The spatiotemporal regulation of organelle positioning is critical for proper cellular function. The movement of organelles and other intracellular cargo is largely driven by the cytoskeletal motor proteins (Hirokawa et al., 2009; Reck-Peterson et al., 2018). Among them, conventional kinesin-1 is the major anterograde motor in cells that is essential for transporting mitochondria (Schwarz, 2013), ER, and Golgi-derived vesicles (Hirokawa et al., 2009) to microtubule plus ends, typically located at the cell periphery.

Kinesin-1 can exist in homodimeric and heterotetrameric forms. Kinesin-1 in the dimeric form is composed of two identical kinesin heavy chains (KHC) that can be divided into three parts: motor, stalk, and tail domains (Figure 1A; Hirokawa et al., 1989). The N-terminal motor domain functions as an engine that converts the chemical energy from ATP to the mechanical force to power kinesin walking along microtubules (Jon Kull et al., 1996). Downstream of the motor domain, a series of coiled-coils dimerize to form the stalk. The regulatory tail at the C-terminus is largely disordered (Seeger et al., 2012). In the heterotetramer form, two copies of the kinesin light chain (KLC) associate with the KHC stalk through its predicted N-terminal coiled-coil domain (Diefenbach et al., 1998; Verhey et al., 1998). The C-terminus of KLC consists of the TPR domain, which functions as a cargo binding platform to link kinesin-1 to various cellular cargo (Cockburn et al., 2018; Pernigo et al., 2013).

Figure 1 with 3 supplements see all

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Figure 1—source data 1

XL-MS data for KIF5B.

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Figure 1—source data 2

XL-MS data for KIF5C.

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Human kinesin-1 contains various isoforms, and dysfunction of them causes diseases. In humans, KHC is encoded by three genes: KIF5A, KIF5B, and KIF5C, which share a very similar motor domain and stalk with minor differences in the C-terminal tail, whereas KLC has four isoforms (KLC1–4). These isoforms showed distinct tissue expression patterns. KIF5B and KLC2 are ubiquitously expressed, whereas KIF5A, KIF5C, and KLC1 are neuron-enriched (Kanai et al., 2000; Rahman et al., 1998). Mutations in KIF5A and KIF5C result in defects in axonal transport and thus can cause neurodevelopmental and neurodegenerative pathologies (Crimella et al., 2012; Nicolas et al., 2018; Poirier et al., 2013; Willemsen et al., 2014).

When not bound to cargo, kinesin-1 exists in an autoinhibited state. Several early studies have proposed a model where the motility of KHC is regulated through the direct interaction between the motor and tail domains (Coy et al., 1999; Dietrich et al., 2008; Friedman and Vale, 1999; Stock et al., 1999). This interaction is facilitated by the folding of KHC at a break between CC2 and CC3, called ‘hinge,’ which positions an isoleucine–alanine–lysine (IAK) motif in the tail domain to bind in between the motor domains (Figure 1A; Kaan et al., 2011). The association between tail and motor domains restricts the relative movement of the motor domains, inhibiting KHC’s enzymatic and microtubule-binding activities (Hackney and Stock, 2000; Kaan et al., 2011).

Despite this prevailing model, recent data suggest that mutating the IAK motif or deleting the hinge does not increase the processivity of kinesin-1, making the current model controversial. Mutations in the IAK motif have been reported to disrupt kinesin-1 autoinhibition in cells, enzymatic assays, and single-molecule assays performed with cell lysates (Cai et al., 2007a; Kelliher et al., 2018; Seiler et al., 2000). However, recent in vitro single-molecule measurement using purified protein suggests that mutations in IAK did not result in a substantial increase in processive motility but increased the landing rate (Chiba et al., 2022). Similarly, deletion of the hinge was traditionally demonstrated to increase the ATPase activity and frequency of processive KHC dimer motility (Coy et al., 1999; Friedman and Vale, 1999; Kelliher et al., 2018), while recent data suggest that KHC without the hinge tends to oligomerize and shows little increase in processivity (Chiba et al., 2022). The contradictory data regarding the IAK motif and hinge indicate that kinesin-1 autoinhibition involves more than these two elements.

Kinesin-1 motility is further regulated by KLCs, where the incorporation of KLCs into heterotetrameric kinesin-1 motors inhibits microtubule binding in vitro and in vivo (Verhey et al., 1998). For instance, cellular FRET experiments implied that KLC keeps kinesin-1 in the folded state but separates the motor domain further apart (Cai et al., 2007a). Recently, in vitro single-molecule assays further demonstrated that the presence of KLCs suppresses the kinesin-1 motility (Chiba et al., 2022). However, it remains unclear whether KLCs stabilize the inhibited state of the heavy chain or promote the formation of a new structural state. Furthermore, how cargo binding to KLCs activates kinesin-1 is still an open question.

Microtubule-associated proteins function as an additional layer to regulate motor protein activity. For instance, MAP7 increases the landing rate and processivity of kinesin-1 by binding to coiled-coil 2 and recruiting kinesin-1 onto microtubules (Ferro et al., 2022; Hooikaas et al., 2019; Monroy et al., 2018). MAP7 contains an N-terminal microtubule-binding domain and a C-terminal kinesin-binding domain connected by an unstructured linker (Hooikaas et al., 2019). Interestingly, the MAP7 kinesin binding domain alone is sufficient to promote the landing rate and processivity of kinesin-1 (Hooikaas et al., 2019), suggesting that binding MAP7 to CC2 disrupts the autoinhibited state. Furthermore, truncated kinesin-1 homodimer KIF5B(1–560) that lacks the hinge and downstream elements can be further activated by MAP7 kinesin binding domain (Hooikaas et al., 2019), suggesting that autoinhibition is still present in KIF5B(1–560), which the current model can not explain.

Recently, a study combining AlphaFold structure prediction and negative staining EM proposed a new hinge position to allow the stalk to fold on itself (Weijman et al., 2022). While this study is an important prediction of KHC bends, there is minimal data to provide an overall description of how kinesin-1 adopts a folded, inhibited state. Moreover, this study did not address how the folded conformation relates to motor domain inhibition.

Here, we combined crosslinking mass spectrometry (XL-MS), negative stain electron microscopy (EM), and AlphaFold structure prediction to probe the conformation of autoinhibited full-length kinesin-1 homodimer and kinesin-1 heterotetramer. First, we performed structural studies with negative stain EM to characterize the folded conformation of kinesin-1 homodimers and heterotetramers. Both biochemical and structural analysis showed that kinesin-1 exists in folded and extended conformations. To determine the folding pattern of kinesin-1, we combined protein structure prediction using AlphaFold and XL-MS to derive an integrative molecular model of the autoinhibited full-length kinesin-1. For the kinesin-1 homodimer, we found that it does not simply fold in half via the originally proposed hinge but rather adopts a hierarchical folding pattern. A newly identified hinge in coiled-coil 3 allows the stalk to fold back on itself. The motor domain also scaffolds back to dock onto coiled-coil 2, positioning it in a head-to-tail conformation. XL-MS analysis of the heterotetramer revealed that the KLC does not change the folding pattern of the heavy chain, indicating that the light chain does not promote a new structural state but stabilizes the inhibited state. We validated our proposed autoinhibition model via mutagenesis studies to show that disruption of multiple regions is required to fully activate the full-length kinesin-1. We demonstrate that autoinhibition requires more interactions than the inhibitory tail peptide, providing the first comprehensive explanation of autoinhibition. Our model offers a conceptual framework for understanding how activation factors such as MAP7 and cargo adaptors relieve autoinhibition to promote full activation.

Our integrative modeling approach provides the first comprehensive description of the kinesin-1 autoinhibition mechanism (Figure 7). Overall, our results point to hierarchical intramolecular interactions that generate a folded autoinhibited state of kinesin-1, and several important findings can be highlighted.

Figure 7

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First, kinesin-1 does not simply fold in half via the originally proposed hinge between the CC2 and CC3a (Coy et al., 1999; Friedman and Vale, 1999). Our results demonstrate that this previously proposed hinge is instead a highly structured region that adopts a short antiparallel coiled-coil in both the dimeric (KIF5B and KIF5C) and tetrameric (KIF5B/C+KLC1) states (Figure 2—figure supplement 1 and Figure 4—figure supplement 1). This finding explains why deletion of the hinge did not result in an extended conformation for Drosophila KHC (Coy et al., 1999) and why removal of the hinge resulted in an only a partial increase in kinesin-1 activity (Chiba et al., 2022; Friedman and Vale, 1999; Kelliher et al., 2018). Our results also demonstrate that the folding of kinesin-1 depends on a short (~4 aa) break in CC3, which serves as a hinge that allows CC3b and CC4 to interact with CC2 and CC3a. Our results are consistent with and extend the work of Weijman et al., 2022. Surprisingly, mutation of this hinge (called the elbow by Weijman et al., 2022) to generate an extended coiled-coil across CC3 did not fully relieve autoinhibition in single-molecule assays. We interpret this result to mean that other regions of KIF5B can generate breaks in the coiled-coil stalk region that enable intramolecular interactions between the motor domain, stalk, and tail.

Second, we identified a novel role for CC2 in the autoinhibition of the two motor domains. In the folded state of the full-length KIF5B model, the two motor domains fold back, and one of them docks on top of CC2 in a manner that blocks the microtubule-binding interface of the motor domain. Positioning of one motor domain along CC2 also enables the C-terminus of CC4 and the tail to be positioned in between the two motor heads and contribute to autoinhibition. In the context of the truncated (1–565) protein, the motor-CC2 interaction results in a protein that, while active in single-molecule motility assays, is still inhibited when compared to the minimally dimeric construct (1–420).

Third, we confirm and extend the role of the tail domain, particularly the IAK motif, in kinesin-1 autoinhibition. Early studies suggested that the IAK motif plays an important role in autoinhibition based on truncations of the KHC from the C-terminus and a tail-bound motor domain structure (Hackney and Stock, 2000; Kaan et al., 2011; Stock et al., 1999). More recent work, however, showed that mutating IAK to AAA did not cause a substantial increase in processive motility but instead increased the landing rate (Chiba et al., 2022). In our hands, mutation of the IAK region resulted in only a partial increase of kinesin-1 activity for Drosophila KHC (Kelliher et al., 2018) and human KIF5B in cell lysate (Figure 5). Furthermore, KIF5B with IAK changed to AAA still adopts a folded conformation under EM and XL-MS (Figure 5—figure supplement 2), suggesting that the removal of IAK alone is insufficient to open up kinesin-1. Since our purified IAK mutant has mScarlet protein at the C-terminus, we observed an additional globular density in between the motor domains (Figure 5—figure supplement 2B), indicating that the regulatory tail is still in proximity to the motor domain in the absence of IAK motif.

Interestingly, we observed that deleting the whole tail (constructs 1–890 and 1–909) can achieve a higher landing rate than simply mutating the IAK residues, but the tail deletions showed lower dwell times (Figure 5B and C, Figure 5—figure supplement 1A and B ) and increased velocities (Figure 5—figure supplement 1C). We believe the tail functions as a whole element to regulate kinesin-1 activity. It may stabilize the autoinhibited state of kinesin-1 and reduce the off rate when kinesin-1 walks along microtubules. In our model, the tail domain should lie very close to the motor domain as its upstream CC4 is crosslinked to the motor domains (Figure 2C). However, since the tail region of kinesin-1 lacks enough lysine residues and is disordered, we could not observe it via EM and XL-MS, and thus cannot comment on the conformation of the tail and location of IAK motif in the autoinhibited state.

Fourth, the addition of KLC did not change the folding pattern of the heavy chain. From this, we propose that the role of KLCs is to stabilize the folded state of the heavy chain, consistent with previous work (Chiba et al., 2022; Verhey et al., 1998). Compared to the kinesin-1 homodimer, the addition of the light chain pushes CC4 closer to the motor domain (Figure 4B), which may facilitate its insertion in between the motor domain. This finding is consistent with our previous work showing that the addition of KLC results in a lower FRET efficiency (larger distance) between the two motor domains (Cai et al., 2007a) and that the N-terminal coiled-coil region of KLC, not the TPR domain, is required for driving KHC further into the autoinhibited state (Chiba et al., 2022; Verhey et al., 1998).

Our model of autoinhibition provides a framework to propose the mechanism of kinesin-1 activation by cargoes and MAPs (Figure 7). Kinesin-1 binding partners such as JIP3 (Sun et al., 2011), TRAK1/2 (Canty et al., 2021; Fenton et al., 2021; Henrichs et al., 2020), JIP1 (Fu and Holzbaur, 2013), and HAP1 (Twelvetrees et al., 2019) increase kinesin-1 dimer motility in vitro. Here, we selected TRAK1 as our target and further map the TRAK1 binding site on kinesin-1 to be in between the CC3b and CC4 (Figure 6E), which overlaps with the KLC binding site, suggesting the incompatibility for simultaneous binding. The association of TRAK1 between CC3b and CC4 may induce a conformational change to release CC4 from motor domains, thus opening the folding within the stalk, as suggested by the decreased number of crosslinks within kinesin-1 after binding to TRAK1 (Figure 6E). Besides activating kinesin-1, TRAK1 also serves as a cargo adaptor for the dynein motor (Canty et al., 2021). However, the relationship between the kinesin-1 and dynein binding sites is less well understood. Here, after examining the XL-MS data, we realized that the kinesin-1 binding site on TRAK1 is in the upstream region of the CC1 box with only a little overlap with the CC1 box (Figure 6E). Given that the dynein–dynactin complex should interact with the downstream of the CC1 box (Canty et al., 2021; Reck-Peterson et al., 2018), our XL-MS data suggest that there are separate binding sites for kinesin-1 and dynein on TRAK1.

The mechanism of kinesin-1 heterotetramer activation needs further investigation. The TPR domain in KLC functions as a cargo binding platform by binding partner proteins such as Nesprin4 (Roux et al., 2009; Wilson and Holzbaur, 2015), SKIP (Pernigo et al., 2013), and JIP1/3 (Pernigo et al., 2018; Verhey et al., 2001; Figure 7). All these cargoes contain a W-acidic or Y-acidic motif to mediate cargo recognition by KLCs (Cross and Dodding, 2019). In cellular assays, a small molecule that mimics the TPR-W-acidic interaction can activate kinesin-1 (Randall et al., 2017), and attachment of the W-acidic motif to intracellular cargo can result in kinesin-dependent cargo displacement (Kawano et al., 2012). However, in microtubule binding and single-molecule motility assays, binding of the KLC partner proteins JIP1 and SKIP1 was insufficient to activate the kinesin-1 heterotetramer, whereas binding of Nesprin4 could activate when present at saturating concentrations (Blasius et al., 2007; Chiba et al., 2022). In our model, we placed one TPR domain near the CC2 and the other on top of the motor domain (Figure 4D and E), while we also noticed that crosslinked pairs between TPR and KHC are greater than the maximum distance allowed for the BS3 crosslinkers. We propose that cargo binding to TPR may induce a conformational change in KLC that loosens the folding of KHC, the full activation still needs other factors, such as binding a kinesin-1 partner protein (Blasius et al., 2007). High-resolution structures of inhibited kinesin-1 heterotetramer are needed for understanding the detailed molecular mechanism of kinesin-1 inhibition and activation.

Full activation of kinesin-1 for cargo transport appears to require not only cargo adaptor proteins but also microtubule-associated factors such as MAP7 (Figure 7). In cells, MAP7 and its Drosophila homolog ensconsin promote kinesin-1’s microtubule association and cargo transport (Barlan et al., 2013; Chaudhary et al., 2019; Gallaud et al., 2014; Metzger et al., 2012; Sung et al., 2008; Tymanskyj et al., 2018). Using in vitro assays, addition of MAP7 directly recruited kinesin-1 to microtubules and can thereby promote the full activation of TRAK1/2-bound kinesin-1 dimer (Canty et al., 2021) and Nesprin4-bound kinesin-1 heterotetramer (Chiba et al., 2022). Based on our hierarchical folding model for kinesin-1, we suggest that MAP7 facilitates the activation of folded kinesin-1 by removing the inhibitory effects of CC2 on the motor domain. This hypothesis is supported by the findings that (i) MAP7 binds residues 418–526, which span CC2, of KHC (Hooikaas et al., 2019), and (ii) MAP7 can increase the motility of KIF5B(1–560) (Hooikaas et al., 2019), which remains in a partly inhibited state (Figure 5—figure supplement 1D). MAP7’s ability to promote kinesin-1 activation is likely also facilitated by its ability to bind to the microtubules through its N-terminal microtubule-binding domain (Hooikaas et al., 2019).

In summary, our work combined AlphaFold structure prediction, XL-MS, and EM to obtain a comprehensive description of the autoinhibition mechanism of kinesin-1. We revised the previous model by showing that autoinhibited kinesin-1 adopts a hierarchical folding pattern, where multilayer intramolecular interactions are needed to promote kinesin-1 fold into the inhibited state. The activation of kinesin-1 thus required multiple protein partners to release the intramolecular folding. Given the limitations of our studies, we did realize that some crosslinked residues in our model have distances greater than the maximum distance allowed for the BS3 crosslinkers, especially for the crosslinked pairs between TPR and heavy chains, which suggest that our current model could be partially incorrect in specific positional details. Furthermore, we could not fully resolve the role of the tail and TPR domain in maintaining the autoinhibited state. High-resolution structures of kinesin-1 homodimers and heterotetramers are needed to completely understand the autoinhibition and activation mechanisms.

The raw data from our XL-MS experiments were processed using pLink software. The crosslinked peptide pairs identified were outputted from pLink and organized into tabular formats that delineate the positions of the crosslinks. We have included files as Source Data for our manuscript. We also attached protein sequence information for each XL-MS experiment. Below are the instructions on how to interpret the data. KIF5B: We have performed three XL-MS experiments on KIF5B and chose one of them (KIF5B_xlink_sites_1) as representative data to present in our manuscript (Figure 1F, Figure 2). The XL-MS results are: KIF5B_pLINK_1, 2, and 3 for identified crosslinked peptide pairs; KIF5B_xlink_sites_1, 2, and 3 for crosslinked positions in tabular format. KIF5C: We performed one XL-MS analysis on KIF5C and presented it in our manuscript (Figure 1—figure supplement 1F). The XL-MS results are: KIF5C_pLINK for identified crosslinked peptide pairs; KIF5C_xlink_sites for crosslinked positions in tabular format.KIF5B-KLC1: We have performed two XL-MS on KIF5B-KLC1 and selected one of them ( KIF5B-KLC1_xlink_sites_1) as representative data to show in our manuscript (Figure 3—figure supplement 1F and Figure 3—figure supplement 2C). The XL-MS results are: KIF5B-KLC1_pLINK_1 and 2 for identified crosslinked peptide pairs; KIF5B-KLC1_xlink_sites_1 and 2 for crosslinked positions in tabular format. KIF5C-KLC1: We have performed two XL-MS on KIF5C-KLC1 and selected one of them ( KIF5C-KLC1_xlink_sites_1) as representative data to show in our manuscript (Figure 3F, Figure 4, and Figure 3—figure supplement 2D). The XL-MS results are: KIF5C-KLC1_pLINK_1 and 2 for identified crosslinked peptide pairs; KIF5C-KLC1_xlink_sites_1 and 2 for crosslinked positions in tabular format. KIF5B (1-565): We performed one XL-MS on KIF5B (1-565) and presented it in our manuscript (Figure 5—figure supplement 1D). The XL-MS results are: KIF5B(1_565)_pLINK for identified crosslinked peptide pairs; KIF5B(1_565)_xlink_sites for crosslinked positions in tabular format.KIF5B_IAK_AAA: We performed one XL-MS on KIF5B (IAK/AAA) and presented it in our manuscript (Figure 5—figure supplement 2C). The XL-MS results are: KIF5B_IAK_AAA_pLINK for identified crosslinked peptide pairs; KIF5B_IAK_AAA_xlink_sites for crosslinked positions in tabular format. TRAK1-KIF5B: We conducted one XL-MS analysis on TRAK1-KIF5B and presented it in our manuscript (Figure 6E). The XL-MS results are: TRAK1_KIF5B_pLINK for identified crosslinked peptide pairs; TRAK1_KIF5B_xlink_sites for crosslinked positions in tabular format.

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Author details

1. Zhenyu Tan

   1. Department of Biophysics, University of Michigan, Ann Arbor, United States
   2. Life Sciences Institute, University of Michigan, Ann Arbor, United States

   Contribution

   Conceptualization, Formal analysis, Investigation, Methodology, Writing - original draft, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-6491-5806

2. Yang Yue

   Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, United States

   Contribution

   Formal analysis, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

3. Felipe Leprevost

   Department of Pathology, University of Michigan, Ann Arbor, United States

   Contribution

   Software, Formal analysis, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

4. Sarah Haynes

   Department of Pathology, University of Michigan, Ann Arbor, United States

   Contribution

   Software, Formal analysis, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

5. Venkatesha Basrur

   Department of Pathology, University of Michigan, Ann Arbor, United States

   Contribution

   Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

6. Alexey I Nesvizhskii

   1. Department of Pathology, University of Michigan, Ann Arbor, United States
   2. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States

   Contribution

   Supervision, Funding acquisition, Writing - review and editing

   Competing interests

   No competing interests declared

7. Kristen J Verhey

   Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, United States

   Contribution

   Conceptualization, Formal analysis, Supervision, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-9329-4981

8. Michael A Cianfrocco

   1. Life Sciences Institute, University of Michigan, Ann Arbor, United States
   2. Department of Biological Chemistry, University of Michigan, Ann Arbor, United States

   Contribution

   Conceptualization, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Investigation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing

   For correspondence

   mcianfro@umich.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-2067-4999

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