1
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Sumiyoshi R, Yamagishi M, Furuta A, Nishizaka T, Furuta K, Cross RA, Yajima J. Tether-scanning the kinesin motor domain reveals a core mechanical action. Proc Natl Acad Sci U S A 2024; 121:e2403739121. [PMID: 39012822 PMCID: PMC11287258 DOI: 10.1073/pnas.2403739121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Natural kinesin motors are tethered to their cargoes via short C-terminal or N-terminal linkers, whose docking against the core motor domain generates directional force. It remains unclear whether linker docking is the only process contributing directional force or whether linker docking is coupled to and amplifies an underlying, more fundamental force-generating mechanical cycle of the kinesin motor domain. Here, we show that kinesin motor domains tethered via double-stranded DNAs (dsDNAs) attached to surface loops drive robust microtubule (MT) gliding. Tethering using dsDNA attached to surface loops disconnects the C-terminal neck-linker and the N-terminal cover strand so that their dock-undock cycle cannot exert force. The most effective attachment positions for the dsDNA tether are loop 2 or loop 10, which lie closest to the MT plus and minus ends, respectively. In three cases, we observed minus-end-directed motility. Our findings demonstrate an underlying, potentially ancient, force-generating core mechanical action of the kinesin motor domain, which drives, and is amplified by, linker docking.
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Affiliation(s)
- Rieko Sumiyoshi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
| | - Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
| | - Akane Furuta
- Kobe Frontier Research Center, National Institute of Information and Communications Technology, Kobe, Hyogo651-2492, Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, Toshima-ku, Tokyo171-8588, Japan
| | - Ken’ya Furuta
- Kobe Frontier Research Center, National Institute of Information and Communications Technology, Kobe, Hyogo651-2492, Japan
| | - Robert A. Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, CoventryCV4 7AL, United Kingdom
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo153-8902, Japan
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2
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Gicking AM, Ma TC, Feng Q, Jiang R, Badieyan S, Cianfrocco MA, Hancock WO. Kinesin-1, -2, and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport. eLife 2022; 11:e82228. [PMID: 36125250 PMCID: PMC9545524 DOI: 10.7554/elife.82228] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022] Open
Abstract
Bidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2, and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2, and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells.
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Affiliation(s)
- Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State UniversityUniversity ParkUnited States
| | - Tzu-Chen Ma
- Department of Biomedical Engineering, Pennsylvania State UniversityUniversity ParkUnited States
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State UniversityUniversity ParkUnited States
| | - Rui Jiang
- Department of Biomedical Engineering, Pennsylvania State UniversityUniversity ParkUnited States
| | - Somayesadat Badieyan
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Michael A Cianfrocco
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State UniversityUniversity ParkUnited States
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3
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Kinesin-14 motors participate in a force balance at microtubule plus-ends to regulate dynamic instability. Proc Natl Acad Sci U S A 2022; 119:2108046119. [PMID: 35173049 PMCID: PMC8872730 DOI: 10.1073/pnas.2108046119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2022] [Indexed: 01/08/2023] Open
Abstract
Kinesin-14 motors represent an essential class of molecular motors that bind to microtubules and then walk toward the microtubule minus-end. However, whether these motors can interact with growing plus-ends of microtubules to impact the lengthening of microtubules remains unknown. We found that Kinesin-14 motors could bind to a protein that resides at growing microtubule plus-ends and then pull this protein away from the growing end. This interaction acted to disrupt microtubule growth and decrease microtubule lengths in cells, likely by exerting minus-end–directed forces at the microtubule tip to alter the configuration of the growing microtubule plus-end. This work demonstrates general principles for the diverse roles that force-generating molecular motors can play in regulating cellular processes. Kinesin-14 molecular motors represent an essential class of proteins that bind microtubules and walk toward their minus-ends. Previous studies have described important roles for Kinesin-14 motors at microtubule minus-ends, but their role in regulating plus-end dynamics remains controversial. Kinesin-14 motors have been shown to bind the EB family of microtubule plus-end binding proteins, suggesting that these minus-end–directed motors could interact with growing microtubule plus-ends. In this work, we explored the role of minus-end–directed Kinesin-14 motor forces in controlling plus-end microtubule dynamics. In cells, a Kinesin-14 mutant with reduced affinity to EB proteins led to increased microtubule lengths. Cell-free biophysical microscopy assays were performed using Kinesin-14 motors and an EB family marker of growing microtubule plus-ends, Mal3, which revealed that when Kinesin-14 motors bound to Mal3 at growing microtubule plus-ends, the motors subsequently walked toward the minus-end, and Mal3 was pulled away from the growing microtubule tip. Strikingly, these interactions resulted in an approximately twofold decrease in the expected postinteraction microtubule lifetime. Furthermore, generic minus-end–directed tension forces, generated by tethering growing plus-ends to the coverslip using λ-DNA, led to an approximately sevenfold decrease in the expected postinteraction microtubule growth length. In contrast, the inhibition of Kinesin-14 minus-end–directed motility led to extended tip interactions and to an increase in the expected postinteraction microtubule lifetime, indicating that plus-ends were stabilized by nonmotile Kinesin-14 motors. Together, we find that Kinesin-14 motors participate in a force balance at microtubule plus-ends to regulate microtubule lengths in cells.
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4
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Goldstein-Levitin A, Pandey H, Allhuzaeel K, Kass I, Gheber L. Intracellular functions and motile properties of bi-directional kinesin-5 Cin8 are regulated by neck linker docking. eLife 2021; 10:71036. [PMID: 34387192 PMCID: PMC8456603 DOI: 10.7554/elife.71036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/13/2021] [Indexed: 12/03/2022] Open
Abstract
In this study, we analyzed intracellular functions and motile properties of neck-linker (NL) variants of the bi-directional S. cerevisiae kinesin-5 motor, Cin8. We also examined – by modeling – the configuration of H-bonds during NL docking. Decreasing the number of stabilizing H-bonds resulted in partially functional variants, as long as a conserved backbone H-bond at the N-latch position (proposed to stabilize the docked conformation of the NL) remained intact. Elimination of this conserved H-bond resulted in production of a non-functional Cin8 variant. Surprisingly, additional H-bond stabilization of the N-latch position, generated by replacement of the NL of Cin8 by sequences of the plus-end directed kinesin-5 Eg5, also produced a nonfunctional variant. In that variant, a single replacement of N-latch asparagine with glycine, as present in Cin8, eliminated the additional H-bond stabilization and rescued the functional defects. We conclude that exact N-latch stabilization during NL docking is critical for the function of bi-directional kinesin-5 Cin8.
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Affiliation(s)
| | - Himanshu Pandey
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Kanary Allhuzaeel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itamar Kass
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,InterX LTD, Ramat-Gan, Israel
| | - Larisa Gheber
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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5
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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: 0.7] [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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6
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Banerjee S, Chakraborty S, Sreepada A, Banerji D, Goyal S, Khurana Y, Haldar S. Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry. Annu Rev Biophys 2021; 50:419-445. [PMID: 33646813 DOI: 10.1146/annurev-biophys-090420-083836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
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Affiliation(s)
- Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Abhijit Sreepada
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Devshuvam Banerji
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shashwat Goyal
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Yajushi Khurana
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
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7
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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: 11] [Impact Index Per Article: 2.8] [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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8
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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: 11] [Impact Index Per Article: 2.8] [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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9
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The mechanochemistry of the kinesin-2 KIF3AC heterodimer is related to strain-dependent kinetic properties of KIF3A and KIF3C. Proc Natl Acad Sci U S A 2020; 117:15632-15641. [PMID: 32571914 DOI: 10.1073/pnas.1916343117] [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] [Indexed: 01/29/2023] Open
Abstract
KIF3AC is a mammalian neuron-specific kinesin-2 implicated in intracellular cargo transport. It is a heterodimer of KIF3A and KIF3C motor polypeptides which have distinct biochemical and motile properties as engineered homodimers. Single-molecule motility assays show that KIF3AC moves processively along microtubules at a rate faster than expected given the motility rates of the KIF3AA and much slower KIF3CC homodimers. To resolve the stepping kinetics of KIF3A and KIF3C motors in homo- and heterodimeric constructs and determine their transport potential under load, we assayed motor activity using interferometric scattering microscopy and optical trapping. The distribution of stepping durations of KIF3AC molecules is described by a rate (k 1 = 11 s-1) without apparent kinetic asymmetry. Asymmetry was also not apparent under hindering or assisting mechanical loads in the optical trap. KIF3AC shows increased force sensitivity relative to KIF3AA yet is more capable of stepping against mechanical load than KIF3CC. Interestingly, the behavior of KIF3C mirrors prior studies of kinesins with increased interhead compliance. Microtubule gliding assays containing 1:1 mixtures of KIF3AA and KIF3CC result in speeds similar to KIF3AC, suggesting the homodimers mechanically impact each other's motility to reproduce the behavior of the heterodimer. Our observations are consistent with a mechanism in which the stepping of KIF3C can be activated by KIF3A in a strain-dependent manner, similar to application of an assisting load. These results suggest that the mechanochemical properties of KIF3AC can be explained by the strain-dependent kinetics of KIF3A and KIF3C.
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10
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Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH. Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. Chem Rev 2019; 119:6788-6821. [DOI: 10.1021/acs.chemrev.8b00760] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Pavel I. Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - George H. Lorimer
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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11
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Goldtzvik Y, Mugnai ML, Thirumalai D. Dynamics of Allosteric Transitions in Dynein. Structure 2018; 26:1664-1677.e5. [PMID: 30270176 DOI: 10.1016/j.str.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/19/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
Cytoplasmic dynein, whose motor domain belongs to the AAA+ family, walks on microtubules toward the minus end. Using the available structures in different nucleotide states, we performed simulations of a coarse-grained model to elucidate the dynamics of allosteric transitions. Binding of ATP closes the cleft between the AAA1 and AAA2 domains, triggering conformational changes in the rest of the motor domain, thus forming the pre-power stroke state. Interactions with the microtubule, modeled implicitly, enhance ADP release rate, and the formation of the post-power stroke state. The dynamics of the linker (LN), which reversibly changes from a straight to a bent state, is heterogeneous. Persistent interactions between the LN and the insert loops in the AAA2 domain prevent the formation of pre-power stroke state when ATP is bound to AAA3, thus locking dynein in a repressed non-functional state. Application of mechanical force to the LN restores motility in the repressed state.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | | | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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12
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Gilbert SP, Guzik-Lendrum S, Rayment I. Kinesin-2 motors: Kinetics and biophysics. J Biol Chem 2018; 293:4510-4518. [PMID: 29444824 DOI: 10.1074/jbc.r117.001324] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Kinesin-2s are major transporters of cellular cargoes. This subfamily contains both homodimeric kinesins whose catalytic domains result from the same gene product and heterodimeric kinesins with motor domains derived from two different gene products. In this Minireview, we focus on the progress to define the biochemical and biophysical properties of the kinesin-2 family members. Our understanding of their mechanochemical capabilities has been advanced by the ability to identify the kinesin-2 genes in multiple species, expression and purification of these motors for single-molecule and ensemble assays, and development of new technologies enabling quantitative measurements of kinesin activity with greater sensitivity.
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Affiliation(s)
- Susan P Gilbert
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Stephanie Guzik-Lendrum
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Ivan Rayment
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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13
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Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin. Proc Natl Acad Sci U S A 2017; 114:E9838-E9845. [PMID: 29087307 DOI: 10.1073/pnas.1706014114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Kinesin walks processively on microtubules (MTs) in an asymmetric hand-over-hand manner consuming one ATP molecule per 16-nm step. The individual contributions due to docking of the approximately 13-residue neck linker to the leading head (deemed to be the power stroke) and diffusion of the trailing head (TH) that contributes in propelling the motor by 16 nm have not been quantified. We use molecular simulations by creating a coarse-grained model of the MT-kinesin complex, which reproduces the measured stall force as well as the force required to dislodge the motor head from the MT, to show that nearly three-quarters of the step occurs by bidirectional stochastic motion of the TH. However, docking of the neck linker to the leading head constrains the extent of diffusion and minimizes the probability that kinesin takes side steps, implying that both the events are necessary in the motility of kinesin and for the maintenance of processivity. Surprisingly, we find that during a single step, the TH stochastically hops multiple times between the geometrically accessible neighboring sites on the MT before forming a stable interaction with the target binding site with correct orientation between the motor head and the [Formula: see text] tubulin dimer.
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14
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Liu D, Liu X, Shang Z, Sindelar CV. Structural basis of cooperativity in kinesin revealed by 3D reconstruction of a two-head-bound state on microtubules. eLife 2017; 6. [PMID: 28504639 PMCID: PMC5459574 DOI: 10.7554/elife.24490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/09/2017] [Indexed: 12/26/2022] Open
Abstract
The detailed basis of walking by dimeric molecules of kinesin along microtubules has remained unclear, partly because available structural methods have been unable to capture microtubule-bound intermediates of this process. Utilizing novel electron cryomicroscopy methods, we solved structures of microtubule-attached, dimeric kinesin bound to an ATP analog. We find that under these conditions, the kinesin dimer can attach to the microtubule with either one or two motor domains, and we present sub-nanometer resolution reconstructions of both states. The former structure reveals a novel kinesin conformation that revises the current understanding of how ATP binding is coupled to forward stepping of the motor. The latter structure indicates how tension between the two motor domains keeps their cycles out of phase in order to stimulate directional motility. The methods presented here pave the way for future structural studies of a variety of challenging macromolecules that bind to microtubules and other filaments.
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Affiliation(s)
- Daifei Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Xueqi Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Zhiguo Shang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
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15
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Guan R, Zhang L, Su QP, Mickolajczyk KJ, Chen GY, Hancock WO, Sun Y, Zhao Y, Chen Z. Crystal structure of Zen4 in the apo state reveals a missing conformation of kinesin. Nat Commun 2017; 8:14951. [PMID: 28393873 PMCID: PMC5394238 DOI: 10.1038/ncomms14951] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 02/15/2017] [Indexed: 12/25/2022] Open
Abstract
Kinesins hydrolyse ATP to transport intracellular cargoes along microtubules. Kinesin neck linker (NL) functions as the central mechano-chemical coupling element by changing its conformation through the ATPase cycle. Here we report the crystal structure of kinesin-6 Zen4 in a nucleotide-free, apo state, with the NL initial segment (NIS) adopting a backward-docked conformation and the preceding α6 helix partially melted. Single-molecule fluorescence resonance energy transfer (smFRET) analyses indicate the NIS of kinesin-1 undergoes similar conformational changes under tension in the two-head bound (2HB) state, whereas it is largely disordered without tension. The backward-docked structure of NIS is essential for motility of the motor. Our findings reveal a key missing conformation of kinesins, which provides the structural basis of the stable 2HB state and offers a tension-based rationale for an optimal NL length to ensure processivity of the motor.
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Affiliation(s)
- Ruifang Guan
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Science, Tsinghua University, Beijing 100084, China
| | - Lei Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing 100101, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Keith J Mickolajczyk
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Geng-Yuan Chen
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yongfang Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing 100101, China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Science, Tsinghua University, Beijing 100084, China
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16
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Hancock WO. The Kinesin-1 Chemomechanical Cycle: Stepping Toward a Consensus. Biophys J 2016; 110:1216-25. [PMID: 27028632 DOI: 10.1016/j.bpj.2016.02.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/23/2016] [Accepted: 02/03/2016] [Indexed: 10/22/2022] Open
Abstract
Kinesin-1 serves as a model for understanding fundamentals of motor protein mechanochemistry and for interpreting functional diversity across the kinesin superfamily. Despite sustained work over the last three decades, disagreements remain regarding the events that trigger the two key transitions in the stepping cycle: detachment of the trailing head from the microtubule and binding of the tethered head to the next tubulin binding site. This review describes the conflicting views of these events and highlights recent work that sheds light on these long-standing controversies. It concludes by presenting a consensus kinesin-1 chemomechanical that incorporates recent work, resolves discrepancies, and highlights key questions for future experimental work. It is hoped that this model provides a framework for understanding how diverse kinesins are tuned for their specific cellular roles.
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Affiliation(s)
- William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania.
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17
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Chen GY, Mickolajczyk KJ, Hancock WO. The Kinesin-5 Chemomechanical Cycle Is Dominated by a Two-heads-bound State. J Biol Chem 2016; 291:20283-20294. [PMID: 27402829 DOI: 10.1074/jbc.m116.730697] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/29/2022] Open
Abstract
Single-molecule microscopy and stopped-flow kinetics assays were carried out to understand the microtubule polymerase activity of kinesin-5 (Eg5). Four lines of evidence argue that the motor primarily resides in a two-heads-bound (2HB) state. First, upon microtubule binding, dimeric Eg5 releases both bound ADPs. Second, microtubule dissociation in saturating ADP is 20-fold slower for the dimer than for the monomer. Third, ATP-triggered mant-ADP release is 5-fold faster than the stepping rate. Fourth, ATP binding is relatively fast when the motor is locked in a 2HB state. Shortening the neck-linker does not facilitate rear-head detachment, suggesting a minimal role for rear-head-gating. This 2HB state may enable Eg5 to stabilize incoming tubulin at the growing microtubule plus-end. The finding that slowly hydrolyzable ATP analogs trigger slower nucleotide release than ATP suggests that ATP hydrolysis in the bound head precedes stepping by the tethered head, leading to a mechanochemical cycle in which processivity is determined by the race between unbinding of the bound head and attachment of the tethered head.
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Affiliation(s)
- Geng-Yuan Chen
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Keith J Mickolajczyk
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - William O Hancock
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
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18
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Direct observation of intermediate states during the stepping motion of kinesin-1. Nat Chem Biol 2016; 12:290-7. [PMID: 26928936 DOI: 10.1038/nchembio.2028] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/06/2016] [Indexed: 11/08/2022]
Abstract
The dimeric motor protein kinesin-1 walks along microtubules by alternatingly hydrolyzing ATP and moving two motor domains ('heads'). Nanometer-precision single-molecule studies demonstrated that kinesin takes regular 8-nm steps upon hydrolysis of each ATP; however, the intermediate states between steps have not been directly visualized. Here, we employed high-temporal resolution dark-field microscopy to directly visualize the binding and unbinding of kinesin heads to or from microtubules during processive movement. Our observations revealed that upon unbinding from microtubules, the labeled heads were displaced rightward and underwent tethered diffusive movement. Structural and kinetic analyses of wild-type and mutant kinesins with altered neck linker lengths provided evidence that rebinding of the unbound head to the rear-binding site is prohibited by a tension increase in the neck linker and that ATP hydrolysis by the leading head is suppressed when both heads are bound to the microtubule, thereby explaining how the two heads coordinate to move in a hand-over-hand manner.
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19
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Lisowski B, Kuśmierz Ł, Żabicki M, Bier M. "Cargo-mooring" as an operating principle for molecular motors. J Theor Biol 2015; 374:26-34. [PMID: 25794652 DOI: 10.1016/j.jtbi.2015.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 01/26/2015] [Accepted: 03/04/2015] [Indexed: 11/27/2022]
Abstract
Navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell׳s crucial components, such as organelles and vesicles filled with neurotransmitter. They generate force and pull cargo, as they literally walk along the polymeric tracks, e.g. microtubules. What we suggest in this paper is that the motor protein is not really pulling its load. The load is subject to diffusion and the motor may be doing little else than rectifying the fluctuations, i.e. ratcheting the load׳s diffusion. Below we present a detailed model to show how such ratcheting can quantitatively account for observed data. The consequence of such a mechanism is the dependence of the transport׳s speed and efficacy not only on the motor, but also on the cargo (especially its size) and on the environment (i.e. its viscosity and structure). Current experimental works rarely provide this type of information for in vivo studies. We suggest that even small differences between assays can impact the outcome. Our results agree with those obtained in wet laboratories and provide novel insight in a molecular motor׳s functioning.
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Affiliation(s)
- Bartosz Lisowski
- M. Smoluchowski Institute of Physics Jagiellonian University, Kraków, Poland; Unit of Pharmacoepidemiology and Pharmacoeconomics, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland.
| | - Łukasz Kuśmierz
- M. Smoluchowski Institute of Physics Jagiellonian University, Kraków, Poland; AGH University of Science and Technology, Institute of Automatics, Al. Mickiewicza 30, 30-059, Krakow, Poland
| | - Michał Żabicki
- M. Smoluchowski Institute of Physics Jagiellonian University, Kraków, Poland
| | - Martin Bier
- Department of Physics, East Carolina University, Greenville, NC 27858, USA
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20
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Andreasson JOL, Milic B, Chen GY, Guydosh NR, Hancock WO, Block SM. Examining kinesin processivity within a general gating framework. eLife 2015; 4. [PMID: 25902401 PMCID: PMC4453223 DOI: 10.7554/elife.07403] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/21/2015] [Indexed: 12/22/2022] Open
Abstract
Kinesin-1 is a dimeric motor that transports cargo along microtubules, taking 8.2-nm steps in a hand-over-hand fashion. The ATP hydrolysis cycles of its two heads are maintained out of phase by a series of gating mechanisms, which lead to processive runs averaging ∼1 μm. A key structural element for inter-head coordination is the neck linker (NL), which connects the heads to the stalk. To examine the role of the NL in regulating stepping, we investigated NL mutants of various lengths using single-molecule optical trapping and bulk fluorescence approaches in the context of a general framework for gating. Our results show that, although inter-head tension enhances motor velocity, it is crucial neither for inter-head coordination nor for rapid rear-head release. Furthermore, cysteine-light mutants do not produce wild-type motility under load. We conclude that kinesin-1 is primarily front-head gated, and that NL length is tuned to enhance unidirectional processivity and velocity. DOI:http://dx.doi.org/10.7554/eLife.07403.001 In cells, molecules are moved from one location to another by motor proteins. Kinesins are a large family of such motors that transport their cargos along long filaments known as microtubules. Most kinesin molecules are formed from two identical protein chains. Each chain has a motor region at one end (called the head) that can attach to microtubules. The other end of each protein chain wraps around its partner to form a common stalk region (called the tail) that links to the cargo being carried. The two kinesin heads are connected to the tail via a ‘neck linker’ region, and they advance along the microtubule in strict alternation, similar to the way our legs move when walking. During each step, the front head remains tightly associated with the filament as the trailing head releases itself, advances beyond the front head, and reattaches to become the new leading head. The two heads need to coordinate their activities, so that at any given time, they're not at the same stage in the process. For example, if both heads remained bound to the microtubule at the same time, the motor would not be able to advance. If they both released, the motor would fall off the filament and diffuse away. However, the process by which the heads coordinate is not fully understood, and different models for how this process works have been proposed. Now, Andreasson, Milic et al. have examined the role played by the neck linker in coordinating the motor's movement using a technique known as ‘optical trapping’. The experiments involved attaching microscopic beads to the motor proteins, which serve as markers that can be tracked. The beads can also be used to exert controlled forces on the kinesin molecules, to see how they respond to different loads. Andreasson, Milic et al. extended the length of neck linker by inserting extra amino acids (which are the building blocks of proteins) into this region of the protein. It was found that kinesins can still walk even when each neck linker was extended by up to six additional amino acids. However, introducing even a single amino acid into the linker relaxed the normal tension that exists between the heads when these are both bound to the filament. This resulted in slowed speeds, shorter distances of travel, and less ability to sustain loads. The experimental results suggest that the length of the neck linker in naturally occurring kinesins may be optimized to support maximum movement. Based on their data, Andreasson, Milic et al. propose a general framework for understanding the communication that needs to take place between the heads in order to walk in a coordinated manner. Further work is required to understand if motor proteins other than kinesins can also be understood with this same framework. DOI:http://dx.doi.org/10.7554/eLife.07403.002
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Affiliation(s)
| | - Bojan Milic
- Department of Biology, Stanford University, Stanford, United States
| | - Geng-Yuan Chen
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | | | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Steven M Block
- Department of Biology, Stanford University, Stanford, United States
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21
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Andreasson JOL, Shastry S, Hancock WO, Block SM. The Mechanochemical Cycle of Mammalian Kinesin-2 KIF3A/B under Load. Curr Biol 2015; 25:1166-75. [PMID: 25866395 DOI: 10.1016/j.cub.2015.03.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 12/11/2022]
Abstract
The response of motor proteins to external loads underlies their ability to work in teams and determines the net speed and directionality of cargo transport. The mammalian kinesin-2, KIF3A/B, is a heterotrimeric motor involved in intraflagellar transport and vesicle motility in neurons. Bidirectional cargo transport is known to result from the opposing activities of KIF3A/B and dynein bound to the same cargo, but the load-dependent properties of kinesin-2 are poorly understood. We used a feedback-controlled optical trap to probe the velocity, run length, and unbinding kinetics of mouse KIF3A/B under various loads and nucleotide conditions. The kinesin-2 motor velocity is less sensitive than kinesin-1 to external forces, but its processivity diminishes steeply with load, and the motor was observed occasionally to slip and reattach. Each motor domain was characterized by studying homodimeric constructs, and a global fit to the data resulted in a comprehensive pathway that quantifies the principal force-dependent kinetic transitions. The properties of the KIF3A/B heterodimer are intermediate between the two homodimers, and the distinct load-dependent behavior is attributable to the properties of the motor domains and not to the neck linkers or the coiled-coil stalk. We conclude that the force-dependent movement of KIF3A/B differs significantly from conventional kinesin-1. Against opposing dynein forces, KIF3A/B motors are predicted to rapidly unbind and rebind, resulting in qualitatively different transport behavior from kinesin-1.
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Affiliation(s)
| | - Shankar Shastry
- Department of Bioengineering, Pennsylvania State University, University Park, PA 16802, USA
| | - William O Hancock
- Department of Bioengineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Steven M Block
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
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22
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Dogan MY, Can S, Cleary FB, Purde V, Yildiz A. Kinesin's front head is gated by the backward orientation of its neck linker. Cell Rep 2015; 10:1967-73. [PMID: 25818289 DOI: 10.1016/j.celrep.2015.02.061] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/20/2015] [Accepted: 02/26/2015] [Indexed: 11/25/2022] Open
Abstract
Kinesin-1 is a two-headed motor that takes processive 8-nm hand-over-hand steps and transports intracellular cargos toward the plus-end of microtubules. Processive motility requires a gating mechanism to coordinate the mechanochemical cycles of the two heads. Kinesin gating involves neck linker (NL), a short peptide that interconnects the heads, but it remains unclear whether gating is facilitated by the NL orientation or tension. Using optical trapping, we measured the force-dependent microtubule release rate of kinesin monomers under different nucleotide conditions and pulling geometries. We find that pulling NL in the backward direction inhibits nucleotide binding and subsequent release from the microtubule. This inhibition is independent of the magnitude of tension (2-8 pN) exerted on NL. Our results provide evidence that the front head of a kinesin dimer is gated by the backward orientation of its NL until the rear head releases from the microtubule.
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Affiliation(s)
- Merve Yusra Dogan
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sinan Can
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Frank B Cleary
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vedud Purde
- Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Ahmet Yildiz
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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23
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Cochran JC. Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines. Biophys Rev 2015; 7:269-299. [PMID: 28510227 DOI: 10.1007/s12551-014-0150-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/16/2014] [Indexed: 11/25/2022] Open
Abstract
Molecular motors are enzymes that convert chemical potential energy into controlled kinetic energy for mechanical work inside cells. Understanding the biophysics of these motors is essential for appreciating life as well as apprehending diseases that arise from motor malfunction. This review focuses on kinesin motor enzymology with special emphasis on the literature that reports the chemistry, structure and physics of several different kinesin superfamily members.
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Affiliation(s)
- J C Cochran
- Department of Molecular & Cellular Biochemistry, Indiana University, Simon Hall Room 405C, 212 S. Hawthorne Dr., Bloomington, IN, 47405, USA.
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24
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Kim JI, Chang HJ, Na S. Identification of tail binding effect of kinesin-1 using an elastic network model. Biomech Model Mechanobiol 2015; 14:1107-17. [PMID: 25676575 DOI: 10.1007/s10237-015-0657-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/05/2015] [Indexed: 12/15/2022]
Abstract
Kinesin is a motor protein that delivers cargo inside a cell. Kinesin has many different families, but they perform basically same function and have same motions. The walking motion of kinesin enables the cargo delivery inside the cell. Autoinhibition of kinesin is important because it explains how function of kinesin inside a cell is stopped. Former researches showed that tail binding is related to autoinhibition of kinesin. In this work, we performed normal mode analysis with elastic network model using different conformation of kinesin to determine the effect of tail binding by considering four models such as functional form, autoinhibited form, autoinhibited form without tail, and autoinhibited form with carbon structure. Our calculation of the thermal fluctuation and cross-correlation shows the change of tail-binding region in structural motion. Also strain energy of kinesin showed that elimination of tail binding effect leads the structure to have energetically similar behavior with the functional form.
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Affiliation(s)
- Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul, 136-701, Republic of Korea
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25
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Chen GY, Arginteanu DFJ, Hancock WO. Processivity of the kinesin-2 KIF3A results from rear head gating and not front head gating. J Biol Chem 2015; 290:10274-94. [PMID: 25657001 DOI: 10.1074/jbc.m114.628032] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 01/12/2023] Open
Abstract
The kinesin-2 family motor KIF3A/B works together with dynein to bidirectionally transport intraflagellar particles, melanosomes, and neuronal vesicles. Compared with kinesin-1, kinesin-2 is less processive, and its processivity is more sensitive to load, suggesting that processivity may be controlled by different gating mechanisms. We used stopped-flow and steady-state kinetics experiments, along with single-molecule and multimotor assays to characterize the entire kinetic cycle of a KIF3A homodimer that exhibits motility similar to that of full-length KIF3A/B. Upon first encounter with a microtubule, the motor rapidly exchanges both mADP and mATP. When adenosine 5'-[(β,γ)-imido]triphosphate was used to entrap the motor in a two-head-bound state, exchange kinetics were unchanged, indicating that rearward strain in the two-head-bound state does not alter nucleotide binding to the front head. A similar lack of front head gating was found when intramolecular strain was enhanced by shortening the neck linker domain from 17 to 14 residues. In single-molecule assays in ADP, the motor dissociates at 2.1 s(-1), 20-fold slower than the stepping rate, demonstrating the presence of rear head gating. In microtubule pelleting assays, the KD(Mt) is similar in ADP and ATP. The data and accompanying simulations suggest that, rather than KIF3A processivity resulting from strain-dependent regulation of nucleotide binding (front head gating), the motor spends a significant fraction of its hydrolysis cycle in a low affinity state but dissociates only slowly from this state. This work provides a mechanism to explain differences in the load-dependent properties of kinesin-1 and kinesin-2.
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Affiliation(s)
- Geng-Yuan Chen
- From the Department of Biomedical Engineering Pennsylvania State University University Park, Pennsylvania 16802
| | - David F J Arginteanu
- From the Department of Biomedical Engineering Pennsylvania State University University Park, Pennsylvania 16802
| | - William O Hancock
- From the Department of Biomedical Engineering Pennsylvania State University University Park, Pennsylvania 16802
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26
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The AAA3 domain of cytoplasmic dynein acts as a switch to facilitate microtubule release. Nat Struct Mol Biol 2014; 22:73-80. [PMID: 25486306 PMCID: PMC4286497 DOI: 10.1038/nsmb.2930] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/06/2014] [Indexed: 11/24/2022]
Abstract
Cytoplasmic dynein is an AAA+ motor responsible for intracellular cargo transport and force generation along microtubules (MTs). Unlike kinesin and myosin, dynein contains multiple ATPase subunits, with AAA1 serving as the primary catalytic site. ATPase activity at AAA3 is also essential for robust motility, but its role in dynein’s mechanochemical cycle remains unclear. Here, we introduced transient pauses in Saccharomyces cerevisiae dynein motility by using a slowly hydrolyzing ATP analog. Analysis of pausing behavior revealed that AAA3 hydrolyzes nucleotide an order of magnitude slower than AAA1 and the two sites do not coordinate. ATPase mutations to AAA3 abolish the ability of dynein to modulate MT release. Nucleotide hydrolysis at AAA3 lifts this “MT gate” to fast motility. These results suggest that AAA3 acts as a switch that repurposes cytoplasmic dynein for fast cargo transport and MT anchoring tasks in cells.
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27
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Kinesin's neck-linker determines its ability to navigate obstacles on the microtubule surface. Biophys J 2014; 106:1691-700. [PMID: 24739168 DOI: 10.1016/j.bpj.2014.02.034] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/14/2014] [Accepted: 02/27/2014] [Indexed: 01/12/2023] Open
Abstract
The neck-linker is a structurally conserved region among most members of the kinesin superfamily of molecular motor proteins that is critical for kinesin's processive transport of intracellular cargo along the microtubule surface. Variation in the neck-linker length has been shown to directly modulate processivity in different kinesin families; for example, kinesin-1, with a shorter neck-linker, is more processive than kinesin-2. Although small differences in processivity are likely obscured in vivo by the coupling of most cargo to multiple motors, longer and more flexible neck-linkers may allow different kinesins to navigate more efficiently around the many obstacles, including microtubule-associated proteins (MAPs), that are found on the microtubule surface within cells. We hypothesize that, due to its longer neck-linker, kinesin-2 can more easily navigate obstacles (e.g., MAPs) on the microtubule surface than kinesin-1. We used total internal reflection fluorescence microscopy to observe single-molecule motility from different kinesin-1 and kinesin-2 neck-linker chimeras stepping along microtubules in the absence or presence of two Tau isoforms, 3RS-Tau and 4RL-Tau, both of which are MAPs that are known to differentially affect kinesin-1 motility. Our results demonstrate that unlike kinesin-1, kinesin-2 is insensitive to the presence of either Tau isoform, and appears to have the ability to switch protofilaments while stepping along the microtubule when challenged by an obstacle, such as Tau. Thus, although kinesin-1 may be more processive, the longer neck-linker length of kinesin-2 allows it to be better optimized to navigate the complex microtubule landscape. These results provide new insight, to our knowledge, into how kinesin-1 and kinesin-2 may work together for the efficient delivery of cargo in cells.
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28
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Shang Z, Zhou K, Xu C, Csencsits R, Cochran JC, Sindelar CV. High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation. eLife 2014; 3:e04686. [PMID: 25415053 PMCID: PMC4383081 DOI: 10.7554/elife.04686] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/20/2014] [Indexed: 12/12/2022] Open
Abstract
Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is
essential for a wide range of vital processes in eukaryotes. We obtained insight into
this process by developing atomic models for no-nucleotide and ATP states of the
monomeric kinesin motor domain on microtubules from cryo-EM reconstructions at
5–6 Å resolution. By comparing these models with existing X-ray
structures of ADP-bound kinesin, we infer a mechanistic scheme in which microtubule
attachment, mediated by a universally conserved ‘linchpin’ residue in
kinesin (N255), triggers a clamshell opening of the nucleotide cleft and accompanying
release of ADP. Binding of ATP re-closes the cleft in a manner that tightly couples
to translocation of cargo, via kinesin's ‘neck linker’ element. These
structural transitions are reminiscent of the analogous nucleotide-exchange steps in
the myosin and F1-ATPase motors and inform how the two heads of a kinesin dimer
‘gate’ each other to promote coordinated stepping along
microtubules. DOI:http://dx.doi.org/10.7554/eLife.04686.001 The inside of a cell is a dynamic environment. Large molecules such as proteins are
commonly transported within a cell by ‘motor proteins’, which move
along a network of filaments called microtubules. One group of motor proteins, the
kinesins, typically have one end called a motor domain that attaches itself to a
microtubule. The other end links to the cargo being carried, and a flexible
‘neck’ region connects the two ends of the motor protein. Kinesins are bound together in pairs. The flexible neck region allows each motor
domain in a pair to move past that of the other, allowing the kinesin to
‘walk’ along a microtubule in a step-like manner. Each step requires
one motor domain to alternately tightly associate with, and then release from, a
microtubule filament. This alternating cycle is coordinated by kinesin binding to and
breaking down a molecule called ATP to form another molecule called ADP, which
releases the energy needed for its next step. This repeating cycle is possible because a motor domain changes shape when it binds
to a microtubule. This shape change stimulates the release of ADP, freeing up room
for a new ATP molecule to bind to the motor domain. Although relatively small, these
structural changes produce larger changes in the flexible neck region that enable the
individual motor domains within a kinesin pair to co-ordinate their movement and move
efficiently. Many previous studies have investigated these shape changes using a
technique called cryo-electron microscopy, which rapidly freezes samples and allows
their structure to be recorded in high detail. However, the small size of the motor
domains and their changes in shape means that this technique was not able to reveal
the structures in full detail. Shang et al. now exploit recent advances in cryo-electron microscopy to examine the
structural changes of individual kinesin motor domains in greater detail. Images of
motor domains bound to microtubules were made while the motor domain was in one of
two different states: not bound to ATP or ADP, or bound to a chemically modified form
of ATP that cannot be broken down. Shang et al. then used these images to produce
models of the motor domains and compared the models with previously published images.
This revealed a cleft in the kinesin motor domain that opens when it attaches to a
microtubule. This cleft's ‘clamshell-like’ opening allows ADP to be
released; it then closes when a molecule of ATP binds to it. The opening and closing of the cleft causes the changes in the ‘neck
linker’ of the kinesin that enable the motor protein to transport its cargo,
and so links ATP binding to the movement of the motor protein. Shang et al. suggest
that similar processes may also occur in other motor proteins that have not been as
well studied as the kinesins. DOI:http://dx.doi.org/10.7554/eLife.04686.002
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Affiliation(s)
- Zhiguo Shang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Kaifeng Zhou
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Chen Xu
- Department of Biology, Brandeis University, Waltham, United States
| | - Roseann Csencsits
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Jared C Cochran
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
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29
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Prevo B, Peterman EJG. Förster resonance energy transfer and kinesin motor proteins. Chem Soc Rev 2014; 43:1144-55. [PMID: 24071719 DOI: 10.1039/c3cs60292c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Förster Resonance Energy Transfer (FRET) is the phenomenon of non-radiative transfer of electronic excitations from a donor fluorophore to an acceptor, mediated by electronic dipole-dipole coupling. The transfer rate and, as a consequence, efficiency depend non-linearly on the distance between the donor and the acceptor. FRET efficiency can thus be used as an effective and accurate reporter of distance between two fluorophores and changes thereof. Over the last 50 years or so, FRET has been used as a spectroscopic ruler to measure conformations and conformational changes of biomolecules. More recently, FRET has been combined with microscopy, ultimately allowing measurement of FRET between a single donor and a single acceptor pair. In this review, we will explain the physical foundations of FRET and how FRET can be applied to biomolecules. We will highlight the power of the different FRET approaches by focusing on its application to the motor protein kinesin, which undergoes several conformational changes driven by enzymatic action, that ultimately result in unidirectional motion along microtubule filaments, driving active transport in the cell. Single-molecule and ensemble FRET studies of different aspects of kinesin have provided numerous insights into the complex chemomechanical mechanism of this fascinating protein.
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Affiliation(s)
- Bram Prevo
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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30
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Joshi M, Duan D, Drew D, Jia Z, Davis D, Campbell RL, Allingham JS. Kar3Vik1 mechanochemistry is inhibited by mutation or deletion of the C terminus of the Vik1 subunit. J Biol Chem 2013; 288:36957-70. [PMID: 24240171 DOI: 10.1074/jbc.m113.492264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Force production by kinesins has been linked to structural rearrangements of the N and C termini of their motor domain upon nucleotide binding. In recent crystal structures, the Kar3-associated protein Vik1 shows unexpected homology to these conformational states even though it lacks a nucleotide-binding site. This conservation infers a degree of commonality in the function of the N- and C-terminal regions during the mechanochemical cycle of all kinesins and kinesin-related proteins. We tested this inference by examining the functional effects on Kar3Vik1 of mutating or deleting residues in Vik1 that are involved in stabilizing the C terminus against the core and N terminus of the Vik1 motor homology domain (MHD). Point mutations at two moderately conserved residues near the Vik1 C terminus impaired microtubule gliding and microtubule-stimulated ATP turnover by Kar3Vik1. Deletion of the seven C-terminal residues inhibited Kar3Vik1 motility much more drastically. Interestingly, none of the point mutants seemed to perturb the ability of Kar3Vik1 to bind microtubules, whereas the C-terminal truncation mutant did. Molecular dynamics simulations of these C-terminal mutants showed distinct root mean square fluctuations in the N-terminal region of the Vik1 MHD that connects it to Kar3. Here, the degree of motion in the N-terminal portion of Vik1 highly correlated with that in the C terminus. These observations suggest that the N and C termini of the Vik1 MHD form a discrete folding motif that is part of a communication pathway to the nucleotide-binding site of Kar3.
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Affiliation(s)
- Monika Joshi
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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31
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Ribeck N, Saleh OA. DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand. PLoS One 2013; 8:e79237. [PMID: 24250825 PMCID: PMC3826741 DOI: 10.1371/journal.pone.0079237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/20/2013] [Indexed: 01/12/2023] Open
Abstract
The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, ‘occluded’ strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.
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Affiliation(s)
- Noah Ribeck
- Department of Physics, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Omar A. Saleh
- Department of Materials and Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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32
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Nam W, Epureanu BI. Metrics for characterizing collective transport by multiple dimeric kinesins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:051916. [PMID: 23214823 DOI: 10.1103/physreve.86.051916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/03/2012] [Indexed: 06/01/2023]
Abstract
Kinesin is a processive molecular motor which transports various cellular cargos by converting chemical energy into mechanical movements. Although the motion of a single molecule has been characterized in several studies, the dynamics of collective transport remains controversial. Since the chemical reactions fueling molecular motors are stochastic processes, the movements of coupled motors are not perfectly synchronized. The goal of this study is to develop metrics to analyze the level of synchronization of coupled (stochastic) motors. The correlation among movements of coupled motors, the slackness, the cooperativity, and the power loss of kinesins are explored using the developed metrics. These metrics can be extended to characterize collective work done by other molecular motors also.
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Affiliation(s)
- Woochul Nam
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA.
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33
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Sardar HS, Gilbert SP. Microtubule capture by mitotic kinesin centromere protein E (CENP-E). J Biol Chem 2012; 287:24894-904. [PMID: 22637578 DOI: 10.1074/jbc.m112.376830] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Centromere protein E, CENP-E, is a kinetochore-associated kinesin-7 that establishes the microtubule-chromosome linkage and transports monooriented chromosomes to the spindle equator along kinetochore fibers of already bioriented chromosomes. As a processive kinesin, CENP-E uses a hand-over-hand mechanism, yet a number of studies suggest that CENP-E exhibits mechanistic differences from other processive kinesins that may be important for its role in chromosome congression. The results reported here show that association of CENP-E with the microtubule is unusually slow at 0.08 μM(-1) s(-1) followed by slow ADP release at 0.9 s(-1). ATP binding and hydrolysis are fast with motor dissociation from the microtubule at 1.4 s(-1), suggesting that CENP-E head detachment from the microtubule, possibly controlled by phosphate release, determines the rate of stepping during a processive run because the rate of microtubule gliding corresponds to 1.4 steps/s. We hypothesize that the unusually slow CENP-E microtubule association step favors CENP-E binding of stable microtubules over dynamic ones, a mechanism that would bias CENP-E binding to kinetochore fibers.
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Affiliation(s)
- Harjinder S Sardar
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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34
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Hyeon C, Onuchic JN. A structural perspective on the dynamics of kinesin motors. Biophys J 2012; 101:2749-59. [PMID: 22261064 DOI: 10.1016/j.bpj.2011.10.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/11/2011] [Accepted: 10/31/2011] [Indexed: 10/14/2022] Open
Abstract
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments, we envisaged how kinesin, a prototype of biological machines, generates force and regulates its dynamics to sustain persistent motor action. A structure-based model, which can be versatile in adapting its structure to external stresses while maintaining its native fold, was employed to account for several features of kinesin dynamics along the biochemical cycle. This analysis complements our current understandings of kinesin dynamics and connections to experiments. We propose a thermodynamic cycle for kinesin that emphasizes the mechanical and regulatory role of the neck linker and clarify issues related to the motor directionality, and the difference between the external stalling force and the internal tension responsible for the head-head coordination. The comparison between the thermodynamic cycle of kinesin and macroscopic heat engines highlights the importance of structural change as the source of work production in biomolecular machines.
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Affiliation(s)
- Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
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35
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McKinley SA, Athreya A, Fricks J, Kramer PR. Asymptotic analysis of microtubule-based transport by multiple identical molecular motors. J Theor Biol 2012; 305:54-69. [PMID: 22575549 DOI: 10.1016/j.jtbi.2012.03.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/09/2012] [Accepted: 03/27/2012] [Indexed: 12/25/2022]
Abstract
We describe a system of stochastic differential equations (SDEs) which model the interaction between processive molecular motors, such as kinesin and dynein, and the biomolecular cargo they tow as part of microtubule-based intracellular transport. We show that the classical experimental environment fits within a parameter regime which is qualitatively distinct from conditions one expects to find in living cells. Through an asymptotic analysis of our system of SDEs, we develop a means for applying in vitro observations of the nonlinear response by motors to forces induced on the attached cargo to make analytical predictions for two parameter regimes that have thus far eluded direct experimental observation: (1) highly viscous in vivo transport and (2) dynamics when multiple identical motors are attached to the cargo and microtubule.
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Affiliation(s)
- Scott A McKinley
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA.
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36
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Zhang Z, Thirumalai D. Dissecting the kinematics of the kinesin step. Structure 2012; 20:628-40. [PMID: 22483110 DOI: 10.1016/j.str.2012.02.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 01/19/2012] [Accepted: 02/09/2012] [Indexed: 01/04/2023]
Abstract
Kinesin walks processively on microtubules in an asymmetric hand-over-hand manner with each step spanning 16 nm. We used molecular simulations to determine the fraction of a single step due to conformational changes in the neck linker, and that due to diffusion of the tethered head. Stepping is determined largely by two energy scales, one favoring neck-linker docking and the other, ε(h)(MT-TH), between the trailing head (TH) and the microtubule. Neck-linker docking and an optimal value of ε(h)(MT-TH) are needed to minimize the probability that the TH takes side steps. There are three major stages in the kinematics of a step. In the first, the neck linker docks, resulting in ∼(5-6) nm movements of the trailing head. The TH moves an additional (6-8) nm in stage II by anisotropic translational diffusion. In the third stage, spanning ∼(3-4) nm, the step is complete with the TH binding to the αβ-tubulin binding site.
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Affiliation(s)
- Zhechun Zhang
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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37
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LIPOWSKY REINHARD, BEEG JANINA, DIMOVA RUMIANA, KLUMPP STEFAN, LIEPELT STEFFEN, MÜLLER MELANIEJI, VALLERIANI ANGELO. ACTIVE BIO-SYSTEMS: FROM SINGLE MOTOR MOLECULES TO COOPERATIVE CARGO TRANSPORT. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048009000946] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Living cells contain a large number of molecular motors that convert the chemical energy released from nucleotide hydrolysis into mechanical work. This review focusses on stepping motors that move along cytoskeletal filaments. The behavior of these motors involves three distinct nonequilibrium processes that cover a wide range of length and time scales: (i) Directed stepping of single motors bound to a filament; (ii) Composite motor walks of single motors consisting of directed stepping interrupted by diffusive motion; and (iii) Cooperative transport by teams of several motors. On the molecular scale, the energy conversion of these motors leads to single steps along the filaments with a step size of about 10 nm. The corresponding chemomechanical coupling is governed by several distinct motor cycles, which represent the dominant pathways for different values of nucleotide concentrations and load force. For the kinesin motor, the competition of two such cycles determines the stall force, at which the motor velocity vanishes and the motor reverses the direction of its motion. Because of thermal noise, the stepping motors unbind from the filaments after a certain run time and run length. For kinesin, the run time is about 1 s and the run length is about 1 μm for high ATP concentration and low load force. On length scales that are large compared to the run length, a single motor undergoes composite walks consisting of directed stepping interrupted by diffusive motion. The relative importance of bound and unbound motor states depends on the binding and unbinding rates of the motors. The effective transport velocity and diffusion coefficient of the motors are determined by the geometry of the compartments, in which the motors move. The effective diffusion coefficient can be enhanced by several orders of magnitude if the motors undergo active diffusion by interacting with certain filament patterns. In vivo, stepping motors are responsible for the transport of vesicles and other types of intracellular cargo particles that shuttle between the different cell compartments. This cargo transport is usually performed by teams of motors. If all motors belong to the same molecular species, the cooperative action of the motors leads to uni-directional transport with a strongly increased run length and to a characteristic force dependence of the velocity distributions. If two antagonistic species of motors pull on the cargo, they perform a stochastic tug-of-war, which is characterized by a subtle force balance between the two motor teams and leads to seven distinct patterns of uni- and bi-directional transport. So far, all experimental observations on bi-directional transport are consistent with such a tug-of-war. Finally, the traffic of interacting motors is also briefly discussed. Depending on their mutual interactions and the compartment geometry, the motors form various spatio-temporal patterns such as traffic jams, and undergo nonequilibrium phase transitions between such transport patterns.
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Affiliation(s)
- REINHARD LIPOWSKY
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - JANINA BEEG
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - RUMIANA DIMOVA
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - STEFAN KLUMPP
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - STEFFEN LIEPELT
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - MELANIE J. I. MÜLLER
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
| | - ANGELO VALLERIANI
- Department of Theory & Bio-Systems, MPI of Colloids and Interfaces, Science Park, 14424 Potsdam, Germany
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38
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Abstract
Kinesin-1 is an ATP-driven, processive motor that transports cargo along microtubules in a tightly regulated stepping cycle. Efficient gating mechanisms ensure that the sequence of kinetic events proceeds in proper order, generating a large number of successive reaction cycles. To study gating, we created two mutant constructs with extended neck-linkers and measured their properties using single-molecule optical trapping and ensemble fluorescence techniques. Due to a reduction in the inter-head tension, the constructs access an otherwise rarely populated conformational state where both motor heads remain bound to the microtubule. ATP-dependent, processive backstepping and futile hydrolysis were observed under moderate hindering loads. Based on measurements, we formulated a comprehensive model for kinesin motion that incorporates reaction pathways for both forward and backward stepping. In addition to inter-head tension, we find that neck-linker orientation is also responsible for ensuring gating in kinesin.
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39
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A seesaw model for intermolecular gating in the kinesin motor protein. Biophys Rev 2011; 3:85-100. [PMID: 21765878 PMCID: PMC3117274 DOI: 10.1007/s12551-011-0049-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 05/19/2011] [Indexed: 11/01/2022] Open
Abstract
Recent structural observations of kinesin-1, the founding member of the kinesin group of motor proteins, have led to substantial gains in our understanding of this molecular machine. Kinesin-1, similar to many kinesin family members, assembles to form homodimers that use alternating ATPase cycles of the catalytic motor domains, or "heads", to proceed unidirectionally along its partner filament (the microtubule) via a hand-over-hand mechanism. Cryo-electron microscopy has now revealed 8-Å resolution, 3D reconstructions of kinesin-1•microtubule complexes for all three of this motor's principal nucleotide-state intermediates (ADP-bound, no-nucleotide, and ATP analog), the first time filament co-complexes of any cytoskeletal motor have been visualized at this level of detail. These reconstructions comprehensively describe nucleotide-dependent changes in a monomeric head domain at the secondary structure level, and this information has been combined with atomic-resolution crystallography data to synthesize an atomic-level "seesaw" mechanism describing how microtubules activate kinesin's ATP-sensing machinery. The new structural information revises or replaces key details of earlier models of kinesin's ATPase cycle that were based principally on crystal structures of free kinesin, and demonstrates that high-resolution characterization of the kinesin-microtubule complex is essential for understanding the structural basis of the cycle. I discuss the broader implications of the seesaw mechanism within the cycle of a fully functional kinesin dimer and show how the seesaw can account for two types of "gating" that keep the ATPase cycles of the two heads out of sync during processive movement.
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40
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Bruno L, Salierno M, Wetzler DE, Despósito MA, Levi V. Mechanical properties of organelles driven by microtubule-dependent molecular motors in living cells. PLoS One 2011; 6:e18332. [PMID: 21483765 PMCID: PMC3069964 DOI: 10.1371/journal.pone.0018332] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 02/25/2011] [Indexed: 11/18/2022] Open
Abstract
The organization of the cytoplasm is regulated by molecular motors which transport organelles and other cargoes along cytoskeleton tracks. Melanophores have pigment organelles or melanosomes that move along microtubules toward their minus and plus end by the action of cytoplasmic dynein and kinesin-2, respectively. In this work, we used single particle tracking to characterize the mechanical properties of motor-driven organelles during transport along microtubules. We tracked organelles with high temporal and spatial resolutions and characterized their dynamics perpendicular to the cytoskeleton track. The quantitative analysis of these data showed that the dynamics is due to a spring-like interaction between melanosomes and microtubules in a viscoelastic microenvironment. A model based on a generalized Langevin equation explained these observations and predicted that the stiffness measured for the motor complex acting as a linker between organelles and microtubules is ∼ one order smaller than that determined for motor proteins in vitro. This result suggests that other biomolecules involved in the interaction between motors and organelles contribute to the mechanical properties of the motor complex. We hypothesise that the high flexibility observed for the motor linker may be required to improve the efficiency of the transport driven by multiple copies of motor molecules.
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Affiliation(s)
- Luciana Bruno
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 1, Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Marcelo Salierno
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Diana E. Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Marcelo A. Despósito
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 1, Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Valeria Levi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
- * E-mail:
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41
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Renewal-Reward Process Formulation of Motor Protein Dynamics. Bull Math Biol 2011; 73:2452-82. [DOI: 10.1007/s11538-011-9632-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 01/18/2011] [Indexed: 11/26/2022]
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42
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Xie P. Mechanism of processive movement of monomeric and dimeric kinesin molecules. Int J Biol Sci 2010; 6:665-74. [PMID: 21060728 PMCID: PMC2974169 DOI: 10.7150/ijbs.6.665] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/19/2010] [Indexed: 11/05/2022] Open
Abstract
Kinesin molecules are motor proteins capable of moving along microtubule by hydrolyzing ATP. They generally have several forms of construct. This review focuses on two of the most studied forms: monomers such as KIF1A (kinesin-3 family) and dimers such as conventional kinesin (kinesin-1 family), both of which can move processively towards the microtubule plus end. There now exist numerous models that try to explain how the kinesin molecules convert the chemical energy of ATP hydrolysis into the mechanical energy to "power" their processive movement along microtubule. Here, we attempt to present a comprehensive review of these models. We further propose a new hybrid model for the dimeric kinesin by combining the existing models and provide a framework for future studies in this subject.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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43
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Thermodynamics and kinetics of molecular motors. Biophys J 2010; 98:2401-9. [PMID: 20513383 DOI: 10.1016/j.bpj.2010.02.040] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 02/03/2010] [Accepted: 02/16/2010] [Indexed: 11/20/2022] Open
Abstract
Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules.
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44
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Fehr AN, Gutiérrez-Medina B, Asbury CL, Block SM. On the origin of kinesin limping. Biophys J 2009; 97:1663-70. [PMID: 19751671 DOI: 10.1016/j.bpj.2009.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 07/06/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022] Open
Abstract
Kinesin is a dimeric motor with twin catalytic heads joined to a common stalk. Kinesin molecules move processively along microtubules in a hand-over-hand walk, with the two heads advancing alternately. Recombinant kinesin constructs with short stalks have been found to "limp", i.e., exhibit alternation in the dwell times of successive steps. Limping behavior implies that the molecular rearrangements underlying even- and odd-numbered steps must differ, but the mechanism by which such rearrangements lead to limping remains unsolved. Here, we used an optical force clamp to measure individual, recombinant dimers and test candidate explanations for limping. Introducing a covalent cross-link into the stalk region near the heads had no effect on limping, ruling out possible stalk misregistration during coiled-coil formation as a cause. Limping was equally unaffected by mutations that produced 50-fold changes in stalk stiffness, ruling out models where limping arises from an asymmetry in torsional strain. However, limping was enhanced by perturbations that increased the vertical component of load on the motor, including increases in bead size or net load, and decreases in the stalk length. These results suggest that kinesin heads take different vertical trajectories during alternate steps, and that the rates for these motions are differentially sensitive to load.
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Affiliation(s)
- Adrian N Fehr
- Department of Applied Physics, Stanford University, Stanford, California, USA
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45
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Verbrugge S, Lechner B, Woehlke G, Peterman EJG. Alternating-site mechanism of kinesin-1 characterized by single-molecule FRET using fluorescent ATP analogues. Biophys J 2009; 97:173-82. [PMID: 19580755 DOI: 10.1016/j.bpj.2009.02.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 01/30/2009] [Accepted: 02/10/2009] [Indexed: 11/19/2022] Open
Abstract
Kinesin-1 motor proteins move along microtubules in repetitive steps of 8 nm at the expense of ATP. To determine nucleotide dwell times during these processive runs, we used a Förster resonance energy transfer method at the single-molecule level that detects nucleotide binding to kinesin motor heads. We show that the fluorescent ATP analog used produces processive motility with kinetic parameters altered <2.5-fold compared with normal ATP. Using our confocal fluorescence kinesin motility assay, we obtained fluorescence intensity time traces that we then analyzed using autocorrelation techniques, yielding a time resolution of approximately 1 ms for the intensity fluctuations due to fluorescent nucleotide binding and release. To compare these experimental autocorrelation curves with kinetic models, we used Monte-Carlo simulations. We find that the experimental data can only be described satisfactorily on the basis of models assuming an alternating-site mechanism, thus supporting the view that kinesin's two motor domains hydrolyze ATP and step in a sequential way.
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Affiliation(s)
- Sander Verbrugge
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
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46
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Abstract
The motor protein Kinesin-1 drives intracellular transport along microtubules, with each of its two motor domains taking 16-nm steps in a hand-over-hand fashion. The way in which a single-motor domain moves during a step is unknown. Here, we use Förster resonance energy transfer (FRET) between fluorescent labels on both motor domains of a single kinesin. This approach allows us to resolve the relative distance between the motor domains and their relative orientation, on the submillisecond timescale, during processive stepping. We observe transitions between high and low FRET values for certain kinesin constructs, depending on the location of the labels. These results reveal that, during a step, a kinesin motor domain dwells in a well-defined intermediate position for approximately 3 ms.
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47
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Spetzler D, Ishmukhametov R, Hornung T, Day LJ, Martin J, Frasch WD. Single molecule measurements of F1-ATPase reveal an interdependence between the power stroke and the dwell duration. Biochemistry 2009; 48:7979-85. [PMID: 19610671 PMCID: PMC2737049 DOI: 10.1021/bi9008215] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increases in the power stroke and dwell durations of single molecules of Escherichia coli F(1)-ATPase were measured in response to viscous loads applied to the motor and inhibition of ATP hydrolysis. The load was varied using different sizes of gold nanorods attached to the rotating gamma subunit and/or by increasing the viscosity of the medium using PEG-400, a noncompetitive inhibitor of ATPase activity. Conditions that increase the duration of the power stroke were found to cause 20-fold increases in the length of the dwell. These results suggest that the order of hydrolysis, product release, and substrate binding may change as the result of external load on the motor or inhibition of hydrolysis.
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Affiliation(s)
| | | | | | - Lixia Jin Day
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ 85287-4501, USA
| | - James Martin
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ 85287-4501, USA
| | - Wayne D. Frasch
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ 85287-4501, USA
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48
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Guydosh NR, Block SM. Direct observation of the binding state of the kinesin head to the microtubule. Nature 2009; 461:125-8. [PMID: 19693012 DOI: 10.1038/nature08259] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 07/01/2009] [Indexed: 11/09/2022]
Abstract
The dimeric motor protein kinesin-1 converts chemical energy from ATP hydrolysis into mechanical work used to transport cargo along microtubules. Cargo attached to the kinesin stalk moves processively in 8-nm increments as its twin motor domains (heads) carry out an asymmetric, 'hand-over-hand' walk. The extent of individual head interactions with the microtubule during stepping, however, remains controversial. A major experimental limitation has been the lack of a means to monitor the attachment of an individual head to the microtubule during movement, necessitating indirect approaches. Here we report the development of a single-molecule assay that can directly report head binding in a walking kinesin molecule, and show that only a single head is bound to the microtubule between steps at low ATP concentrations. A bead was linked to one of the two kinesin heads by means of a short DNA tether and used to apply rapidly alternating hindering and assisting loads with an optical trap. The time-dependent difference between forwards and backwards displacements of the bead alternated between two discrete values during stepping, corresponding to those intervals when the linked head adopted a bound or an unbound state. The linked head could only rebind the microtubule once ATP had become bound to its partner head.
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Affiliation(s)
- Nicholas R Guydosh
- Biophysics Program, Stanford University, Stanford, California 94305, USA
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49
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Abstract
Kinesin I can walk on a microtubule for distances as long as several micrometers. However, it is still unclear how this molecular motor can remain attached to the microtubule through the hundreds of mechanochemical cycles necessary to achieve this remarkable degree of processivity. We have addressed this issue by applying ensemble and single-molecule fluorescence methods to study the process of kinesin stepping, and our results lead to 4 conclusions. First, under physiologic conditions, approximately 75% of processively moving kinesin molecules are attached to the microtubule via both heads, and in this conformation, they are resistant to dissociation. Second, the remaining 25% of kinesin molecules, which are in an "ATP waiting state" and are strongly attached to the microtubule via only one head, are intermittently in a conformation that cannot bind ATP and therefore are resistant to nucleotide-induced dissociation. Third, the forward step in the kinesin ATPase cycle is very fast, accounting for <5% of the total cycle time, which ensures that the lifetime of this ATP waiting state is relatively short. Finally, by combining nanometer-level single-molecule fluorescence localization with higher ATP concentrations than used previously, we have determined that in this ATP waiting state, the ADP-containing head of kinesin is located 8 nm behind the attached head, in a location where it can interact with the microtubule lattice. These 4 features reduce the likelihood that a kinesin I motor will dissociate and contribute to making this motor so highly processive.
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50
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Muthukrishnan G, Zhang Y, Shastry S, Hancock WO. The processivity of kinesin-2 motors suggests diminished front-head gating. Curr Biol 2009; 19:442-7. [PMID: 19278641 DOI: 10.1016/j.cub.2009.01.058] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/15/2022]
Abstract
Kinesin-2 motors, which are involved in intraflagellar transport and cargo transport along cytoplasmic microtubules, differ from motors in the canonical kinesin-1 family by having a heterodimeric rather than homodimeric structure and possessing a three amino acid insertion in their neck linker domain. To determine how these structural features alter the chemomechanical coupling in kinesin-2, we used single-molecule bead experiments to measure the processivity and velocity of mouse kinesin-2 heterodimer (KIF3A/B) and the engineered homodimers KIF3A/A and KIF3B/B and compared their behavior to Drosophila kinesin-1 heavy chain (KHC). Single-motor run lengths of kinesin-2 were 4-fold shorter than those of kinesin-1. Extending the kinesin-1 neck linker by three amino acids led to a similar reduction in processivity. Furthermore, kinesin-2 processivity varied inversely with ATP concentration. Stochastic simulations of the kinesin-1 and kinesin-2 hydrolysis cycles suggest that "front-head gating," in which rearward tension prevents ATP binding to the front head when both heads are bound to the microtubule, is diminished in kinesin-2. Because the mechanical tension that underlies front-head gating must be transmitted through the neck linker domains, we propose that the diminished coordination in kinesin-2 is a result of its longer and, hence, more compliant neck linker element.
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Affiliation(s)
- Gayatri Muthukrishnan
- Department of Bioengineering, The Pennsylvania State University, 205 Hallowell Building, University Park, PA 16802, USA
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