm beads. The step size of the forward and backward steps was 8.2 nm even over a wide range of loads. Histograms of the dwell times of backward steps and detachment fit well to two independent exponential equations with fast (~0.4 ms) and slow (>3 ms) time constants, indicating the existence of a fast step in addition to the conventional slow step. The dwell times of the fast steps were almost independent of the load and ATP concentration, while those of the slow backward steps and detachment depended on those. We constructed the kinetic model to explain the fast and slow steps under a wide range of loads.
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Affiliation(s)
- Yuichi Kondo
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Hideo Higuchi
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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10
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Zhang C, Guo C, Russell RW, Quinn CM, Li M, Williams JC, Gronenborn AM, Polenova T. Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation. Nat Commun 2022; 13:6795. [PMID: 36357375 PMCID: PMC9649657 DOI: 10.1038/s41467-022-34026-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Chunting Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Mingyue Li
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
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11
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Microtubule Dumbbells to Assess the Effect of Force Geometry on Single Kinesin Motors. Methods Mol Biol 2022; 2478:559-583. [PMID: 36063334 PMCID: PMC9987583 DOI: 10.1007/978-1-0716-2229-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The cytoskeletal motors myosin, kinesin, and dynein and their corresponding tracks, actin and microtubules, are force generating ATPases responsible for motility and morphological changes at the intracellular, cellular, and tissue levels. The pioneering application of optical tweezers to measure the force-producing properties of cytoskeletal motors has provided an unparalleled understanding of their mechanochemistry. The mechanosensitivity of processive, microtubule-based motors has largely been studied in the optical trap using the "single-bead" assay, where a bead-attached motor is held adjacent to a cytoskeletal filament as it processively steps along it. However, because of the geometrical constraints in the conventional single-bead assay, the motor-filament bond is not only loaded parallel to the long axis of the filament, but also perpendicular to the long axis of the filament. This perpendicular force, which is inherent in the conventional single-bead assay, accelerates the motor-filament detachment and has not been carefully considered in prior experiments. An alternative approach is the "three-bead" assay, which was developed for the study of non-processive myosin motors. The vertical force component is minimized in this assay, and the total opposing force is mainly parallel to the microtubule. Experiments with kinesin show that microtubule attachment durations can be highly variable and last for up to tenfold longer times in the three-bead assay, compared to the single-bead assay. Thus, the ability of kinesin to bear mechanical load and remain attached to microtubules depends on the forces in more than one dimension. In this chapter, we provide detailed methods for preparing the proteins, buffers, flow chambers, and bead-filament assemblies for performing the three-bead assay with microtubules and their motors.
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12
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Xie P. Dynamics of kinesin motor proteins under longitudinal and sideways loads. J Theor Biol 2021; 530:110879. [PMID: 34437882 DOI: 10.1016/j.jtbi.2021.110879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/10/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China
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13
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Ariga T, Tateishi K, Tomishige M, Mizuno D. Noise-Induced Acceleration of Single Molecule Kinesin-1. PHYSICAL REVIEW LETTERS 2021; 127:178101. [PMID: 34739268 DOI: 10.1103/physrevlett.127.178101] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
The movement of single kinesin molecules was observed while applying noisy external forces that mimic intracellular active fluctuations. We found kinesin accelerates under noise, especially when a large hindering load is added. The behavior quantitatively conformed to a theoretical model that describes the kinesin movement with simple two-state reactions. The universality of the kinetic theory suggests that intracellular enzymes share a similar noise-induced acceleration mechanism, i.e., active fluctuations in cells are not just noise but are utilized to promote various physiological processes.
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Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, 755-8505 Yamaguchi, Japan
| | - Keito Tateishi
- Graduate School of Medicine, Yamaguchi University, 755-8505 Yamaguchi, Japan
| | - Michio Tomishige
- Department of Physical Sciences, Aoyama Gakuin University, 252-5258 Kanagawa, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, 819-0395 Fukuoka, Japan
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14
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Abstract
Kinesin-1 is a motor protein that can step processively on microtubule by hydrolyzing ATP molecules, playing an essential role in intracellular transports. To better understand the mechanochemical coupling of the motor stepping cycle, numerous structural, biochemical, single molecule, theoretical modeling and numerical simulation studies have been undertaken for the kinesin-1 motor. Recently, a novel ultraresolution optical trapping method was employed to study the mechanics of the kinesin-1 motor and new results were supplemented to its stepping dynamics. In this commentary, the new single molecule results are explained well theoretically with one of the models presented in the literature for the mechanochemical coupling of the kinesin-1 motor. With the model, various prior experimental results for dynamics of different families of N-terminal kinesin motors have also been explained quantitatively.
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15
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Hasnain S, Mugnai ML, Thirumalai D. Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin. J Phys Chem B 2021; 125:10432-10444. [PMID: 34499499 DOI: 10.1021/acs.jpcb.1c02218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A substantial increase in the temporal resolution of the stepping of dimeric molecular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was employed to measure the stepping trajectories of conventional kinesin (Kin1) using the time-dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head, and (2) the rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.
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Affiliation(s)
- Sabeeha Hasnain
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
| | - Mauro L Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin 78712, Texas, United States
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16
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Goldtzvik Y, Thirumalai D. Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. J Chem Theory Comput 2021; 17:5358-5368. [PMID: 34251798 DOI: 10.1021/acs.jctc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conventional kinesin, a motor protein that transports cargo within cells, walks by taking multiple steps toward the plus end of the microtubule (MT). While significant progress has been made in understanding the details of the walking mechanism of kinesin, there are many unresolved issues. From a computational perspective, a central challenge is the large size of the system, which limits the scope of time scales accessible in standard computer simulations. Here, we create a general multiscale coarse-grained model for motors that enables us to simulate the stepping process of motors on polar tracks (actin and MT) with a focus on kinesin. Our approach greatly shortens the computation times without a significant loss in detail, thus allowing us to better describe the molecular basis of the stepping kinetics. The small number of parameters, which are determined by fitting to experimental data, allows us to develop an accurate method that may be adopted to simulate stepping in other molecular motors. The model enables us to simulate a large number of steps, which was not possible previously. We show in agreement with experiments that due to the docking of the neck linker (NL) of kinesin, sometimes deemed as the power stroke, the space explored diffusively by the tethered head is severely restricted, allowing the step to be completed in tens of microseconds. We predict that increasing the interaction strength between the NL and the motor head, achievable by mutations in the NL, decreases the stepping time but reaches a saturation value. Furthermore, the full three-dimensional dynamics of the cargo are fully resolved in our model, contributing to the predictive power and allowing us to study the important aspects of cargo-motor interactions.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
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17
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Wilson JO, Zaragoza AD, Xu J. Tuning ensemble-averaged cargo run length via fractional change in mean kinesin number. Phys Biol 2021; 18. [PMID: 33827070 DOI: 10.1088/1478-3975/abf5b3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/07/2021] [Indexed: 11/12/2022]
Abstract
The number of motors carrying cargos in biological cells is not well-defined, instead varying from cargo to cargo about a statistical mean. Predictive understanding of motility in cells therefore requires quantitative insights into mixed ensembles of cargos. Toward this goal, here we employed Monte Carlo simulations to investigate statistical ensembles of cargos carried by a Poisson-distributed number of motors. Focusing on the key microtubule-based motor kinesin-1, our simulations utilized experimentally determined single-kinesin characteristics and alterations in kinesin's on- and off-rates caused by cellular factors and/or physical load. We found that a fractional increase in mean kinesin number enhances the ensemble-averaged cargo run length and amplifies run-length sensitivity to changes in single-kinesin on-rate and off-rate. These tuning effects can be further enhanced as solution viscosity increases over the range reported for cells. Together, our data indicate that the physiological range of kinesin number sensitively tunes the motility of mixed cargo populations. These effects have rich implications for quantitative and predictive understanding of cellular motility and its regulation.
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Affiliation(s)
- John O Wilson
- Physics, University of California, Merced, CA, United States of America
| | - Arturo D Zaragoza
- Mechanical Engineering, University of California, Merced, CA, United States of America
| | - Jing Xu
- Physics, University of California, Merced, CA, United States of America
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18
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Shinde A, Illath K, Gupta P, Shinde P, Lim KT, Nagai M, Santra TS. A Review of Single-Cell Adhesion Force Kinetics and Applications. Cells 2021; 10:577. [PMID: 33808043 PMCID: PMC8000588 DOI: 10.3390/cells10030577] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cells exert, sense, and respond to the different physical forces through diverse mechanisms and translating them into biochemical signals. The adhesion of cells is crucial in various developmental functions, such as to maintain tissue morphogenesis and homeostasis and activate critical signaling pathways regulating survival, migration, gene expression, and differentiation. More importantly, any mutations of adhesion receptors can lead to developmental disorders and diseases. Thus, it is essential to understand the regulation of cell adhesion during development and its contribution to various conditions with the help of quantitative methods. The techniques involved in offering different functionalities such as surface imaging to detect forces present at the cell-matrix and deliver quantitative parameters will help characterize the changes for various diseases. Here, we have briefly reviewed single-cell mechanical properties for mechanotransduction studies using standard and recently developed techniques. This is used to functionalize from the measurement of cellular deformability to the quantification of the interaction forces generated by a cell and exerted on its surroundings at single-cell with attachment and detachment events. The adhesive force measurement for single-cell microorganisms and single-molecules is emphasized as well. This focused review should be useful in laying out experiments which would bring the method to a broader range of research in the future.
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Affiliation(s)
- Ashwini Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Kavitha Illath
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Gupta
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Ki-Taek Lim
- Department of Biosystems Engineering, Kangwon National University, Chuncheon-Si, Gangwon-Do 24341, Korea;
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan;
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
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19
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Xu H, Hou R, Tong T, Li H. Diffusion Biased by a Soft Neck Linker Regulates Kinesin Stepping. J Phys Chem B 2021; 125:2627-2635. [PMID: 33667100 DOI: 10.1021/acs.jpcb.1c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conventional kinesin is a high-performance motor that moves primarily toward the plus end of microtubules and occasionally toward the opposite direction. The physical mechanism of this directional stepping remains unclear. Here we develop a kinetic two-cycle model incorporating kinesin forward and backward stepping, in which the neck linker zippering and ATP catalysis process are conserved in backward steps. This model is quantitatively validated by a variety of experimental data, including load dependence of velocity, stepping ratio, and dwell time. The physical mechanism of kinesin stepping regulated by a biased diffusion process is identified by analyzing the load dependence and relevant thermodynamic properties of the model. Furthermore, the model suggests the kinesin directionality is optimized resulting from fulfilling a thermodynamic constraint. Our modeling provides a chemomechanical coupling mechanism that connects the flexibility of the neck linker zippering effect for direction rectification and the measured performance into a consistent frame.
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Affiliation(s)
- Huijuan Xu
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Quantum Optics and Quantum Information, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ruizheng Hou
- Department of Applied Physics, School of Science, Xi'an University of Technology, Xi'an 710048, China
| | - Tong Tong
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Quantum Optics and Quantum Information, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hongrong Li
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Quantum Optics and Quantum Information, Xi'an Jiaotong University, Xi'an 710049, China
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20
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Zaniewski TM, Gicking AM, Fricks J, Hancock WO. A kinetic dissection of the fast and superprocessive kinesin-3 KIF1A reveals a predominant one-head-bound state during its chemomechanical cycle. J Biol Chem 2020; 295:17889-17903. [PMID: 33082143 PMCID: PMC7939386 DOI: 10.1074/jbc.ra120.014961] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The kinesin-3 family contains the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle and give rise to their unique properties are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to WT KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and -2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate-limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate-limiting transition in the KIF1A stepping cycle. Thus, KIF1A's activity can be explained by a fast rear-head detachment rate, a rate-limiting step of tethered-head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly bound post-hydrolysis state.
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Affiliation(s)
- Taylor M Zaniewski
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Allison M Gicking
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona, USA
| | - William O Hancock
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA.
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21
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Klobusicky JJ, Fricks J, Kramer PR. Effective behavior of cooperative and nonidentical molecular motors. RESEARCH IN THE MATHEMATICAL SCIENCES 2020; 7:29. [PMID: 33870090 PMCID: PMC8049358 DOI: 10.1007/s40687-020-00230-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/04/2020] [Indexed: 06/12/2023]
Abstract
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1 and kinesin-2) which can each attach and detach from a microtubule. The dynamics of the motor and cargo in each phase are governed by stochastic differential equations, and the switching rates depend on the spatial configuration of the motor and cargo. This system is analyzed in a limit where the detached motors have faster dynamics than the cargo, which in turn has faster dynamics than the attached motors. The attachment and detachment rates are also taken to be slow relative to the spatial dynamics. Through an application of iterated stochastic averaging to this system, and the use of renewal-reward theory to stitch together the progress within each switching phase, we obtain explicit analytical expressions for the effective drift, diffusivity, and processivity of the motor-cargo system. Our approach accounts in particular for jumps in motor-cargo position that occur during attachment and detachment events, as the cargo tracking variable makes a rapid adjustment due to the averaged fast scales. The asymptotic formulas are in generally good agreement with direct stochastic simulations of the detailed model based on experimental parameters for various pairings of kinesin-1 and kinesin-2 under assisting, hindering, or no load.
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Affiliation(s)
| | - John Fricks
- Arizona State University, School of Mathematical and Statistical Sciences, Tempe, AZ, USA
| | - Peter R Kramer
- Rensselaer Polytechnic Institute, Mathematical Science Department, Troy, NY, USA
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22
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Toleikis A, Carter NJ, Cross RA. Backstepping Mechanism of Kinesin-1. Biophys J 2020; 119:1984-1994. [PMID: 33091340 PMCID: PMC7732724 DOI: 10.1016/j.bpj.2020.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023] Open
Abstract
Kinesin-1 is an ATP-driven molecular motor that transports cellular cargo along microtubules. At low loads, kinesin-1 almost always steps forward, toward microtubule plus ends, but at higher loads, it can also step backward. Backsteps are usually 8 nm but can be larger. These larger backward events of 16 nm, 24 nm, or more are thought to be slips rather than steps because they are too fast to consist of multiple, tightly coupled 8-nm steps. Here, we propose that not only these larger backsteps, but all kinesin-1 backsteps, are slips. We show first that kinesin waits before forward steps for less time than before backsteps and detachments; second, we show that kinesin waits for the same amount of time before backsteps and detachments; and third, we show that by varying the microtubule type, we can change the ratio of backsteps to detachments without affecting forward stepping. Our findings indicate that backsteps and detachments originate from the same state and that this state arises later in the mechanochemical cycle than the state that gives rise to forward steps. To explain our data, we propose that, in each cycle of ATP turnover, forward kinesin steps can only occur before Pi release, whereas backslips and detachments can only occur after Pi release. In the scheme we propose, Pi release gates access to a weak binding K⋅ADP-K⋅ADP state that can slip back along the microtubule, re-engage, release ADP, and try again to take an ATP-driven forward step. We predict that this rescued detachment pathway is key to maintaining kinesin processivity under load.
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Affiliation(s)
- Algirdas Toleikis
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Nicholas J Carter
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom.
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23
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How Kinesin-1 Utilize the Energy of Nucleotide: The Conformational Changes and Mechanochemical Coupling in the Unidirectional Motion of Kinesin-1. Int J Mol Sci 2020; 21:ijms21186977. [PMID: 32972035 PMCID: PMC7555842 DOI: 10.3390/ijms21186977] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
Kinesin-1 is a typical motile molecular motor and the founding member of the kinesin family. The most significant feature in the unidirectional motion of kinesin-1 is its processivity. To realize the fast and processive movement on the microtubule lattice, kinesin-1 efficiently transforms the chemical energy of nucleotide binding and hydrolysis to the energy of mechanical movement. The chemical and mechanical cycle of kinesin-1 are coupled to avoid futile nucleotide hydrolysis. In this paper, the research on the mechanical pathway of energy transition and the regulating mechanism of the mechanochemical cycle of kinesin-1 is reviewed.
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24
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Khataee H, Mahamdeh M, Neufeld Z. Processivity of molecular motors under vectorial loads. Phys Rev E 2020; 102:022406. [PMID: 32942474 DOI: 10.1103/physreve.102.022406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 11/06/2022]
Abstract
Molecular motors are cellular machines that drive the spatial organization of the cells by transporting cargos along intracellular filaments. Although the mechanical properties of single molecular motors are relatively well characterized, it remains elusive how the geometry of a load imposed on a motor affects its processivity, i.e., the average distance that a motor moves per interaction with a filament. Here, we theoretically explore this question for a single-kinesin molecular motor by analyzing the load dependence of the stepping and detachment processes. We find that the processivity of the kinesin increases with lowering the load angle between the kinesin and the microtubule filament, due to the deceleration of the detachment rate. When the load angle is large, the processivity is predicted to enhance with accelerating the stepping rate through an optimal distribution of the load over the kinetic transition rates underlying a mechanical step of the motor. These results provide new insights into understanding of the design of potential synthetic biomolecular machines that can travel long distances with high velocities.
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Affiliation(s)
- Hamid Khataee
- School of Mathematics and Physics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammed Mahamdeh
- Harvard Medical School, Harvard University, Boston, Massachusetts 02115, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02129, USA
| | - Zoltan Neufeld
- School of Mathematics and Physics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
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25
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Rydzek S, Shein M, Bielytskyi P, Schütz AK. Observation of a Transient Reaction Intermediate Illuminates the Mechanochemical Cycle of the AAA-ATPase p97. J Am Chem Soc 2020; 142:14472-14480. [DOI: 10.1021/jacs.0c03180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Simon Rydzek
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Pavlo Bielytskyi
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Anne K. Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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26
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Hunter B, Allingham JS. These motors were made for walking. Protein Sci 2020; 29:1707-1723. [PMID: 32472639 DOI: 10.1002/pro.3895] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
Kinesins are a diverse group of adenosine triphosphate (ATP)-dependent motor proteins that transport cargos along microtubules (MTs) and change the organization of MT networks. Shared among all kinesins is a ~40 kDa motor domain that has evolved an impressive assortment of motility and MT remodeling mechanisms as a result of subtle tweaks and edits within its sequence. Several elegant studies of different kinesin isoforms have exposed the purpose of structural changes in the motor domain as it engages and leaves the MT. However, few studies have compared the sequences and MT contacts of these kinesins systematically. Along with clever strategies to trap kinesin-tubulin complexes for X-ray crystallography, new advancements in cryo-electron microscopy have produced a burst of high-resolution structures that show kinesin-MT interfaces more precisely than ever. This review considers the MT interactions of kinesin subfamilies that exhibit significant differences in speed, processivity, and MT remodeling activity. We show how their sequence variations relate to their tubulin footprint and, in turn, how this explains the molecular activities of previously characterized mutants. As more high-resolution structures become available, this type of assessment will quicken the pace toward establishing each kinesin's design-function relationship.
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Affiliation(s)
- Byron Hunter
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - John S Allingham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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27
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Ohashi KG, Han L, Mentley B, Wang J, Fricks J, Hancock WO. Load-dependent detachment kinetics plays a key role in bidirectional cargo transport by kinesin and dynein. Traffic 2020; 20:284-294. [PMID: 30809891 DOI: 10.1111/tra.12639] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Abstract
Bidirectional cargo transport along microtubules is carried out by opposing teams of kinesin and dynein motors. Despite considerable study, the factors that determine whether these competing teams achieve net anterograde or retrograde transport in cells remain unclear. The goal of this work is to use stochastic simulations of bidirectional transport to determine the motor properties that most strongly determine overall cargo velocity and directionality. Simulations were carried out based on published optical tweezer characterization of kinesin-1 and kinesin-2, and for available data for cytoplasmic dynein and the dynein-dynactin-BicD2 (DDB) complex. By varying dynein parameters and analyzing cargo trajectories, we find that net cargo transport is predicted to depend minimally on the dynein stall force, but strongly on dynein load-dependent detachment kinetics. In simulations, dynein is dominated by kinesin-1, but DDB and kinesin-1 are evenly matched, recapitulating recent experimental work. Kinesin-2 competes less well against dynein and DDB, and overall, load-dependent motor detachment is the property that most determines a motor's ability to compete in bidirectional transport. It follows that the most effective intracellular regulators of bidirectional transport are predicted to be those that alter motor detachment kinetics rather than motor velocity or stall force.
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Affiliation(s)
- Kazuka G Ohashi
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania
| | - Lifeng Han
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - Brandon Mentley
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania
| | - Jiaxuan Wang
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania
| | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - William O Hancock
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania
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28
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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29
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Peña A, Sweeney A, Cook AD, Locke J, Topf M, Moores CA. Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy. Structure 2020; 28:450-457.e5. [PMID: 32084356 PMCID: PMC7139217 DOI: 10.1016/j.str.2020.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/12/2019] [Accepted: 01/28/2020] [Indexed: 01/23/2023]
Abstract
Kinesin-5 motors are vital mitotic spindle components, and disruption of their function perturbs cell division. We investigated the molecular mechanism of the human kinesin-5 inhibitor GSK-1, which allosterically promotes tight microtubule binding. GSK-1 inhibits monomeric human kinesin-5 ATPase and microtubule gliding activities, and promotes the motor's microtubule stabilization activity. Using cryoelectron microscopy, we determined the 3D structure of the microtubule-bound motor-GSK-1 at 3.8 Å overall resolution. The structure reveals that GSK-1 stabilizes the microtubule binding surface of the motor in an ATP-like conformation, while destabilizing regions of the motor around the empty nucleotide binding pocket. Density corresponding to GSK-1 is located between helix-α4 and helix-α6 in the motor domain at its interface with the microtubule. Using a combination of difference mapping and protein-ligand docking, we characterized the kinesin-5-GSK-1 interaction and further validated this binding site using mutagenesis. This work opens up new avenues of investigation of kinesin inhibition and spindle perturbation.
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Affiliation(s)
- Alejandro Peña
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Aaron Sweeney
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Alexander D Cook
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Julia Locke
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK.
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30
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Xie P. Theoretical Analysis of Dynamics of Kinesin Molecular Motors. ACS OMEGA 2020; 5:5721-5730. [PMID: 32226850 PMCID: PMC7097908 DOI: 10.1021/acsomega.9b03738] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 05/07/2023]
Abstract
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.
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31
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Ariga T, Tomishige M, Mizuno D. Experimental and theoretical energetics of walking molecular motors under fluctuating environments. Biophys Rev 2020; 12:503-510. [PMID: 32173796 DOI: 10.1007/s12551-020-00684-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/02/2020] [Indexed: 01/10/2023] Open
Abstract
Molecular motors are nonequilibrium open systems that convert chemical energy to mechanical work. Their energetics are essential for various dynamic processes in cells, but largely remain unknown because fluctuations typically arising in small systems prevent investigation of the nonequilibrium behavior of the motors in terms of thermodynamics. Recently, Harada and Sasa proposed a novel equality to measure the dissipation of nonequilibrium small systems. By utilizing this equality, we have investigated the nonequilibrium energetics of the single-molecule walking motor kinesin-1. The dissipation from kinesin movement was measured through the motion of an attached probe particle and its response to external forces, indicating that large hidden dissipation exists. In this short review, aiming to readers who are not familiar with nonequilibrium physics, we briefly introduce the theoretical basis of the dissipation measurement as well as our recent experimental results and mathematical model analysis and discuss the physiological implications of the hidden dissipation in kinesin. In addition, further perspectives on the efficiency of motors are added by considering their actual working environment: living cells.
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Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, Ube, Japan.
| | - Michio Tomishige
- Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan
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32
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Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1. Sci Rep 2019; 9:16973. [PMID: 31740721 PMCID: PMC6861319 DOI: 10.1038/s41598-019-53550-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
Abstract
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.
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33
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Tjioe M, Shukla S, Vaidya R, Troitskaia A, Bookwalter CS, Trybus KM, Chemla YR, Selvin PR. Multiple kinesins induce tension for smooth cargo transport. eLife 2019; 8:50974. [PMID: 31670658 PMCID: PMC6904222 DOI: 10.7554/elife.50974] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
How cargoes move within a crowded cell—over long distances and at speeds nearly the same as when moving on unimpeded pathway—has long been mysterious. Through an in vitro force-gliding assay, which involves measuring nanometer displacement and piconewtons of force, we show that multiple mammalian kinesin-1 (from 2 to 8) communicate in a team by inducing tension (up to 4 pN) on the cargo. Kinesins adopt two distinct states, with one-third slowing down the microtubule and two-thirds speeding it up. Resisting kinesins tend to come off more rapidly than, and speed up when pulled by driving kinesins, implying an asymmetric tug-of-war. Furthermore, kinesins dynamically interact to overcome roadblocks, occasionally combining their forces. Consequently, multiple kinesins acting as a team may play a significant role in facilitating smooth cargo motion in a dense environment. This is one of few cases in which single molecule behavior can be connected to ensemble behavior of multiple motors. The inside of a cell is a crowded space, full of proteins and other molecules. Yet, the molecular motors that transport some of those molecules within the cell move at the same speed as they would in pure water – about one micrometer per second. How the molecular motors could achieve such speeds in crowded cells was unclear. Nevertheless, Tjioe et al. suspected that the answer might be related to how multiple motors work together. Molecular motors move by walking along filaments inside the cell and pulling their cargo from one location to another. Other molecules that bind to the filaments should, in theory, act like “roadblocks” and impede the movement of the cargo. Tjioe et al. studied a motor protein called kinesin, which walks on filaments called microtubules. But instead of looking at these motors moving along microtubules inside a cell, Tjioe et al. used a simpler system where the cell was eliminated, and all parts were purified. Specifically, Tjioe et al. tethered purified motors to a piece of glass and then observed them under an extremely accurate microscope as they moved free-floating, fluorescently labelled microtubules. The microtubules, in this scenario, were acting like cargoes, where many kinesins could bind. Each kinesin motor also had a small chemical tag that could emit light. By following the movement of the lights, it was possible to calculate what each kinesin was doing and how the cargo moved. When more than one kinesin molecule was acting, the tension and speed of one kinesin affected the movement of the others. In any group of kinesins, about two-thirds of kinesin pulled the cargo, and unexpectedly, about one-third tended to resist and slow the cargo. These latter kinesins were moved along with the group without actually driving the cargo. These resisting kinesins did come off more rapidly than the driving kinesins, meaning the cargo should be able to quickly bypass roadblocks. This would help to keep the whole group travelling in the right direction at a steady pace.
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Affiliation(s)
- Marco Tjioe
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Saurabh Shukla
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Rohit Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Alice Troitskaia
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Carol S Bookwalter
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Yann R Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
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34
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How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics. Proc Natl Acad Sci U S A 2019; 116:23091-23099. [PMID: 31659052 DOI: 10.1073/pnas.1913650116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Conventional kinesin, responsible for directional transport of cellular vesicles, takes multiple nearly uniform 8.2-nm steps by consuming one ATP molecule per step as it walks toward the plus end of the microtubule (MT). Despite decades of intensive experimental and theoretical studies, there are gaps in the elucidation of key steps in the catalytic cycle of kinesin. How the motor waits for ATP to bind to the leading head is controversial. Two experiments using a similar protocol have arrived at different conclusions. One asserts that kinesin waits for ATP in a state with both the heads bound to the MT, whereas the other shows that ATP binds to the leading head after the trailing head detaches. To discriminate between the 2 scenarios, we developed a minimal model, which analytically predicts the outcomes of a number of experimental observable quantities (the distribution of run length, the distribution of velocity [[Formula: see text]], and the randomness parameter) as a function of an external resistive force (F) and ATP concentration ([T]). The differences in the predicted bimodality in [Formula: see text] as a function of F between the 2 models may be amenable to experimental testing. Most importantly, we predict that the F and [T] dependence of the randomness parameters differ qualitatively depending on the waiting states. The randomness parameters as a function of F and [T] can be quantitatively measured from stepping trajectories with very little prejudice in data analysis. Therefore, an accurate measurement of the randomness parameter and the velocity distribution as a function of load and nucleotide concentration could resolve the apparent controversy.
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35
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Liu S, Majeed W, Grigaitis P, Betts MJ, Climer LK, Starkuviene V, Storrie B. Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization. Front Cell Dev Biol 2019; 7:126. [PMID: 31428608 PMCID: PMC6687757 DOI: 10.3389/fcell.2019.00126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
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.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Waqar Majeed
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Pranas Grigaitis
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Matthew J Betts
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Leslie K Climer
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Vytaute Starkuviene
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany.,Institute of Pharmacology and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.,Institute of Biosciences, Vilnius University Life Sciences Centre, Vilnius, Lithuania
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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36
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Li G, Tu ZC. Stochastic thermodynamics with odd controlling parameters. Phys Rev E 2019; 100:012127. [PMID: 31499855 DOI: 10.1103/physreve.100.012127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Indexed: 06/10/2023]
Abstract
Stochastic thermodynamics extends the notions and relations of classical thermodynamics to small systems that experience strong fluctuations. The definitions of work and heat and the microscopically reversible condition are two key concepts in the current framework of stochastic thermodynamics. Herein, we apply stochastic thermodynamics to small systems with odd controlling parameters and find that the definition of heat and the microscopically reversible condition are incompatible. Such a contradiction also leads to a revision to the fluctuation theorems and nonequilibrium work relations. By introducing adjoint dynamics, we find that the total entropy production can be separated into three parts, with two of them satisfying the integral fluctuation theorem. Revising the definitions of work and heat and the microscopically reversible condition allows us to derive two sets of modified nonequilibrium work relations, including the Jarzynski equality, the detailed Crooks work relation, and the integral Crooks work relation. We consider the strategy of shortcuts to isothermality as an example and give a more sophisticated explanation for the Jarzynski-like equality derived from shortcuts to isothermality.
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Affiliation(s)
- Geng Li
- Department of Physics, Beijing Normal University, Beijing 100875, China
- CAS Key Laboratory for Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Z C Tu
- Department of Physics, Beijing Normal University, Beijing 100875, China
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37
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Ilan Y. Randomness in microtubule dynamics: an error that requires correction or an inherent plasticity required for normal cellular function? Cell Biol Int 2019; 43:739-748. [DOI: 10.1002/cbin.11157] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/28/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Yaron Ilan
- Department of MedicineHadassah‐Hebrew University Medical CenterJerusalem IL91120 Israel
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38
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Chakraborty M, Tarasovetc EV, Zaytsev AV, Godzi M, Figueiredo AC, Ataullakhanov FI, Grishchuk EL. Microtubule end conversion mediated by motors and diffusing proteins with no intrinsic microtubule end-binding activity. Nat Commun 2019; 10:1673. [PMID: 30975984 PMCID: PMC6459870 DOI: 10.1038/s41467-019-09411-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/28/2019] [Indexed: 01/31/2023] Open
Abstract
Accurate chromosome segregation relies on microtubule end conversion, the ill-understood ability of kinetochores to transit from lateral microtubule attachment to durable association with dynamic microtubule plus-ends. The molecular requirements for this conversion and the underlying biophysical mechanisms are elusive. We reconstituted end conversion in vitro using two kinetochore components: the plus end-directed kinesin CENP-E and microtubule-binding Ndc80 complex, combined on the surface of a microbead. The primary role of CENP-E is to ensure close proximity between Ndc80 complexes and the microtubule plus-end, whereas Ndc80 complexes provide lasting microtubule association by diffusing on the microtubule wall near its tip. Together, these proteins mediate robust plus-end coupling during several rounds of microtubule dynamics, in the absence of any specialized tip-binding or regulatory proteins. Using a Brownian dynamics model, we show that end conversion is an emergent property of multimolecular ensembles of microtubule wall-binding proteins with finely tuned force-dependent motility characteristics.
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Affiliation(s)
- Manas Chakraborty
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, CV4 7AL, UK
| | - Ekaterina V Tarasovetc
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anatoly V Zaytsev
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maxim Godzi
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Ana C Figueiredo
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Fazly I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 119991, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia.
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39
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Cargo diffusion shortens single-kinesin runs at low viscous drag. Sci Rep 2019; 9:4104. [PMID: 30858425 PMCID: PMC6411862 DOI: 10.1038/s41598-019-40550-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/18/2019] [Indexed: 02/03/2023] Open
Abstract
Molecular motors such as kinesin-1 drive active, long-range transport of cargos along microtubules in cells. Thermal diffusion of the cargo can impose a randomly directed, fluctuating mechanical load on the motor carrying the cargo. Recent experiments highlighted a strong asymmetry in the sensitivity of single-kinesin run length to load direction, raising the intriguing possibility that cargo diffusion may non-trivially influence motor run length. To test this possibility, here we employed Monte Carlo-based simulations to evaluate the transport of cargo by a single kinesin. Our simulations included physiologically relevant viscous drag on the cargo and interrogated a large parameter space of cytoplasmic viscosities, cargo sizes, and motor velocities that captures their respective ranges in living cells. We found that cargo diffusion significantly shortens single-kinesin runs. This diffusion-based shortening is countered by viscous drag, leading to an unexpected, non-monotonic variation in run length as viscous drag increases. To our knowledge, this is the first identification of a significant effect of cargo diffusion on motor-based transport. Our study highlights the importance of cargo diffusion and load-detachment kinetics on single-motor functions under physiologically relevant conditions.
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40
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The structure of the catalytic domain of the ATP synthase from Mycobacterium smegmatis is a target for developing antitubercular drugs. Proc Natl Acad Sci U S A 2019; 116:4206-4211. [PMID: 30683723 DOI: 10.1073/pnas.1817615116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from Mycobacterium smegmatis which hydrolyzes ATP very poorly. The structure of the α3β3-component of the catalytic domain is similar to those in active F1-ATPases in Escherichia coli and Geobacillus stearothermophilus However, its ε-subunit differs from those in these two active bacterial F1-ATPases as an ATP molecule is not bound to the two α-helices forming its C-terminal domain, probably because they are shorter than those in active enzymes and they lack an amino acid that contributes to the ATP binding site in active enzymes. In E. coli and G. stearothermophilus, the α-helices adopt an "up" state where the α-helices enter the α3β3-domain and prevent the rotor from turning. The mycobacterial F1-ATPase is most similar to the F1-ATPase from Caldalkalibacillus thermarum, which also hydrolyzes ATP poorly. The βE-subunits in both enzymes are in the usual "open" conformation but appear to be occupied uniquely by the combination of an adenosine 5'-diphosphate molecule with no magnesium ion plus phosphate. This occupation is consistent with the finding that their rotors have been arrested at the same point in their rotary catalytic cycles. These bound hydrolytic products are probably the basis of the inhibition of ATP hydrolysis. It can be envisaged that specific as yet unidentified small molecules might bind to the F1 domain in Mycobacterium tuberculosis, prevent ATP synthesis, and inhibit the growth of the pathogen.
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41
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Malaby HL, Lessard DV, Berger CL, Stumpff J. KIF18A's neck linker permits navigation of microtubule-bound obstacles within the mitotic spindle. Life Sci Alliance 2019; 2:2/1/e201800169. [PMID: 30655363 PMCID: PMC6337737 DOI: 10.26508/lsa.201800169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 01/24/2023] Open
Abstract
KIF18A (kinesin-8) is required for mammalian mitotic chromosome alignment. KIF18A confines chromosome movement to the mitotic spindle equator by accumulating at the plus-ends of kinetochore microtubule bundles (K-fibers), where it functions to suppress K-fiber dynamics. It is not understood how the motor accumulates at K-fiber plus-ends, a difficult feat requiring the motor to navigate protein dense microtubule tracks. Our data indicate that KIF18A's relatively long neck linker is required for the motor's accumulation at K-fiber plus-ends. Shorter neck linker (sNL) variants of KIF18A display a deficiency in accumulation at the ends of K-fibers at the center of the spindle. Depletion of K-fiber-binding proteins reduces the KIF18A sNL localization defect, whereas their overexpression reduces wild-type KIF18A's ability to accumulate on this same K-fiber subset. Furthermore, single-molecule assays indicate that KIF18A sNL motors are less proficient in navigating microtubules coated with microtubule-associated proteins. Taken together, these results support a model in which KIF18A's neck linker length permits efficient navigation of obstacles to reach K-fiber ends during mitosis.
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Affiliation(s)
- Heidi Lh Malaby
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Dominique V Lessard
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Christopher L Berger
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
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42
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Force Dependence of Velocity and Run Length of Kinesin-1, Kinesin-2 and Kinesin-5 Family Molecular Motors. Molecules 2019; 24:molecules24020287. [PMID: 30646587 PMCID: PMC6358798 DOI: 10.3390/molecules24020287] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 11/17/2022] Open
Abstract
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.
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43
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Fujimoto K, Morita Y, Iino R, Tomishige M, Shintaku H, Kotera H, Yokokawa R. Simultaneous Observation of Kinesin-Driven Microtubule Motility and Binding of Adenosine Triphosphate Using Linear Zero-Mode Waveguides. ACS NANO 2018; 12:11975-11985. [PMID: 30418736 DOI: 10.1021/acsnano.8b03803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single-molecule fluorescence observation of adenosine triphosphate (ATP) is a powerful tool to elucidate the chemomechanical coupling of ATP with a motor protein. However, in total internal reflection fluorescence microscopy (TIRFM), available ATP concentration is much lower than that in the in vivo environment. To achieve single-molecule observation with a high signal-to-noise ratio, zero-mode waveguides (ZMWs) are utilized even at high fluorescent molecule concentrations in the micromolar range. Despite the advantages of ZMWs, the use of cytoskeletal filaments for single-molecule observation has not been reported because of difficulties in immobilization of cytoskeletal filaments in the cylindrical aperture of ZMWs. Here, we propose linear ZMWs (LZMWs) to visualize enzymatic reactions on cytoskeletal filaments, specifically kinesin-driven microtubule motility accompanied by ATP binding/unbinding. Finite element method simulation revealed excitation light confinement in a 100 nm wide slit of LZMWs. Single-molecule observation was then demonstrated with up to 1 μM labeled ATP, which was 10-fold higher than that available in TIRFM. Direct observation of binding/unbinding of ATP to kinesins that propel microtubules enabled us to find that a significant fraction of ATP molecules bound to kinesins were dissociated without hydrolysis. This highlights the advantages of LZMWs for single-molecule observation of proteins that interact with cytoskeletal filaments such as microtubules, actin filaments, or intermediate filaments.
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Affiliation(s)
- Kazuya Fujimoto
- Department of Micro Engineering , Kyoto University , Kyoto 615-8540 , Japan
| | - Yuki Morita
- Department of Micro Engineering , Kyoto University , Kyoto 615-8540 , Japan
| | - Ryota Iino
- Institute for Molecular Science , National Institutes of Natural Sciences , Okazaki , Aichi 444-8787 , Japan
| | - Michio Tomishige
- College of Science and Engineering , Aoyama Gakuin University , Kanagawa 252-5258 , Japan
| | - Hirofumi Shintaku
- Department of Micro Engineering , Kyoto University , Kyoto 615-8540 , Japan
| | - Hidetoshi Kotera
- Department of Micro Engineering , Kyoto University , Kyoto 615-8540 , Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering , Kyoto University , Kyoto 615-8540 , Japan
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44
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Ariga T, Tomishige M, Mizuno D. Nonequilibrium Energetics of Molecular Motor Kinesin. PHYSICAL REVIEW LETTERS 2018; 121:218101. [PMID: 30517811 DOI: 10.1103/physrevlett.121.218101] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/18/2018] [Indexed: 06/09/2023]
Abstract
Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum of the dissipation and work did not amount to the input free energy change, indicating large hidden dissipation exists. Possible sources of the hidden dissipation were explored by analyzing the Langevin dynamics of the probe, which incorporates the two-state Markov stepper as a kinesin model. We conclude that internal dissipation is dominant.
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Affiliation(s)
- Takayuki Ariga
- Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| | - Michio Tomishige
- Department of Physics and Mathematics, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
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45
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Sasaki K, Kaya M, Higuchi H. A Unified Walking Model for Dimeric Motor Proteins. Biophys J 2018; 115:1981-1992. [PMID: 30396511 DOI: 10.1016/j.bpj.2018.09.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 01/17/2023] Open
Abstract
Dimeric motor proteins, kinesin-1, cytoplasmic dynein-1, and myosin-V, move stepwise along microtubules and actin filaments with a regular step size. The motors take backward as well as forward steps. The step ratio r and dwell time τ, which are the ratio of the number of backward steps to the number of forward steps and the time between consecutive steps, respectively, were observed to change with the load. To understand the movement of motor proteins, we constructed a unified and simple mathematical model to explain the load dependencies of r and of τ measured for the above three types of motors quantitatively. Our model consists of three states, and the forward and backward steps are represented by the cycles of transitions visiting different pairs of states among the three, implying that a backward step is not the reversal of a forward step. Each of r and τ is given by a simple expression containing two exponential functions. The experimental data for r and τ for dynein available in the literature are not sufficient for a quantitative analysis, which is in contrast to those for kinesin and myosin-V. We reanalyze the data to obtain r and τ of native dynein to make up the insufficient data to fit them to the model. Our model successfully describes the behavior of r and τ for all of the motors in a wide range of loads from large assisting loads to superstall loads.
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Affiliation(s)
- Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan.
| | - Motoshi Kaya
- Department of Physics, University of Tokyo, Hongo Bunkyo-ku, Tokyo, Japan
| | - Hideo Higuchi
- Department of Physics, University of Tokyo, Hongo Bunkyo-ku, Tokyo, Japan; Universal Biology Institute, Graduate School of Science, University of Tokyo, Hongo Bunkyo-ku, Tokyo, Japan.
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Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor-microtubule interaction strength. Proc Natl Acad Sci U S A 2018; 115:E7950-E7959. [PMID: 30093386 DOI: 10.1073/pnas.1801820115] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinesin-8 motors, which move in a highly processive manner toward microtubule plus ends where they act as depolymerases, are essential regulators of microtubule dynamics in cells. To understand their navigation strategy on the microtubule lattice, we studied the 3D motion of single yeast kinesin-8 motors, Kip3, on freely suspended microtubules in vitro. We observed short-pitch, left-handed helical trajectories indicating that kinesin-8 motors frequently switch protofilaments in a directionally biased manner. Intriguingly, sidestepping was not directly coupled to forward stepping but rather depended on the average dwell time per forward step under limiting ATP concentrations. Based on our experimental findings and numerical simulations we propose that effective sidestepping toward the left is regulated by a bifurcation in the Kip3 step cycle, involving a transition from a two-head-bound to a one-head-bound conformation in the ATP-waiting state. Results from a kinesin-1 mutant with extended neck linker hint toward a generic sidestepping mechanism for processive kinesins, facilitating the circumvention of intracellular obstacles on the microtubule surface.
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Rank M, Frey E. Crowding and Pausing Strongly Affect Dynamics of Kinesin-1 Motors along Microtubules. Biophys J 2018; 115:1068-1081. [PMID: 30146266 PMCID: PMC6139881 DOI: 10.1016/j.bpj.2018.07.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/27/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular motors of the kinesin-1 family move in a directed and processive fashion along microtubules. It is generally accepted that steric hindrance of motors leads to crowding effects; however, little is known about the specific interactions involved. We employ an agent-based lattice gas model to study the impact of interactions that enhance the detachment of motors from crowded filaments on their collective dynamics. The predictions of our model quantitatively agree with the experimentally observed concentration dependence of key motor characteristics including their run length, dwell time, velocity, and landing rate. From the anomalous stepping statistics of individual motors that exhibit relatively long pauses, we infer that kinesin-1 motors sometimes lapse into an inactive state. Hereby, the formation of traffic jams amplifies the impact of single inactive motors and leads to a crowding dependence of the frequencies and durations of the resulting periods of no or slow motion. We interpret these findings and conclude that kinesin-1 spends a significant fraction of its stepping cycle in a weakly bound state in which only one of its heads is bound to the microtubule.
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Affiliation(s)
- Matthias Rank
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, München, Germany.
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48
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Gardini L, Heissler SM, Arbore C, Yang Y, Sellers JR, Pavone FS, Capitanio M. Dissecting myosin-5B mechanosensitivity and calcium regulation at the single molecule level. Nat Commun 2018; 9:2844. [PMID: 30030431 PMCID: PMC6054644 DOI: 10.1038/s41467-018-05251-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/22/2018] [Indexed: 11/08/2022] Open
Abstract
Myosin-5B is one of three members of the myosin-5 family of actin-based molecular motors. Despite its fundamental role in recycling endosome trafficking and in collective actin network dynamics, the molecular mechanisms underlying its motility are inherently unknown. Here we combine single-molecule imaging and high-speed laser tweezers to dissect the mechanoenzymatic properties of myosin-5B. We show that a single myosin-5B moves processively in 36-nm steps, stalls at ~2 pN resistive forces, and reverses its directionality at forces >2 pN. Interestingly, myosin-5B mechanosensitivity differs from that of myosin-5A, while it is strikingly similar to kinesin-1. In particular, myosin-5B run length is markedly and asymmetrically sensitive to force, a property that might be central to motor ensemble coordination. Furthermore, we show that Ca2+ does not affect the enzymatic activity of the motor unit, but abolishes myosin-5B processivity through calmodulin dissociation, providing important insights into the regulation of postsynaptic cargoes trafficking in neuronal cells.
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Affiliation(s)
- Lucia Gardini
- LENS-European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
- National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy
| | - Sarah M Heissler
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-8015, USA
| | - Claudia Arbore
- LENS-European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Yi Yang
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-8015, USA
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - James R Sellers
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-8015, USA
| | - Francesco S Pavone
- LENS-European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
- National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS-European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy.
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49
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Guo SK, Shi XX, Wang PY, Xie P. Processivity of dimeric kinesin-1 molecular motors. FEBS Open Bio 2018; 8:1332-1351. [PMID: 30087836 PMCID: PMC6070657 DOI: 10.1002/2211-5463.12486] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
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.
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Affiliation(s)
- Si-Kao Guo
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Xiao-Xuan Shi
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
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McHugh T, Drechsler H, McAinsh AD, Carter NJ, Cross RA. Kif15 functions as an active mechanical ratchet. Mol Biol Cell 2018; 29:1743-1752. [PMID: 29771628 PMCID: PMC6080711 DOI: 10.1091/mbc.e18-03-0151] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Kif15 is a kinesin-12 that contributes critically to bipolar spindle assembly in humans. Here we use force-ramp experiments in an optical trap to probe the mechanics of single Kif15 molecules under hindering or assisting loads and in a variety of nucleotide states. While unloaded Kif15 is established to be highly processive, we find that under hindering loads, Kif15 takes <∼10 steps. As hindering load is increased, Kif15 forestep:backstep ratio decreases exponentially, with stall occurring at 6 pN. In contrast, under assisting loads, Kif15 detaches readily and rapidly, even from its AMPPNP state. Kif15 mechanics thus depend markedly on the loading direction. Kif15 interacts with a binding partner, Tpx2, and we show that Tpx2 locks Kif15 to microtubules under both hindering and assisting loads. Overall, our data predict that Kif15 in the central spindle will act as a mechanical ratchet, supporting spindle extension but resisting spindle compression.
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Affiliation(s)
- Toni McHugh
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Hauke Drechsler
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Andrew D McAinsh
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Nicolas J Carter
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
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