ATP Reorients the Neck Linker of Kinesin in Two Sequential Steps
Open accessAbstract
Recent models of the kinesin mechanochemical cycle provide some conflicting information on how the neck linker contributes to movement. Some spectroscopic approaches suggest a nucleotide-induced order-to-disorder transition in the neck linker. However, cryoelectron microscopic imaging suggests instead that nucleotide alters the orientation of the neck linker when docked on the microtubule surface. Furthermore, since these studies utilized transition state or non-hydrolyzable nucleotide analogs, it is not clear at what point in the ATPase cycle this reorientation of the neck linker occurs. We have addressed this issue by developing a strategy to examine the effect of nucleotide on the orientation of the neck linker based on the technique of fluorescence resonance energy transfer. Transient kinetic studies utilizing this approach support a model in which ATP binding leads to two sequential isomerizations, the second of which reorients the neck linker in relation to the microtubule surface.
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Previous studies with K349 show that the rate of docking of the neck linker places an upper limit on kh of ∼800 s−1.
“our previous studies with K349 show that the rate of docking of the neck linker places an upper limit on kh of ∼800 s−1 (23”
From Stepping and Stretching (2003) · cites this paper as [23]
The Discussion (page unavailable) proposes that a neck-linker reorientation step is rate-limiting for ATP hydrolysis, supporting the claimed relationship in qualified form. But the Results give a reorientation rate of 367 ± 51 s−1 at 10 °C, and the passages found do not establish an upper limit on kh of approximately 800 s−1. (LLM, conf=0.84)
Experimental — accuracy not yet measuredKinetic characterizations of K349 and K413 show that only one step in the mechanochemical cycle is affected: the rate of ADP-induced dissociation, which is accelerated 19-fold compared with wild-type.
“Our kinetic characterizations of K349 and K413 has shown that only one step in the mechanochemical cycle is affected (18, 23, and this work). This is the rate of ADP-induced dissociation, which is accelerated 19-fold compared with wild-type (Fig. 4).”
From Stepping and Stretching (2003) · cites this paper as [23]
The Results (page unavailable) measure ADP-induced dissociation in a construct derived from K349. They do not establish that this is the only affected step in K349 and K413, or report a 19-fold acceleration relative to wild-type. (LLM, conf=0.82)
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Cited by
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Walking the walk: how kinesin and dynein coordinate their steps
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“Evidence is accumulating for a neck-linker conformational change [23–26], but how necklinker docking is affected by load and the precise role of neck-linker conformational changes in head–head coordination are still open questions.”
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“Although evidence for this conformational change has been obtained (Rosenfeld et al., 2001; Skiniotis et al., 2003; Tomishige et al., 2006), it still remains controversial whether the neck linker docking powers kinesin movement (Schief and Howard, 2001; Block, 2007; Carter and Cross, 2005).”
BackgroundThe kinetic mechanism of kinesin.
Cross, R. (2004) · TIBS -Trends in Biochemical Sciences. Regular ed · doi:10.1016/j.tibs.2004.04.010 · Cited by 204 · see citing works
Rosenfeld, S. S., Fordyce, P. M., Jefferson, G. M., King, P. H., & Block, S. M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300849200 · Cited by 188 · see citing works
Self-citationExamining kinesin processivity within a general gating framework
Andreasson, J. O. L., Milic, B., Chen, G.-Y., Guydosh, N. R., Hancock, W. O., & Block, S. M. (2015) · eLife · doi:10.7554/elife.07403 · Cited by 197 · see citing works
“DOI: 10.7554/eLife.07403 1 of 22 NL docking (Rice et al., 1999; Schnitzer et al., 2000; Rosenfeld et al., 2001; Asenjo et al., 2006; Tomishige et al., 2006; Khalil et al., 2008; Sindelar and Downing, 2010; Clancy et al., 2011).”
InfluentialForce Generation in Kinesin Hinges on Cover-Neck Bundle Formation
Hwang, W., Lang, M. J., & Karplus, M. (2008) · Structure · doi:10.1016/j.str.2007.11.008 · Cited by 161 · see citing works
“The mechanism that involves a power stroke followed by a diffusive search is consistent with two substeps observed in experiments, a fast (cid:2) 25 m s step followed by a slower one (Nish-iyama et al., 2001; Rosenfeld et al., 2001).”
MINFLUX dissects the unimpeded walking of kinesin-1
Wirth, J. O., Scheiderer, L., Engelhardt, T., Engelhardt, J., Matthias, J., & Hell, S. W. (2023) · Science · doi:10.1126/science.ade2650 · Cited by 186 · see citing works
“Upon binding of ATP to the microtubule-bound leading head (31), the neck linker of the leading head partially docks (41, 42), moving the unbound head towards its next binding site and rotating the coiled-coil domain around its axis.”
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Thermodynamic properties of the kinesin neck-region docking to the catalytic core.
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“Immediately adjacent to the catalytic core is the neck linker, a ;15 amino acid segment which has been shown to be critical for force generation and directionality (Case et al., 1997, 2000; Henningsen and Schliwa, 1997; Rice et al., 1999; Rosenfeld et al., 2001).”
BackgroundThe structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement
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Backsteps induced by nucleotide analogs suggest the front head of kinesin is gated by strain
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Kinesin processivity is gated by phosphate release
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Mickolajczyk, K. J., Deffenbaugh, N. C., Arroyo, J. O., Andrecka, J., Kukura, P., & Hancock, W. O. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517638112 · Cited by 120 · see citing works
“Our results are most consistent with a two-step model of the powerstroke in which ATP binding only partially docks the NL and hydrolysis completes docking to accelerate tethered head attachment (19, 41, 48).”
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“Wehad previously shown thatMD/MTstoichiometric ratios from 1:4 to 1:15 gave similar kinetic results (31, 48).”
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Docking and Rolling, a Model of How the Mitotic Motor Eg5 Works
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BackgroundLoop L5 Acts as a Conformational Latch in the Mitotic Kinesin Eg5*
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Self-citationKinesin’s Front Head Is Gated by the Backward Orientation of Its Neck Linker
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“Studies of kinesin motility have revealed that interhead coordination is mediated through neck linker (NL), a 14 amino acid peptide that connects each of the kinesin heads to the common stalk (Asenjo et al., 2006; Block, 2007; Rosenfeld et al., 2001; Sindelar and Downing, 2010).”
Measuring Kinesin's First Step
Rosenfeld, S. S., Xing, J., Jefferson, G. M., Cheung, H. C., & King, P. H. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205261200 · Cited by 54 · see citing works
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“Rosenfeld and coworkers observed the fluorescence of probes placed on the neck linker, showing that the transition involved two steps, and providing further evidence for this model (Rosenfeld et al., 2001, 2002).”
Pathway of ATP hydrolysis by monomeric kinesin Eg5.
Cochran, J. C., Krzysiak, T. C., & Gilbert, S. (2006) · Biochemistry · doi:10.1021/bi0608562 · Cited by 50 · see citing works
The Loop 5 Element Structurally and Kinetically Coordinates Dimers of the Human Kinesin-5, Eg5
Waitzman, J. S., Larson, A. G., Cochran, J. C., Naber, N. I., Cooke, R., Kull, F. J., Pate, E., & Rice, S. E. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.10.032 · Cited by 39 · see citing works
The structural kinetics of switch-1 and the neck linker explain the functions of kinesin-1 and Eg5
Muretta, J. M., Jun, Y., Gross, S. P., Major, J. A., Thomas, D. D., & Rosenfeld, S. S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512305112 · Cited by 37 · see citing works
“For both constructs, the rates of NL docking and MT dissociation are similar to each other and are ∼four- to sevenfold slower than that for switch-1 opening (8, 16), suggesting that ADP-induced changes in MT affinity occur hand-in-hand with corresponding changes in the state of the NL but not with the state of switch-…”
BackgroundMethodResultInfluentialSelf-citationKinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines
Cochran, J. C. (2015) · Biophysical Reviews · doi:10.1007/s12551-014-0150-6 · Cited by 38 · see citing works
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Mechanical Design of Translocating Motor Proteins
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“Transitions between one or more substeps can be observed using methods such as stopped flow [50, 55], by tracking donor-acceptor distances in fluorescence resonance energy transfer (FRET) [62, 63], and polarization states of fluorophore-labeled segments of the motor [21, 72].”
BackgroundNew Insights into the Mechanism of Force Generation by Kinesin-5 Molecular Motors
Goulet, A., & Moores, C. A. (2013) · International review of cytology · doi:10.1016/b978-0-12-407696-9.00008-7 · Cited by 25 · see citing works
A Kinesin Switch I Arginine to Lysine Mutation Rescues Microtubule Function*
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“Snapshots” of Ispinesib-induced Conformational Changes in the Mitotic Kinesin Eg5
Kaan, H. Y. K., Major, J. A., Tkocz, K., Kozielski, F., & Rosenfeld, S. S. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.462648 · Cited by 30 · see citing works
“We had previously reported (21) that the limiting anisotropies for fluorescent probes on the Eg5 NL are 0.”
BackgroundSelf-citationThe ATPase Cycle of the Mitotic Motor CENP-E*
Rosenfeld, S., van Duffelen, M., Behnke-Parks, W. M., Beadle, C., Corrreia, J., & Xing, J. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.041210 · Cited by 27 · see citing works
Self-citationFractionation and Characterization of Kinesin II Species in Vertebrate Brain
Berezuk, M. A., & Schroer, T. (2004) · Traffic : the International Journal of Intracellular Transport · doi:10.1111/j.1398-9219.2004.00197.x · Cited by 27 · see citing works
“Parallel biophysical studies have provided insight into the mechanical (6–8) and structural (9,10) details of kinesin-based movement as well as the structural basis for motor polarity (11).”
BackgroundProcessivity of dimeric kinesin‐1 molecular motors
Guo, S., Shi, X., Wang, P., & Xie, P. (2018) · FEBS Open Bio · doi:10.1002/2211-5463.12486 · Cited by 29 · see citing works
Kinesin-2 motors: Kinetics and biophysics
Gilbert, S. P., Guzik-Lendrum, S., & Rayment, I. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.r117.001324 · Cited by 31 · see citing works
“The ATP-promoted isomerization has traditionally been viewed as representing the series of structural transitions that include neck linker docking and orientation of the active site residues around MgATP to form the intermediate poised for ATP hydrolysis (71, 93-95).”
BackgroundInsight into the chemomechanical coupling mechanism of kinesin molecular motors
Xie, P. (2021) · Communications in Theoretical Physics · doi:10.1088/1572-9494/abecd8 · Cited by 30 · see citing works
“The experimental data showed that ADP release is a non-rate-limiting step of the ATPase activity [ 57 ] and the rate of NL docking is much larger than the rate of ATP hydrolysis and Pi release [ 75 ] , implying k D ? k ( + ) and k NL ? k ( + ) .”
Theoretical Analysis of Dynamics of Kinesin Molecular Motors
Xie, P. (2020) · ACS Omega · doi:10.1021/acsomega.9b03738 · Cited by 31 · see citing works
Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin
Dutta, M., Diehl, M., Onuchic, J., & Jana, B. (2018) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1810622115 · Cited by 22 · see citing works
Molecular motors: not quite like clockwork
Amos, L. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-7518-3 · Cited by 24 · see citing works
Force dependence of unbinding rate of kinesin motor during its processive movement on microtubule
Guo, S., Shi, X., Wang, P., & Xie, P. (2019) · Biophysical Chemistry · doi:10.1016/j.bpc.2019.106216 · Cited by 24 · see citing works
Microtubule−Kinesin Interface Mutants Reveal a Site Critical for Communication
Klumpp, L. M., Brendza, K. M., Gatial, J. E., Hoenger, A., Saxton, W. M., & Gilbert, S. P. (2004) · Biochemistry · doi:10.1021/bi035830e · Cited by 20 · see citing works
“An isomerization at 200-300 s-1 has also been detected by mantATP binding kinetics (23), by fluorescence resonance energy transfer (41), and by molecular force clamp (42).”
BackgroundThese motors were made for walking
Hunter, B., & Allingham, J. S. (2020) · Protein Science · doi:10.1002/pro.3895 · Cited by 21 · see citing works
“These conformational changes expose a hydrophobic patch along the side of the motor domain that allows the neck-linker element to partially dock.(17,18) In dimeric transport kinesins (e.”
BackgroundXie, P., Guo, S., & Chen, H. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20194911 · Cited by 19 · see citing works
“Since in the INT state with the MT-head bound with ATP (Figure 2b) its NL docks rapidly [55], we approximate that i .”
BackgroundGuo, S., Wang, W.-C., Wang, P., & Xie, P. (2019) · Molecules · doi:10.3390/molecules24020287 · Cited by 18 · see citing works
Kinesin-2 KIF3AB Exhibits Novel ATPase Characteristics*
Albracht, C., Rank, K. C., Obrzut, S., Rayment, I., & Gilbert, S. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.583914 · Cited by 17 · see citing works
Mechanisms by Which Kinesin-5 Motors Perform Their Multiple Intracellular Functions
Pandey, H., Popov, M., Goldstein-Levitin, A., & Gheber, L. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22126420 · Cited by 24 · see citing works
“In contrast to kinesin-1, where prior to ATP binding the neck linker is disordered [77,88,89], the kinesin-5 neck linker is ordered and points to the minus-end of the MTs [79,90–93].”
BackgroundFrontiers in Protein Structure, Function, and Dynamics
Tripathi, T. (2020) · doi:10.1007/978-981-15-5530-5 · Cited by 15
“In kinesin-1, before ATP binding the NL is more flexible or disordered (Rice et al. 1999; Sindelar and Downing 2010; Rosenfeld et al. 2001) and in Kinesin-5, the NL is structured or more ordered and points toward the minus-end of the MTs (Rosenfeld et al. 2005; Turner et al. 2001; Larson et al.…”
BackgroundModulation of the Kinesin ATPase Cycle by Neck Linker Docking and Microtubule Binding
Zhao, P. Y., Kull, F. J., & Cochran, J. C. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.123067 · Cited by 19 · see citing works
Run length distribution of dimerized kinesin-3 molecular motors: comparison with dimeric kinesin-1
Guo, S.-K., Shi, X.-X., Wang, P.-Y., & Xie, P. (2019) · Scientific Reports · doi:10.1038/s41598-019-53550-2 · Cited by 13 · see citing works
Effect of Kinesin-5 Tail Domain on Motor Dynamics for Antiparallel Microtubule Sliding
Liu, Y.-Y., Wang, Y., Wang, P.-Y., & Xie, P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22157857 · Cited by 10 · see citing works
Spatial relationship between heads of dimeric Ncd in the presence of nucleotides and microtubules.
Hajdo, L., Skowronek, K., & Kasprzak, A. A. (2004) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2003.11.009 · Cited by 9 · see citing works
A common chemomechanical coupling model for orphan and conventional kinesin molecular motors.
Guo, S.-K., & Xie, P. (2020) · Biophysical Chemistry · doi:10.1016/j.bpc.2020.106427 · Cited by 8 · see citing works
Effect of the Neck Linker on Processive Stepping of Kinesin Motor
Xie, P. (2023) · Biophysica · doi:10.3390/biophysica3010004 · Cited by 11 · see citing works
Molecular Mechanism of Processive Stepping of Kinesin Motors
Xie, P. (2021) · Symmetry · doi:10.3390/sym13101799 · Cited by 8 · see citing works
Xie, P. (2021) · Biophysical Chemistry · doi:10.1016/j.bpc.2021.106548 · Cited by 7 · see citing works
Modeling Study of the Dynamics of Kinesin-14 Molecular Motors
Xie, P. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c05820 · Cited by 8 · see citing works
A model of processive walking and slipping of kinesin-8 molecular motors
Xie, P. (2021) · Scientific Reports · doi:10.1038/s41598-021-87532-0 · Cited by 8 · see citing works
Xie, P. (2025) · Biomolecules · doi:10.3390/biom15101453 · Cited by 6 · see citing works
“…[13,16–21], the dynamics of the motor have also been investigated in great detail by using various methods, including biochemical measurement [22–25], single molecule imaging [26–29], single molecule optical trapping [14,15,30–39], coarse-grained and atomistic molecular dynamics (AMD)…”
4.17 Kinesin Structure and Biochemistry
Gilbert, S. P., & Sardar, H. (2012) · Elsevier eBooks · doi:10.1016/b978-0-12-374920-8.00421-5 · Cited by 6 · see citing works
Xie, P. (2025) · Journal of Biological Physics · doi:10.1007/s10867-025-09671-z · Cited by 5 · see citing works
“The value of k NL = 1500 s −1 is the same as that determined before [27, 47] and is consistent with the existing biochemical data [48].”
Goldstein-Levitin, A., Pandey, H., Allhuzaeel, K., Kass, I., & Gheber, L. (2021) · eLife · doi:10.7554/elife.71036 · Cited by 3 · see citing works
Atherton, J., Chegkazi, M. S., Leusciatti, M., Palma, M. D., Peirano, E., Pozzer, L. S., Meli, M., Pasqualato, S., Foran, T., Morra, G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61498-3 · Cited by 9 · see citing works
“This has been suggested on the basisof FRET measurements to anticipate and accelerate ADP release 25 .”
Shi, X., Liu, Y., & Xie, P. (2025) · Biomolecules · doi:10.3390/biom15050717 · Cited by 5 · see citing works
“To be consistent with prior biochemical data [33,37,38], we take k D = 300 s − 1 and k NL = 1500 s − 1 in this section, as achieved before for kinesin-1 [31], giving β = k NL / k D = 5.”
InfluentialEffects of Gold Nanoparticles on the Stepping Trajectories of Kinesin
Hasnain, S., Mugnai, M., & Thirumalai, D. (2020) · bioRxiv · doi:10.1101/2020.02.05.935791 · Cited by 3
A Model for Chemomechanical Coupling of Kinesin-3 Motor
Xie, P. (2024) · Cellular and Molecular Bioengineering · doi:10.1007/s12195-024-00795-1 · Cited by 5 · see citing works
“This value of k NL = 590 s −1 for the kinesin-3 KIF1A is smaller than that (> 800 s −1 ) for the kinesin-1 [43] but is larger than that (about 70 s −1 ) for the kinesin-5 Eg5 [44] measured experimentally before.”
A model of tubulin removal and exchange caused by kinesin motor walking on microtubule lattices.
Xie, P. (2025) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2025.112088 · Cited by 1 · see citing works
Effect of small molecular crowders on dynamics of kinesin molecular motors
Xie, P. (2023) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2023.111685 · Cited by 2 · see citing works
Origin of fast backward steps and detachment of kinesin motor under backward load
Wang, J., Shi, X.-X., Liu, Y.-R., Wang, P., & Xie, P. (2026) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2026.112575
Flexibility of the neck-linker during docking is pivotal for function of bi-directional kinesin
Goldstein-Levitin, A., Allhuzaeel, K., Pandey, H., & Gheber, L. (2020) · bioRxiv · doi:10.1101/2020.05.27.118430
Molecular Motors: Subdomain Dynamics and Mechanochemistry
Singh, M., & Singh, S. K. (2020) · Springer eBooks · doi:10.1007/978-981-15-5530-5_15 · Cited by 1 · see citing works
Measurement of Force-Dependent Release Rates of Cytoskeletal Motors
Can, S., & Yıldız, A. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6421-5_18
Motor proteins of the kinesin superfamily
Hackney, D. D. (2003) · The Enzymes · doi:10.1016/s1874-6047(04)80004-0 · Cited by 1 · see citing works
- Authors
- Rosenfeld, S. S., Jefferson, G. M., & King, P. H.
- Affiliations
- University of Alabama at Birmingham (US)
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2001-10
- Volume
- 276
- Issue
- 43
- Pages
- 40167-40174
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2062419779
- Cited by
- 84
- References
- 26
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 2 · 2023: 4 · 2022: 1 · 2021: 9 · 2020: 4 · 2019: 5 · 2018: 4 · 2016: 1 · 2015: 5 · 2014: 3 · 2013: 2 · 2012: 4
- FWCI
- 1.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5p01ns034856-05)
- National Institute of Neurological Disorders and Stroke (NS 34856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Keywords
- kinesin, neck linker, ATP binding, mechanochemical cycle, isomerization, ATPase cycle, fluorescence resonance energy transfer, transient kinetic analysis, order-disorder transition
- MeSH terms
- Adenosine Triphosphate, Dansyl Compounds, Energy Transfer, Microtubules, Models, Molecular, Models, Theoretical, Protein Conformation, Spectrometry, Fluorescence, Tryptophan, Tubulin, Kinesins, Dimerization, Molecular Motor Proteins
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