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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Nature. Author manuscript; available in PMC Oct 16, 2009.
Published in final edited form as:
PMCID: PMC2762700
NIHMSID: NIHMS4564

The structure of the myosin VI motor reveals the mechanism of directionality reversal

Abstract

We have solved a 2.4Å structure of a truncated version of the reverse direction myosin motor, myosin VI, that contains the motor domain and binding sites for two calmodulins. The structure reveals only minor differences in the motor domain as compared to plus-end directed myosins, with the exception of two unique inserts. The first insert is near the nucleotide-binding pocket, and alters the rates of nucleotide association and dissociation. The second unique insert forms an integral part of the myosin VI converter domain along with a calmodulin bound to a previously unseen binding motif within the insert. This serves to redirect the effective “lever arm” of myosin VI, which includes a second calmodulin bound to an “IQ motif,” towards the pointed (−) end of the actin filament. This repositioning largely accounts for the reverse directionality of this class of myosin motors. We propose a model incorporating a kinesin-like uncoupling/docking mechanism to fully explain the movements of myosin VI.

The myosin superfamily is composed of eighteen classes of molecular motor proteins, the vast majority of which traffic toward the barbed (+) end of actin filaments1. Class VI myosins were the first of the superfamily identified to traffic toward the pointed (−) end of the actin filament2. They function in a number of critical intracellular processes such as vesicular membrane traffic, cell migration, maintenance of stereocilia and mitosis36.

The current view of how myosin motors couple ATP hydrolysis and actin binding to movement is known as the lever arm hypothesis7. In essence the proposed mechanism is that nucleotide binding, hydrolysis and product release are all coupled to small movements within the myosin motor core. These movements are amplified and transmitted via a region that has been termed the “converter” domain to a lever arm consisting of a target helix and associated light chains/calmodulins. The lever arm further amplifies the motions of the converter domain into large directed movements. Consistent with the lever arm hypothesis, the stroke size has been shown to be proportional to the lever arm length8,9,10. In the absence of actin, ATP hydrolysis occurs, but product release is slow, thus trapping the lever arm in a primed or pre-powerstroke position. Binding to actin causes release of products, plus-end-directed movement of the lever arm, and force generation concomitant with formation of strong binding between myosin and actin.

Perhaps because of their reverse directionality, myosin VI motors have a number of additional unusual features. First, the motor domain itself contains two inserts that are unique within the myosin superfamily. The first is near the nucleotide-binding pocket and the second is between the converter and IQ motif. (These correspond to residues C278-A303 and P774-Y812, respectively and are called insert-1 and insert-2 hereafter.) Single molecules of dimeric myosin VI, like myosin V, are capable of taking multiple steps (processive movement) of 30–36nm via a hand-over-hand mechanism along actin filaments11,12. This large step size is surprising within the context of the lever arm hypothesis, in that myosin VI binds only two calmodulins per head13, while myosin V binds six. Furthermore, a construct truncated after the binding site for the second CaM (“IQ motif”) has a stroke (non-processive displacement upon an actin encounter) of 12nm, less than half of the step size of the two-headed molecule14. Thus the true composition of the myosin VI “lever arm” is unclear.

The fact that myosin VI binds two calmodulins per head was surprising since there is only one conventional calmodulin-binding site (IQ motif) per head13. It initially was postulated that the unique insert-2 forms part of the “converter” of myosin VI and redirects the lever arm (i.e. IQ-bound CaM) toward the minus end of an actin filament2. That hypothesis was brought into question by studies on chimeric molecules of myosin V and VI, in which removal or addition of insert-2 did not alter directionality15. The finding that insert-2 provides a second calmodulin binding site13 raises the possibility that its purpose could be to simply lengthen the lever arm. In order to gain insight into the function of these two unique inserts within the myosin VI motor, we determined the crystal structure of two fragments of myosin VI.

RESULTS

Nucleotide-free myosin VI displays partial closure of the actin-binding cleft

We co-expressed calmodulin with porcine myosin VI constructs coding for either the motor domain (containing inserts 1 and 2) alone (aa. 1-816; called hereafter MDins2) or the motor domain and the helical calmodulin-binding domain (“IQ” motif) (aa. 1-859; called hereafter MDins2IQ) in insect SF9 cells. Crystals were obtained in the absence of nucleotide and diffracted to 2.4Å and 2.9Å for the MDins2 and MDins2IQ constructs, respectively. The two refined structures obtained from different crystal forms superimpose very well with an r.m.s. deviation of 0.694Å for 787 Cα atoms of the motor domain (G4-Y812). These structures thus define the nucleotide-free state of myosin VI, which greatly differs from that found for plus-end myosin motors by the reversed-orientation of the lever arm (Fig. 1). The overall conformation of the myosin VI motor domain is however similar to that recently presented for myosin V16 and for the Dictyostelium discoideum myosin II motor in the absence of nucleotide17 : the twist of the central β-sheet in all these structures greatly differs from that found for the post-rigor (ATP-) and pre-powerstroke (ADP.Pi-) states of the motor16,17,18. The myosin V structure has been suggested to be in a “rigor-like” state, meaning that it is the state that myosin populates when bound to actin in the absence of nucleotide16,19. Several differences – which are minor in amplitude but not in significance – distinguishes the myosin VI and II17 nucleotide-free structures from the myosin V rigor-like state. The major cleft in the molecule that closes upon binding to actin is not completely closed in myosin VI, as it is for myosin V (Supplementary movie S1). Moreover, the set of interactions found between the nucleotide-binding elements in the rigor-like state18 are also not found in myosin VI, in relation with differences in the distortion of the central β-sheet (Supplementary movie S2). The kinetics of its interaction with actin20 also demonstrates that in the absence of nucleotide and actin, myosin VI does not populate the rigor-like state. Docking of the nucleotide-free myosin VI structure into reconstructions from electron microscopy images of the acto-myosin VI rigor complex2 confirms however that the state we crystallized is close to the conformation of myosin VI at the end of its powerstroke (Fig. 1a).

Figure 1
Crystal structure of nucleotide-free myosin VI. a, A ribbon diagram representation of the myosin VI structure highlights its two specific inserts, the four subdomains (N-terminal, U50kDa, L50kDa and Converter) of the motor domain and two connectors (relay ...

The role of insert-1 in modulating nucleotide association and dissociation

Myosin VI not only moves in the reverse direction, but has unusual kinetic properties. Most notable is the slow rate (40-fold slower than myosin V) of ATP-induced release of myosin VI from the actomyosin complex20,21. This is primarily due to a weak affinity for ATP, which is weaker than the affinity of either myosin VI or actomyosin VI for ADP (see Supplementary Table S1). The first of the two unique inserts in myosin VI (C278-A303) belongs to the U50kDa subdomain and is located close to the nucleotide binding site, near Switch I (Fig. 1, ,2a).2a). Switch I plays a critical role in binding both the Mg2+ ion and the γ-phosphate of ATP in the active site. It is now believed that sequential conformational rearrangements of switch I are essential to control nucleotide release and binding from the motor22,23. The location of insert-1 leads to the prediction that it may have evolved to provide unique kinetic characteristics that are potentially important for a reverse-directed motor.

Figure 2
Insert-1 modulates nucleotide binding and Switch I flexibility. a, Insert-1 is found at the surface of the U50kDa subdomain near the nucleotide-binding site. b, The same region is shown for myosin V which lacks this insert. Note the conformational change ...

To test the influence of insert-1 on the kinetics of this reverse-direction motor, we have engineered a myosin VI lacking insert-1 (ΔC278-A303) and measured the impact on the actomyosin ATPase activity and nucleotide binding and release. These results show that insert-1 has a critical role in slowing ADP-release and ATP-induced actomyosin dissociation (see data in Supplementary Table S1). Interestingly, the myosin VI structure reveals that the presence of insert-1 does not alter the conformation of switch I relative to the U50kDa subdomain, which is the same in all myosin states visualized to date (Fig. 2). In contrast, the small loop (G304-D313) that follows insert-1 is drastically re-positioned and strongly interacts with Switch I. This loop also protrudes within the nucleotide-binding pocket – resulting in reduction of nucleotide accessibility (Fig. 2). Modeling studies based on the myosin V structure show that when insert-1 is removed, this loop can adopt a conformation close to that adopted by equivalent residues in other myosins, reducing its interactions with Switch I (Fig. 2b). Restrictions in nucleotide binding pocket accessibility explain in large part why the ATP affinity (1/K1′) of actomyosin VI is weak (25mM). Insert-1 likely also influences mobility of switch I relative to the rest of the U50kDa subdomain, which would explain its influence on both ADP-release and ATP-induced dissociation of the motor from actin at saturating ATP concentrations (k+2′). (See supplementary data.)

The role of insert-2 in redirecting the lever arm

Functional studies of chimeric molecules between myosin V and VI were interpreted as evidence that the motor domain, rather than insert-2, provides the major determinants for directionality reversal15. The nucleotide-free myosin VI structure shows, however, that its motor domain is very similar to that of myosin V – including in the position of the converter, the specific subdomain designed to direct lever arm movement in myosin motors. The converter position is controlled by the specific conformation of two connectors – the relay and the SH1 helix (Fig. 1, 3a,b). Importantly, as found in all plus-end myosins, the set of hydrophobic interactions that maintain the relay and the converter closely linked to one another (in all states of the motor) are also conserved in myosin VI. However, there are sequence variations specific for myosin VI which are clustered in the interface between these two connectors (Supplementary Movie S3). Their effect in modulating the precise orientation of the converter is minimal in the nucleotide-free state of myosin VI, but they could play a critical role in other states of the cycle – such as the pre-powerstroke state.

Figure 3
Reorientation of the myosin VI lever arm by its unique converter. a, The proximal part of insert-2 (P774-W787 ; purple/grey) interacts on the surface of the converter, in particular with a loop whose sequence is highly variable among myosin classes, but ...

The truly unique and novel feature of the two myosin VI structures is the reversal of the lever arm direction by insert-2 (P774-Y812 ; Fig. 3). The proximal part of the insert (P774-W787) wraps around the converter, rather than emerging as a straight helix from the converter and the distal part of the insert (W787-Y812) forms a previously unseen calmodulin-binding motif (see Fig. 4). Both the insert and its associated 4Ca2+-calmodulin make specific interactions with the converter (many involving a variable loop (K719-P731) ; Fig. 3a). The net result of these interactions is that the IQ helix emerges approximately 120° from the position that the IQ helix would in any other myosin (Fig. 3b). This redirects the IQ helix and its bound calmodulin (which form a “lever arm”) toward the minus end of the actin filament (Fig. 1).

Figure 4
A new calmodulin binding motif that interacts strongly with 4Ca2+-CaM. a, The overall conformation and polarity of the insert-2/CaM complex (new 1-6-14 motif) is compared to those observed when CaM interacts with myosin light chain kinase (MLCK) (classic ...

Unique structural differences of the myosin VI converter are critical for its close interaction with insert-2 and thus the re-orientation of the lever arm. In particular, the orientation of the last helix of the myosin VI converter differs by about 19° from that found in plus-end myosins when the converters are superimposed (Fig. 3b). This helix is well anchored against the rest of the converter via several large hydrophobic side chains. It ends with a proline (P774) which favors a 90°-turn at the beginning of insert-2, that promotes its wrapping around the converter. The variable loop of the converter and the helix that follows create a small hydrophobic cavity in which small hydrophobic side chains of insert-2 fit (Fig. 3c). A break in the helix of insert-2 at position V784 further extends the surface of interaction with the converter (via W787 and L788) and also allows the calmodulin to be held by the distal part of this insert to interact with the converter – in particular via six salt bridges (Fig. 3d). In contrast, the helix remains straight between insert-2 and the IQ motif and the stiffness at the MD/lever arm junction in this myosin likely is similar to that found for other myosins. The functional converter of myosin VI that redirects the lever arm in the opposite direction in the rigor state thus is composed of the normal converter plus the insert-2/calmodulin.

Insert-2 constitutes a novel calmodulin binding motif

Although the sequence of the myosin VI-specific insert-2 does not correspond to any calmodulin (CaM) binding motif described so far24, we previously reported that it recruits a 4Ca2+-CaM and that dissociation of these Ca2+ ions cannot occur and regulate this interaction under physiological conditions13. Consistent with these observations, the myosin VI structure reveals that the distal part of insert-2 contains a novel CaM binding motif (Fig. 4). Following the precedent for other targets of CaM25, such as the 1-8-14 motif found in the smooth myosin light chain kinase (MLCK), we name this motif 1-6-14 based on the distance between three key hydrophobic residues (W793, W798, L806) that are buried in the interaction with CaM. Compared to other Ca2+-CaM/target (1-8-14) complexes25, the polarity of this Ca2+-CaM/insert-2 complex is similar with the C-lobe of CaM gripping the N-terminal region of the target sequence (Fig. 4a). While the C-lobe of CaM adopts a classic open conformation, that found for the N-lobe differs from any other complex described so far in being more closed by ~20° (Fig. 4b). (It is in fact close to that recently described as a contracted-open conformation26). The target helix thus is found in a much less buried position within this lobe than in a classic open lobe (Fig. 4b). After close inspection of this structure, the selection of such a conformation for the N-lobe seems to be induced by the target motif itself, not the surface contacts this lobe makes with the rest of the motor domain. In particular, the presence of a large hydrophobic side chain in the 6th position, W798, plays a critical role since it interacts strongly with helix A and the last helix of the C-lobe (Fig. 4b). By providing strong hydrophobic interactions and by selecting for relative orientations of the two lobes of CaM that allow them both to interact with the converter, this motif is remarkably well suited to impose a structural role for the recruited CaM (Fig. 4c).

DISCUSSION

What is at first striking about myosin VI is that reverse directionality has been accomplished with only minor changes within the motor domain itself. The first unique insert, insert-1, is not positioned to impact directionality by altering the structure of the motor domain. However, it does have a major impact on kinetic properties by slowing ADP release and creating a long-lived rigor state. Insert-1 is thus essential for the processivity of the motor and would be critical for the anchoring role of myosin VI, which is dependent on slow ATP binding relative to ADP binding27.

The second unique insert, insert-2, is what initially called attention to myosin VI2 and indeed is the most interesting feature of this structure. It reveals that myosin VI has tightly coupled both this insert and a calmodulin to the conventional myosin converter to create a unique converter subdomain. The purpose of this design is to redirect the lever arm toward the minus-end of the actin filament. This undoubtedly is essential for reverse-directionality. For a single-headed myosin, it would reposition the lever arm toward the minus-end of the actin filament in the rigor state (end of powerstroke), and for a two-headed processive myosin, it additionally would bias the unbound lead head toward minus-end-directed binding sites.

The work of Tsiavaliaris et al.28 demonstrated that repositioning the lever arm by 180°, rather than 120° as for myosin VI, is sufficient to reverse the directionality using a single-headed plus-end myosin motor domain. To assess if the repositioning of the lever arm is sufficient to explain the myosin VI stroke, a model for myosin VI at the beginning of the powerstroke was obtained using the pre-powerstroke state of plus-end motors (see Methods). A minus-end directed movement (i.e. reversal) is indeed produced but the component of the displacement parallel to the actin filament would only be ~2.5 nm (Fig. 5a). This is five times less than the 12 nm stroke size measured from optical trap studies for a MDins2IQ molecule14. A similar modeling for a truncated myosin V motor would predict a stroke of ~7 nm (Fig. 5b), which is what was measured in optical trap studies8. Note that for either myosin V or this myosin VI model, the rotation of the converter contributes a plus-end directed stroke. While this contribution adds to the lever arm displacement for a plus-end directed motor, it must be overcome by the lever arm contribution (for example, by increasing lever arm length) for a minus-end directed motor. This is illustrated in a model of the artificial lever arm, which achieved reversal of myosin I28 using a plus-end converter rotation and a 14 nm long lever arm (Fig. 5c).

Figure 5
Directionality of movement and power stroke in myosin motors. a,b, Schematic drawings of the myosin V and VI structural models (see Methods) prior and after force generation (using similar colors as in Fig. 1). Note in particular how conformational changes ...

Since a MDins2IQ myosin VI molecule has an inexplicably large14 minus-end directed stroke2 with a very short (4 nm) lever arm, we must conclude that myosin VI has a quite different pre-powerstroke structure from other myosins. This could be accomplished in at least two fundamentally different ways. First, the position of the converter could differ from that of other characterized myosins in all of the nucleotide states of myosin VI. There is already evidence from cryo-EM that the rotation from the actomyosin ADP (A.M.ADP) to the rigor state is in a different direction2. Since the rearrangements necessary for this transition are of small amplitude, it is possible to imagine that they differ in myosin VI due to the small alterations in the nature of the β-sheet and SH1 helix (Supplementary movies S2 and S3). But major rearrangements occur upon ATP-binding to generate the post-rigor and pre-powerstroke states18 and it is difficult to imagine how these subtle motor domain differences could cause the nearly 90° change in rotation of the converter in the pre-powerstroke state that would be necessary to generate the large step size of the MDins2IQ molecule14 (see Fig. 5d). Such an altered rotation would likely require a major redesign of the motor domain, which the structure of myosin VI clearly reveals did not occur.

The second and more easily envisioned possibility is that myosin VI has not truly reversed the normal myosin powerstroke, but has essentially abolished it and evolved a mechanism similar to that proposed for “conventional” kinesin29,30. In kinesin, it is thought that movement is accomplished by a reversible, nucleotide-state dependent docking and undocking of its neck-linker region. In the two-headed kinesin molecule, intra-molecular strain gates the docking and undocking, while the docked head biases the diffusive search for a new tubulin binding site of the unbound head during processive movement. To apply this mechanism to myosin VI, either the insert-2/CaM or the entire converter subdomain must uncouple from the motor domain in the pre-powerstroke state. In the case of insert-2/CaM, it appears to be an integral part of the converter, and as can be seen in the pre-powerstroke model (Fig. 5a), there would be no steric hindrance between this unique myosin VI converter and the motor domain to drive such an uncoupling. However, we propose that uncoupling of the entire converter from the motor domain could be induced by an SH1 helix unwinding in the post-rigor and pre-powerstroke states (Fig. 5e). A cluster of sequence differences specific for myosin VI are indeed found in the cavity of the SH1 helix (Supplementary movie S3) and there is structural evidence for unwinding of this connector in myosin II following nucleotide binding31. Thus in myosin VI, the SH1-helix would be roughly analogous to the neck-linker of kinesin.

Consistent with this hypothesis is data that placed fluorescent probes either on the IQ-CaM or on the N-terminal subdomain of two-headed myosin VI32. Using FIONA (fluorescence imaging with one nanometer accuracy), large fluctuations in the position of the IQ-CaM, but not in the position of the motor domain, were observed during processive movement. These fluctuations disappeared when ATP was removed and the heads were strongly bound to actin with either ADP or no nucleotide32. Thus, based on these observations and our new structural insights, we hypothesize that myosin VI (M.ADP.Pi) binds to actin with an uncoupled converter domain. In the absence of strain, strong binding to actin accompanies cleft closure via the central β-sheet distortion. These rearrangements would lead to an interface between the SH1 helix and the N-terminal subdomain that would favor recoupling of the converter to the motor domain in the strong actin-binding A.M.ADP state. Recoupling of the lead head for a two-headed processive myosin would be prevented, or greatly slowed, until the rear head detaches. This is consistent with both the FIONA study32 and direct measurements of pyrene-actin quenching (strong binding) with the myosin VI dimer in the presence of ATP33. When ADP dissociates, further cleft closure would lead to a small rotation of the lever arm in the minus-end direction2. The net displacement on actin (stroke) would be the difference in the average position of the lever arm when uncoupled and the stable rigor position.

This uncoupling model could account for ~6–7 nm movement of the MDins2IQ construct, assuming that there is no positional bias of the uncoupled converter (Fig. 5e). However, as depicted in this model, any biasing toward the plus end of the actin filament would increase the stroke and step size. Such biasing might come from the relay, which based on the myosin II structure with an unwound SH1 helix31, would maintain connections with the converter and would be plus-end directed due to the loss of the steric hindrance that normally bends the relay helix in the minus-end direction in the pre-powerstroke state7,31,34. Additional experiments and structures will be necessary to test this proposed mechanism of directionality reversal. Undoubtedly, this unique myosin family member has yet more surprises to reveal.

METHODS

Crystallization and Data collection

Protein expression and purification have been previously described2,13 and are detailed in Supplementary Methods. Crystals of myosin VI were first obtained with the short MDins2IQ [1-839] construct by vapor diffusion. Spontaneous nucleation occurred at 4°C in hanging drops using equal amounts of reservoir solution (containing 8–10% PEG 8000, 50mM Tris pH 8.0, 3% iso-propanol, 3% tert-butanol) and stock solution of the Myosin VI MDins2IQ at 10–12 mg/mL. Crystals of the MDins2 [2-816] and long MDins2IQ [1-859] constructs were initially obtained by cross-seeding with crystals of the short MDins2IQ and then improved by seeding in solution containing 8–10% PEG 8000, 50mM MES pH 6.7, 150mM NH4.SO4, 3% iso-propanol, 3% tert-butanol. Prior to freezing and data collection, the crystals were transferred stepwise into a final cryoprotectant solution containing 16% PEG 8000 with 25% glycerol. X-ray data sets were collected at the European Synchrotron Radiation Facility beamlines at 100 K. The MDins2 construct was crystallized in a monoclinic crystal form, while both MDins2IQ constructs were crystallized in an orthorhombic one. The long MDins2IQ crystals are similar to those of the short MDins2IQ except for the b-axis which length accommodates for the difference in lever arm length. The short MDins2IQ, long MDins2IQ and MDins2 crystals diffracted to 3.5Å, 2.9Å and 2.4Å resolution, respectively. All datasets were integrated and scaled with either the HKL package35 or the CCP4 suite36 programs (see Table 1 and Supplementary Table S2 for statistics on the data collection).

Table 1
Statistics on Data Collection and Refinement

Structure determination and refinement

The myosin VI structure was solved by molecular replacement using the myosin V MDE model (PDB code 1OE9) with the program AMoRe37 using data at 3.5 Å resolution from the short MDins2IQ or the MDins2 crystals. Several steps of rigid body fitting were performed with AMoRe (each subdomain has been considered as a rigid group). Model building and refinement of the motor domain, the insert-2 and its 4Ca2+-bound CaM was carried out at 2.4 Å resolution using data from the MDins2 crystals with Turbo38, and CNS1.139 and Refmac5 (CCP4 suite)36. The long MDins2IQ structure was solved by molecular replacement37 using the coordinates from this 2.4Å refined myosin VI MDins2 structure. Clear density was easily interpreted for the N-terminal part of the IQ helix and most of the C-terminal lobe of its CaM, which were modeled as poly-alanines. The C-terminal part of the IQ motif and most of the N-lobe of its CaM are not stabilized by crystal packing interactions. They have a high level of flexibility in the crystal and were not included in the refined model (See Supplementary Fig. S1). Water molecules have been placed with Arp/Warp program40. Crystallographic statistics are summarized in Table 1. Note that all diagrams for the figures and the movies were computed using MOLSCRIPT/Raster3D41.

Pre-powerstroke state modeling

Models of the myosin VI and V pre-powerstroke states were obtained using known myosin II pre-powerstroke structures. The scallop striated muscle myosin II pre-powerstroke structure42 (1DFL) provided coordinates for the motor domain. Position for the myosin VI and V converter/lever arms were obtained by superimposing their converter with that of the myosin II converter. Similarly, the lever arm for the engineered reverse myosin I motor was obtained from a molecular model31 (D. Manstein, personal communication). Note that this modeled myosin VI pre-powerstroke state assumes that the converter and the insert-2/CaM interactions are not broken during the catalytic cycle, which seems reasonable in view of their strong interactions. Note that no steric clash is generated between the insert-2/CaM and the motor domain when this myosin II converter rotation is applied to myosin VI. The pre-powerstroke and nucleotide-free (1OE9, 2BKI) structural models were docked on F-actin as previously described18 and a schematic drawing is shown for clarity in Fig. 5. The stroke resulting from this model was measured as the component of the displacement parallel to the actin filament.

Supplementary Material

FigS1

Supp data

Supp methods

Supp movie 1

Supp movie 2

Supp movie 3

Supp movie 4

Supp table 1

Supp table 2

Acknowledgments

This work was supported by a grant from the National Institutes of Health (AR-048931) to H.L.S and A.H., grants from the CNRS and the ARC to A.H., as well as predoctoral fellowships from the Quebec government and the FRM to A.B. We thank the staff of the European Synchrotron Radiation Facility for assistance during data collection. We are also grateful to Anna Li and Damien Garbett for technical assistance in preparing the recombinant proteins and to Jérôme Cicolari for assistance in crystallization experiments.

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