Activation of the dynein adenosinetriphosphatase by microtubules

Structure of Motile Cilia

Cilia are tail-like organelles responsible for motility, transportation, and sensory functions in eukaryotic cells. Cilia research has been providing multifaceted questions, attracting biologists of various areas and inducing interdisciplinary studies. In this chapter, we mainly focus on efforts to elucidate the molecular mechanism of ciliary beating motion, a field of research that has a long history and is still ongoing. We also overview topics closely related to the motility mechanism, such as ciliogenesis, cilia-related diseases, and sensory cilia. Subnanometer-scale to submillimeter-scale 3D imaging of the axoneme and the basal body resulted in a wide variety of insights into these questions.

Cryo-electron tomography of motile cilia and flagella

Cryo-electron tomography has been a valuable tool in the analysis of 3D structures of cilia at molecular and cellular levels. It opened a way to reconstruct 3D conformations of proteins in cilia at 3-nm resolution, revealed networks of a number of component proteins in cilia, and has even allowed the study of component dynamics. In particular, we have identified the locations and conformations of all the regular inner and outer dyneins, as well as various regulators such as radial spokes. Since the mid 2000s, cryo-electron tomography has provided us with new knowledge, concepts, and questions in the area of cilia research. Now, after nearly 10 years of application of this technique, we are turning a corner and are at the stage to discuss the next steps. We expect further development of this technique for specimen preparation, data acquisition, and analysis. While combining this tool with other methodologies has already made cryo-electron tomography more biologically significant, we need to continue this cooperation using recently developed biotechnology and cell biology approaches.

In this review, we will provide an up-to-date overview of the biological insights obtained by cryo-electron tomography and will discuss future possibilities of this technique in the context of cilia research.

Displacement-weighted velocity analysis of gliding assays reveals that Chlamydomonas axonemal dynein preferentially moves conspecific microtubules

In vitro gliding assays, in which microtubules are observed to glide over surfaces coated with motor proteins, are important tools for studying the biophysics of motility. Gliding assays with axonemal dyneins have the unusual feature that the microtubules exhibit large variations in gliding speed despite measures taken to eliminate unsteadiness. Because axonemal dynein gliding assays are usually done using heterologous proteins, i.e., dynein and tubulin from different organisms, we asked whether the source of tubulin could underlie the unsteadiness. By comparing gliding assays with microtubules polymerized from Chlamydomonas axonemal tubulin with those from porcine brain tubulin, we found that the unsteadiness is present despite matching the source of tubulin to the source of dynein. We developed a novel, to our knowledge, displacement-weighted velocity analysis to quantify both the velocity and the unsteadiness of gliding assays systematically and without introducing bias toward low motility. We found that the quantified unsteadiness is independent of tubulin source. In addition, we found that the short Chlamydomonas microtubules translocate significantly faster than their porcine counterparts. By modeling the effect of length on velocity, we propose that the observed effect may be due to a higher rate of binding of Chlamydomonas axonemal dynein to Chlamydomonas microtubules than to porcine microtubules.

Differential interactions of the formins INF2, mDia1, and mDia2 with microtubules

Three mammalian formins, although binding microtubules with high affinity, differ dramatically in their microtubule-binding mechanisms. In addition, the ability of one formin (mDia2) to bind actin is strongly inhibited by microtubules, whereas the ability of another formin (INF2) to bind microtubules is strongly inhibited by actin monomers.

A number of cellular processes use both microtubules and actin filaments, but the molecular machinery linking these two cytoskeletal elements remains to be elucidated in detail. Formins are actin-binding proteins that have multiple effects on actin dynamics, and one formin, mDia2, has been shown to bind and stabilize microtubules through its formin homology 2 (FH2) domain. Here we show that three formins, INF2, mDia1, and mDia2, display important differences in their interactions with microtubules and actin. Constructs containing FH1, FH2, and C-terminal domains of all three formins bind microtubules with high affinity (K_d < 100 nM). However, only mDia2 binds microtubules at 1:1 stoichiometry, with INF2 and mDia1 showing saturating binding at approximately 1:3 (formin dimer:tubulin dimer). INF2-FH1FH2C is a potent microtubule-bundling protein, an effect that results in a large reduction in catastrophe rate. In contrast, neither mDia1 nor mDia2 is a potent microtubule bundler. The C-termini of mDia2 and INF2 have different functions in microtubule interaction, with mDia2's C-terminus required for high-affinity binding and INF2's C-terminus required for bundling. mDia2's C-terminus directly binds microtubules with submicromolar affinity. These formins also differ in their abilities to bind actin and microtubules simultaneously. Microtubules strongly inhibit actin polymerization by mDia2, whereas they moderately inhibit mDia1 and have no effect on INF2. Conversely, actin monomers inhibit microtubule binding/bundling by INF2 but do not affect mDia1 or mDia2. These differences in interactions with microtubules and actin suggest differential function in cellular processes requiring both cytoskeletal elements.

Kinetic characterization of tail swing steps in the ATPase cycle of Dictyostelium cytoplasmic dynein

According to the power stroke model of dynein deduced from electron microscopic and fluorescence resonance energy transfer studies, the power stroke and the recovery stroke are expected to take place at the two isomerization steps of the ATPase cycle at the primary ATPase site. Here, we have conducted presteady-state kinetic analyses of these two isomerization steps with the single-headed motor domain of Dictyostelium cytoplasmic dynein by employing fluorescence resonance energy transfer to probe ATPase steps at the primary site and tail positions. Our results show that the recovery stroke at the first isomerization step proceeds quickly ( approximately 180 s(-1)), whereas the power stroke at the second isomerization step is very slow ( approximately 0.2 s(-1)) in the absence of microtubules, and that the presence of microtubules accelerates the second but not the first step. Moreover, a comparison of the microtubule-induced acceleration of the power stroke step and that of steady-state ATP hydrolysis implies the intriguing possibility that microtubules simultaneously accelerate the ATPase activity not only at the primary site but also at other site(s) in the motor domain.

Single-occupancy binding in simple bounded and unbounded systems

The number of substrate molecules that can bind to the active site of an enzyme at one time is constrained. This paper develops boundary conditions that correspond to the constraint of single-occupancy binding. Two simple models of substrate molecules diffusing to a single-occupancy site are considered. In the interval model, a fixed number of substrate molecules diffuse in a bounded domain. In the spherical model, a varying number of molecules diffuse in a domain with boundary conditions that model contact with a reservoir containing a large number of substrate molecules. When the diffusive time scale is much shorter than the time scale for entering the single-occupancy site, the dynamics of binding are accurately described by simple approximations.

Model for unidirectional movement of axonemal and cytoplasmic dynein molecules

A model for the unidirectional movement of dynein is presented based on the structural observations and biochemical experimental results available. In this model, the binding affinity of dynein for microtubule (MT) is independent of its nucleotide state and the change between strong and weak MT-binding is determined naturally by the variation of relative orientation between the stalk and MT, as the stalk rotates following nucleotide-state transition. Thus the enigmatic communication from the adenosine triphosphate (ATP)-binding site in the globular domain to the far MT-binding site in the tip of the stalk, which is a prerequisite in conventional models, is not required. Using the present model, the previous experimental results such as the effect of ATP and adenosine diphosphate (ADP) bindings on dissociation of dynein from MT, the movement of single-headed axonemal dyneins at saturating ATP concentration, the load dependence of step-size for the movement of two-headed cytoplasmic dyneins and the dependence of stall force on ATP concentration can be well explained.

Dynamic allostery of protein alpha helical coiled-coils

Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of approximately 2kBT, consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein.

Alternating site ATPase pathway of rat conventional kinesin

The pathway of ATP hydrolysis by rat kinesin was established by pre-steady-state kinetic methods. A 406-residue long N-terminal fragment was shown by sedimentation equilibrium analysis to form a dimer with a K(d) of 46 nm. The pathway of ATP hydrolysis follows the Gilbert-Johnson pathway determined previously for a similarsized N-terminal fragment of Drosophila conventional kinesin. However, the rates of ADP release were at least 3-fold faster, and ATP hydrolysis was approximately 5-fold faster. Paralleling our previous mechanistic data, these results support an alternating site ATPase pathway, including a captive head state as an intermediate in the kinesin ATPase cycle. The kinetic data presented in this report once again point to the importance of the captive head state and argue against a pathway that short-circuits this key intermediate. In addition, several unique aspects of the rat kinesin kinetics reveal new aspects of the ATPase-coupling mechanism. These studies provide a baseline set of kinetic parameters against which future studies of rat kinesin mutants may be evaluated and directly correlated with the structure of the dimeric kinesin.

A model for the oscillatory motion of single dynein molecules

Axonemal dynein is the molecular motor responsible for the rhythmic beating of eukaryotic cilia and flagella. An individual axonemal dynein molecule is capable of both unidirectional and oscillatory motion along a microtubule (Nature 393 (1998) 711). We propose a model which links the physical motion of a two-headed dynein molecule to its ATP hydrolysis cycle, and which exhibits both processive and oscillatory behaviors. A mathematical analysis of the model is used to make experimentally testable predictions.

Properties of the full-length heavy chains of Tetrahymena ciliary outer arm dynein separated by urea treatment

An important challenge is to understand the functional specialization of dynein heavy chains. The ciliary outer arm dynein from Tetrahymena thermophila is a heterotrimer of three heavy chains, called alpha, beta and gamma. In order to dissect the contributions of the individual heavy chains, we used controlled urea treatment to dissociate Tetrahymena outer arm dynein into a 19S beta/gamma dimer and a 14S alpha heavy chain. The three heavy chains remained full-length and retained MgATPase activity. The beta/gamma dimer bound microtubules in an ATP-sensitive fashion. The isolated alpha heavy chain also bound microtubules, but this binding was not reversed by ATP. The 19S beta/gamma dimer and the 14S alpha heavy chain could be reconstituted into 22S dynein. The intact 22S dynein, the 19S beta/gamma dimer, and the reconstituted dynein all produced microtubule gliding motility. In contrast, the separated alpha heavy chain did not produce movement under a variety of conditions. The intact 22S dynein produced movement that was discontinuous and slower than the movement produced by the 19S dimer. We conclude that the three heavy chains of Tetrahymena outer arm dynein are functionally specialized. The alpha heavy chain may be responsible for the structural binding of dynein to the outer doublet A-tubule and/or the positioning of the beta/gamma motor domains near the surface of the microtubule track.

Diameter oscillation of axonemes in sea-urchin sperm flagella

The 9 + 2 configuration of axonemes is one of the most conserved structures of eukaryotic organelles. Evidence so far has confirmed that bending of cilia and flagella is the result of active sliding of microtubules induced by dynein arms. If the conformational change of dynein motors, which would be a key step of force generation, is occurring in a three-dimensional manner, we can easily expect that the microtubule sliding should contain some transverse component, i.e., a motion in a direction at a right angle to the longitudinal axis of axonemes. Using a modified technique of atomic force microscopy, we found such transverse motion is actually occurring in an oscillatory manner when the axonemes of sea-urchin sperm flagella were adhered onto glass substrates. The motion was adenosine triphosphate-dependent and the observed frequency of oscillation was similar to that of oscillatory sliding of microtubules that had been shown to reflect the physiological activity of dynein arms (S. Kamimura and R. Kamiya. 1989. Nature: 340:476-478; 1992. J. Cell Biol. 116:1443-1454). Maximal amplitude of the diameter oscillation was around 10 nm, which was within a range of morphological change observed with electron microscopy (F. D. Warner. 1978. J. Cell Biol. 77:R19-R26; N. C. Zanetti, D. R. Mitchell, and F. D. Warner. 1979. J. Cell Biol. 80:573-588).

RNA transport in oligodendrocytes from the taiep mutant rat

The results presented here identify a new RNA trafficking phenotype in taiep oligodendrocytes that increases the frequency of reversals and restricts the extent of transport of RNA containing the A2RE transport signal from MBP mRNA. The taiep rat is a myelin mutant characterized by excessive accumulation of microtubules in oligodendrocytes and myelin deficiency in the central nervous system. The taiep RNA trafficking is developmentally correlated with the microtubule accumulation in oligodendrocytes and can be partially suppressed by reducing microtubule density with nocodazole or inhibiting dynein activity by coinjecting anti-dynein antibodies. These results suggest that RNA trafficking in taiep oligodendrocytes is inhibited by enhanced dynein activity that neutralizes or lessens the normal overriding power of the plus-end directed motor kinesin. Altered orientation of microtubules in oligodendrocyte fine processes and a physical barrier created by densely packed microtubules may also contribute to the inhibition of RNA trafficking in taiep oligodendrocytes.

Functional diversity of axonemal dyneins as studied in Chlamydomonas mutants

Cilia and flagella of most organisms are equipped with two kinds of motor protein complex, the inner and outer dynein arms. The two arms were previously thought to be similar to each other, but recent studies using Chlamydomonas mutants indicate that they differ significantly in subunit structure and arrangement within the axoneme. For example, whereas the outer dynein arm exists as a single protein complex containing three heavy chains, the inner dynein arm comprises seven different subspecies each containing one or two discrete heavy chains. Furthermore, the two kinds of arms appear to differ in function also. Most strikingly, our studies suggest that inner-arm dynein, but not outer-arm dynein, is under the control of the central pair microtubules and radial spokes. The axoneme thus appears to be equipped with two rather distinct systems for beating: one involving inner-arm dyneins, the central pair and radial spokes, and the other involving outer-arm dynein alone.

Dynein structure and power stroke

Dynein ATPases are microtubule motors that are critical to diverse processes such as vesicle transport and the beating of sperm tails; however, their mechanism of force generation is unknown. Each dynein comprises a head, from which a stalk and a stem emerge. Here we use electron microscopy and image processing to reveal new structural details of dynein c, an isoform from Chlamydomonas reinhardtii flagella, at the start and end of its power stroke. Both stem and stalk are flexible, and the stem connects to the head by means of a linker approximately 10 nm long that we propose lies across the head. With both ADP and vanadate bound, the stem and stalk emerge from the head 10 nm apart. However, without nucleotide they emerge much closer together owing to a change in linker orientation, and the coiled-coil stalk becomes stiffer. The net result is a shortening of the molecule coupled to an approximately 15-nm displacement of the tip of the stalk. These changes indicate a mechanism for the dynein power stroke.

Myosin cross bridges in skeletal muscles: "rower" molecular motors

Different classes of molecular motors, "rowers" and "porters," have been proposed to describe the chemomechanical transduction of energy. Rowers work in large assemblies and spend a large percentage of time detached from their lattice substrate. Porters behave in the opposite way. We calculated the number of myosin II cross bridges (CB) and the probabilities of attached and detached states in a minimal four-state model in slow (soleus) and fast (diaphragm) mouse skeletal muscles. In both muscles, we found that the probability of CB being detached was approximately 98% and the number of working CB was higher than 10(9)/mm(2). We concluded that muscular myosin II motors were classified in the category of rowers. Moreover, attachment time was higher than time stroke and time for ADP release. The duration of the transition from detached to attached states represented the rate-limiting step of the overall attached time. Thus diaphragm and soleus myosins belong to subtype 1 rowers.

Molecular structure of dynein and motility of a giant sperm axoneme provided with only the outer dynein arm

The peculiar sperm axoneme of the dipteran Asphondylia ruebsaameni is characterized by an extraordinarily high number of microtubule doublets (up to 2,500) arranged in double parallel spirals. Doublets of the inner row of each spiral are tilted, so that their outer arms point towards the B-tubule of the next doublet in the outer row. Doublets are provided with only the outer arm, and no structure related to the central pair/radial spoke complex is present. When analyzed by quick-freeze, deep-etch electron microscopy, the structure of the dynein arms was shown to share the same organization described in other organisms; however, it appears to be somewhat more complex than that previously found in a related dipteran species, Monarthropalpus flavus, since the foot region of the arms displays a globular extra-domain that is intercalated between adjacent arms. Treatment of demembranated sperm with ATP and vanadate induced conformational changes in the dynein arms. SDS-page suggested the presence of a single dynein high molecular weight band or, in the gels with the best electrophoretic resolution, of two very closely spaced bands. This polypeptide positively reacted with a polyclonal antibody raised against a specific amino acid sequence located in the phosphate-binding loop of the dynein catalytic site. Dynein heavy chain-related DNA sequences corresponding to the catalytic phosphate-binding region were amplified by RT-PCR. Two distinct fragments (Asph-ax1 and Asph-ax2) encoding axonemal dynein sequences were identified. Southern blot analysis performed on genomic DNA using these sequences as a probe showed that they are part of different genes. An intron was identified in the Asph-ax1 fragment at a position corresponding to the site of a nucleotide deletion in the putative pseudogene of Monarthropalpus. Asphondylia spermatozoa exhibited in vivo a whirling movement both in the deferent duct and in the spermatheca, but they were unable to undergo processive movement in vitro. They propagated a three-dimensional wave only when constrained in a bent configuration by some mechanical means. The phylogenetic relationships between the two dipteran species, Monarthopalpus and Asphondylia, based on these biochemical and molecular data are also discussed.

RNA trafficking in oligodendrocytes

A2RE and hnRNP A2 have been identified as important cis/trans determinants for MBP RNA trafficking in oligodendrocytes. Since A2RE-like sequences are found in several different transported RNAs, and since hnRNP A2 is expressed in most cell types, this may represent a general RNA trafficking pathway shared by a variety of different RNAs in different cell types. In oligodendrocytes, A2RE/hnRNP A2 determinants are involved in at least four steps in the RNA trafficking pathway: (1) export from the nucleus to the cytoplasm, (2) granule assembly in the perikaryon, (3) transport along microtubules in the processes, and (4) translation activation in the myelin compartment. The components of the cellular machinery mediating each of these steps are known. How A2RE/hnRNP A2 determinants interact with these components to mediate RNA trafficking is being investigated by a combination of: biochemistry to analyze molecular interactions in vitro, imaging to visualize molecular interactions in living cells, and computational modeling to simulate molecular interactions in the Virtual Cell.

Dynein-ADP as a force-generating intermediate revealed by a rapid reactivation of flagellar axoneme

Fragmented flagellar axonemes of sand dollar spermatozoa were reactivated by rapid photolysis of caged ATP. After a time lag of 10 ms, axonemes treated with protease started sliding disintegration. Axonemes without protease digestion started nanometer-scale high-frequency oscillation after a similar time lag. Force development in the sliding disintegration was measured with a flexible glass needle and its time course was corresponded well to that of the dynein-ADP intermediate production estimated using kinetic rates previously reported. However, with a high concentration ( approximately 80 microM) of vanadate, which binds to the dynein-ADP intermediate and forms a stable complex of dynein-ADP-vanadate, the time course of force development in sliding disintegration was not affected at all. In the case of high frequency oscillation, the time lag to start the oscillation, the initial amplitude, and the initial frequency were not affected by vanadate, though the oscillation once started was damped more quickly at higher concentrations of vanadate. These results suggest that during the initial turnover of ATP hydrolysis, force generation of dynein is not blocked by vanadate. A vanadate-insensitive dynein-ADP is postulated as a force-generating intermediate.

A model for flagellar motility

Experimental investigation has provided a wealth of structural, biochemical, and physiological information regarding the motile mechanism of eukaryotic flagella/cilia. This chapter surveys the available literature, selectively focusing on three major objectives. First, it attempts to identify those conserved structural components essential to providing motile function in eukaryotic axonemes. Second, it examines the relationship between these structural elements to determine the interactions that are vital to the mechanism of flagellar/ciliary beating. Third, the vital principles of these interactions are incorporated into a tractable theoretical model, referred to as the Geometric Clutch, and this hypothetical scheme is examined to assess its compatibility with experimental observations.

Microtubules and microtubule motors: mechanisms of regulation

Microtubule-based motility is precisely regulated, and the targets of regulation may be the motor proteins, the microtubules, or both components of this intricately controlled system. Regulation of microtubule behavior can be mediated by cell cycle-dependent changes in centrosomal microtubule nucleating ability and by cell-specific, microtubule-associated proteins (MAPs). Changes in microtubule organization and dynamics have been correlated with changes in phosphorylation. Regulation of motor proteins may be required both to initiate movement and to dictate its direction. Axonemal and cytoplasmic dyneins as well as kinesin can be phosphorylated and this modification may affect the motor activities of these enzymes or their ability to interact with organelles. A more complete understanding of how motors can be modulated by phosphorylation, either of the motor proteins or of other associated substrates, will be necessary in order to understand how bidirectional transport is regulated.

Mechanochemical aspects of axonemal dynein activity studied by in vitro microtubule translocation

We have determined the relationship between microtubule length and translocation velocity from recordings of bovine brain microtubules translocating over a Paramecium 22S dynein substratum in an in vitro assay chamber. For comparison with untreated samples, the 22S dynein has been subjected to detergent and/or to pretreatments that induce phosphorylation of an associated 29 kDa light chain. Control and treated dyneins have been used at the same densities in the translocation assays. In any given condition, translocation velocity (v) shows an initial increase with microtubule length (L) and then reaches a plateau. This situation may be represented by a hyperbola of the general form v = aL/(L+b), which is formally analogous to the Briggs-Haldane relationship, which we have used to interpret our data. The results indicate that the maximum translocation velocity Vo(= a) is increased by pretreatment, whereas the length constant KL(= b), which corresponds to Km, does not change with pretreatment, implying that the mechanochemical properties of the pretreated dyneins differ from those of control dyneins. The conclusion that KL is constant for defined in vitro assays rules out the possibility that the velocity changes seen are caused by changes in geometry in the translocation assays or by the numbers of dyneins or dynein heads needed to produce maximal translocational velocity. From our analysis, we determine that f, the fraction of cycle time during which the dynein is in the force-generating state, is small--roughly 0.01, comparable to the f determined previously for heavy meromyosin. The practical limits of these mechanochemical changes imply that the maximum possible ciliary beat frequency is about 120 Hz, and that in the physiological range of 5-60 Hz, beat frequency could be controlled by varying the numbers of phosphorylated outer arm dyneins along an axonemal microtubule.

Functional multiplicity of motor molecules revealed by a simple kinetic analysis

We present a simple analytical solution for a kinetic model of motor molecule function with multiple arms. This model has a rate of motion proportional to the probability that all arms in a complex are detached from the cytoskeleton and, therefore, we refer to it as obligate cooperativity. The model has the form: v = Vmax/(1 + q/S)n, where Vmax is the maximum velocity, the product nq is the effective Michaelis constant at high [ATP], and n is the number of arms. Values of n = 2 and n = 1 give good fits to the heavy meromyosin and myosin S1 sliding velocity data, respectively, consistent with the number of active sites. Despite the complexity of the eukaryotic axoneme, beat frequency data from Chlamydomonas wild-type and oda mutants are also fit by this model.

Isolation of polypeptides with microtubule-translocating activity from phragmoplasts of tobacco BY-2 cells

As part of our efforts to understand the molecular basis of the microtubule-associated motility that is involved in cytokinesis in higher plant cells, an attempt was made to identify proteins with the ability to translocate microtubules in an extract from isolated phragmoplasts. Homogenization of isolated phragmoplasts in a solution that contained MgATP, MgGTP and a high concentration of NaCl resulted in the release from phragmoplasts of factors with ATPase and GTPase activity that were stimulated by microtubules. A protein fraction with microtubule-dependent ATPase and GTPase activity caused minus-end-headed gliding of microtubules in the presence of ATP or GTP. Polypeptides with microtubule-translocating activity cosedimented with microtubules that had been assembled in vitro from brain tubulin and were dissociated from sedimented microtubules by addition of ATP or GTP. After cosedimentation and dissociation procedures, a 125 kDa polypeptide and a 120 kDa polypeptide were recovered in a fraction that supported minus-end-headed gliding of microtubules. The rate of microtubule gliding that was caused by the fraction that contained the 125 kDa and 120 kDa polypeptides as main components was 1.28 microns/minute in the presence of ATP and 0.50 microns/minute in the presence of GTP. This fraction contained some microtubule-associated polypeptides in addition to the 125 kDa and 120 kDa polypeptides, but a fraction that contained only these additional polypeptides did not cause any translocation of microtubules. Thus, it appeared that the 125 kDa and 120 kDa polypeptides were responsible for translocation of microtubules. These polypeptides with plus-end-directed motor activity may play an important role in formation of the cell plate and in the organization of the phragmoplast.

Pre-steady-state kinetics of the microtubule-kinesin ATPase

The pre-steady-state kinetics of the microtubule-kinesin ATPase were investigated by chemical-quench flow methods using the Drosophila kinesin motor domain (K401) expressed in Escherichia coli [Gilbert, S. P., & Johnson, K. A. (1993) Biochemistry 32, 4677-4684]. The results define a minimal mechanism: M.K + ATP in equilibrium with (M).K.ATP in equilibrium with (M).K.ADP.Pi in equilibrium with M.K.ADP + Pi in equilibrium with M.K + ADP, where M, K, and Pi represent microtubules, kinesin, and inorganic phosphate, respectively, with k+1 = 0.8-3 microM-1 s-1, k-1 = 100-300 s-1, k+2 = 70-120 s-1, k+4 = 10-20 s-1, and k+3 >> k-2 and k+3 >> k+4. Conditions were as follows: 25 degrees C, 20 mM HEPES, pH 7.2 with KOH, 5 mM magnesium acetate, 0.1 mM EDTA, 0.1 mM EGTA, 50 mM potassium acetate, 1 mM DTT. The experiments presented do not determine the step in the cycle where kinesin dissociates from the microtubule or the step at which kinesin reassociates with the microtubule; therefore, the steps that may represent kinesin as the free enzyme are indicated by (M). A burst of ADP product formation was observed during the first turnover of the enzyme in the acid-quench experiments that define the ATP hydrolysis transient. The observation of the burst demonstrates that product release is rate limiting even in the presence of saturating microtubule concentrations. The pulse-chase experiments define the time course of ATP binding to the microtubule-K401 complex. At low ATP concentrations, ATP binding limits the rate of the burst. However, at high concentrations of ATP, ATP binding is faster than the rate of ATP hydrolysis with k+2 = 70-120 s-1. The amplitude of the burst of the ATP binding transient reached a maximum of 0.7 per site at saturating concentrations of ATP and microtubules. The amplitude of less than 1 is attributed to the fast k(off) for ATP (k-1 = 100-300 s-1) that leads to a partitioning of the M.K.ATP complex between ATP hydrolysis (k+2) and ATP release (k-1). These results indicate that ATP binds weakly to the M.K complex (Kd,ATP app approximately 100 microM). ADP release (k+4 = 10-20 s-1) is rate limiting during steady-state turnover, indicating that microtubules activate the kinesin ATPase by increasing k(off),ADP from 0.01 s-1 in the absence of microtubules to 10-20 s-1 at saturating microtubule concentrations.

C/A dynein isolated from sea urchin sperm flagellar axonemes. Enzymatic properties and interaction with microtubules

C/A dynein is a novel dynein isolated from sea urchin sperm flagellar axonemes. It is composed of C and A heavy chains and some additional lower molecular mass polypeptide chains. The characterization of ATPase activity and the interaction of this dynein with microtubules polymerized from calf brain tubulin were investigated in this study. The ATPase activity of C/A dynein (0.3-0.4 mumol Pi/min per mg) was about one half that of outer arm 21 S dynein (0.6-0.8 mumol Pi/min per mg) at 25 degrees C. Vanadate inhibited the ATPase activity with a half-maximal inhibition at 1 microM. C/A dynein absorbed to the glass surface was able to translocate the microtubules towards its plus end. The velocity of the microtubule movement in the presence of 1 mM ATP was 4.0 to 4.5 microns/s at 22 degrees C. C/A dynein binds to and bundles the microtubules even in the presence of ATP. Cross-bridges were found between adjacent microtubules in the bundle with an axial periodicity of about 24 nm. The ATPase activity of C/A dynein was enhanced up to several-fold by the microtubules at concentration as low as 1 mg/ml. On the other hand, 21 S dynein bound to the microtubules with 24 nm axial periodicity only in the absence of ATP. Its ATPase activity was not activated by the microtubules. From these results, it is concluded that the manner of interaction with microtubules of C/A dynein is different from that of the outer arm dynein.

Porters versus rowers: a unified stochastic model of motor proteins

We present a general phenomenological theory for chemical to mechanical energy transduction by motor enzymes which is based on the classical "tight-coupling" mechanism. The associated minimal stochastic model takes explicitly into account both ATP hydrolysis and thermal noise effects. It provides expressions for the hydrolysis rate and the sliding velocity, as functions of the ATP concentration and the number of motor enzymes. It explains in a unified way many results of recent in vitro motility assays. More importantly, the theory provides a natural classification scheme for the motors: it correlates the biochemical and mechanical differences between "porters" such as cellular kinesins or dyneins, and "rowers" such as muscular myosins or flagellar dyneins.

Expression, purification, and characterization of the Drosophila kinesin motor domain produced in Escherichia coli

The Drosophila kinesin heavy-chain gene was truncated to obtain the N-terminal 401 amino acid motor domain (designated K401) containing both the microtubule and ATP binding sites. The plasmid construct with the truncated kinesin gene was used to transform Escherichia coli. After induction, K401 was expressed as soluble kinesin protein at high levels and purified to homogeneity in milligram quantities. The purified protein was active and behaved as native kinesin with respect to its steady-state kinetic properties: K401 demonstrated a very low ATPase activity (kcat = 0.01 s-1) which was stimulated approximately 1000-fold by the addition of microtubules (kcat = 10 s-1; K0.5,MT = 0.9 microM tubulin; Km,ATP = 31 microM). Like native kinesin, K401 when purified contained ADP tightly bound at its active site, and the release of ADP from the active site occurred at a rate equal to the steady-state ATPase kcat. Active-site measurements using [alpha-32P]ATP demonstrated a stoichiometry of one ATPase site per K401 molecule. Like native kinesin, K401 can also hydrolyze MgGTP, and in the presence of microtubules, the rate of hydrolysis was increased dramatically from 0.03 to 16 s-1 (K0.5,MT = 2 microM tubulin; Km,GTP = 3.5 mM). These results establish that an active kinesin motor domain can be bacterially expressed and that this domain, the N-terminal 401 amino acids of the Drosophila kinesin heavy chain without light chains or additional eukaryotic factors, has full catalytic activity with microtubules.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemomechanical cycle of kinesin differs from that of myosin

Motor proteins move unidirectionally along cytoskeletal polymers by coupling translocation to cycles of ATP hydrolysis. The energy from ATP is required both to generate force and to dissociate the motor-filament complex in order to begin a new chemomechanical cycle. For myosin, force production is associated with phosphate release following ATP hydrolysis, whereas dissociation of actomyosin is tightly coupled to the binding of ATP. Dynein, a microtubule motor, uses a similar cycle, suggesting that all cytoskeletal motors might operate by a common mechanism. Here we investigate kinesin's chemomechanical cycle by assaying microtubule movement by single kinesin molecules when intermediate states in the hydrolysis cycle are prolonged with ATP analogues or inhibitors. In contrast to myosin and dynein, kinesin with bound ADP dissociates from microtubules during translocation, whereas kinesin with unhydrolysed nucleotide remains tightly associated with the polymer. These findings imply that kinesin converts ATP energy into mechanical work by a pathway distinct from that of myosin or dynein.

The motile beta/IC1 subunit of sea urchin sperm outer arm dynein does not form a rigor bond

We used in vitro translocation and cosedimentation assays to study the microtubule binding properties of sea urchin sperm outer arm dynein and its beta/IC1 subunit. Microtubules glided on glass-absorbed sea urchin dynein for a period of time directly proportional to the initial MgATP2- concentration and then detached when 70-95% of the MgATP2- was hydrolyzed. Detachment resulted from MgATP2- depletion, because (a) perfusion with fresh buffer containing MgATP2- reconstituted binding and gliding, (b) microtubules glided many minutes with an ATP-regenerating system at ATP concentrations which alone supported gliding for only 1-2 min, and (c) microtubules detached upon total hydrolysis of ATP by an ATP-removal system. The products of ATP hydrolysis antagonized binding and gliding; as little as a threefold excess of ADP/Pi over ATP resulted in complete loss of microtubule binding and translocation by the beta/IC1 subunit. In contrast to the situation with sea urchin dynein, microtubules ceased gliding but remained bound to glass-absorbed Tetrahymena outer arm dynein when MgATP2- was exhausted. Cosedimentation assays showed that Tetrahymena outer arm dynein sedimented with microtubules in an ATP-sensitive manner, as previously reported (Porter, M.E., and K. A. Johnson. J. Biol. Chem. 258: 6575-6581). However, the beta/IC1 subunit of sea urchin dynein did not cosediment with microtubules in the absence of ATP. Thus, this subunit, while capable of generating motility, lacks both structural and rigor-type microtubule binding.

Activation of ATPase activity of 14S dynein from Tetrahymena cilia by microtubules

The ATPase activity of 14S dynein was activated by the presence of microtubule-associated-protein-free microtubules. The activation was 2.5-3.5 fold at 10 mg microtubule/ml, and the activity increased further with increasing microtubule concentration. The microtubule-14S-dynein complex, microtubule bundles with 14S dynein, was treated with a zero-length chemical cross-linker, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC). The ATPase activity of the complex responded to EDC in a biphasic, concentration-dependent manner and, at most, it was enhanced 5-10 fold. The complex treated with EDC was no longer unbundled by addition of ATP, as revealed by electron-microscopic observation. Several ATP analogues, which support in vitro microtubule translocation mediated by 14S dynein, were turned over faster by this mechanochemical enzyme in the presence of microtubules than in their absence. However, some ATP analogues which do not support the translocation were also turned over faster in the presence of microtubules. Thus, microtubule-dynein motility and substrate-turnover activation are not tightly coupled, which indicates that all three major motor systems, actin- heavy-meromyosin, microtubule-kinesin [Shimizu, T., Furusawa, K., Ohashi, S., Toyoshima, Y. Y., Okuno, M., Malik, F. & Vale, R. D. (1991) J. Cell Biol. 112, 1189-1197] and microtubule-dynein, have this characteristic property in common.

Two distinct isoforms of sea urchin egg dynein

Extracts of unfertilized sea urchin eggs contain at least two isoforms of cytoplasmic dynein. One exhibits a weak affinity for microtubules and is primarily soluble. The other isoform, HMr-3, binds to microtubules in an ATP-sensitive manner, but is immunologically distinct from the soluble egg dynein (Porter et al.: Journal of Biological Chemistry 263:6759-6771, 1988). We have now further distinguished these egg dynein isoforms based on differences in NTPase activity. HMr-3 copurifies with NTPase activity, but it hydrolyzes CTP at 10 times the rate of ATP. The soluble egg dynein is similar to flagellar dynein in its nucleotide specificity; its MgCTPase activity is ca. 60% of its MgATPase activity. Non-ionic detergents and salt activate the MgATPase activities of both enzymes relative to their MgCTPase activities, but this effect is more pronounced for the soluble egg dynein than for HMr-3. Sucrose gradient-purified HMr-3 promotes an ATP-sensitive microtubule bundling, as seen with darkfield optics. We have also isolated a 20 S microtubule translocating activity by sucrose gradient fractionation of egg extracts, followed by microtubule affinity and ATP release. This 20 S fraction, which contains the HMr-3 isoform, induces a microtubule gliding activity that is distinct from kinesin. Our observations suggest that soluble dynein resembles axonemal dynein, but that HMr-2 is related to the dynein-like enzymes isolated from a variety of cell types and may represent the cytoplasmic dynein of sea urchin eggs.

Cooperativity in axonemal motion: analysis of a four-state, two-site kinetic model

A kinetic model for axonemal motion based upon a four-state mechanochemical cycle of dynein with two active sites is described. Our model analysis determines the pseudo-steady-state concentrations of enzyme species for specified rate constants, most of which are experimentally determined, with given substrate and product concentrations. The proportion of enzyme species in which both active sites are detached from the microtubule (denoted as "both detached"), numerically calculated from the model, appears to be proportional to experimental observations of flagellar beat frequency. This correlation between beat frequency and the both-detached enzyme species is maintained over a wide range of substrate concentrations and exhibited an apparent positive cooperativity at low substrate concentrations, which we call "obligate cooperativity." The unusual obligate cooperativity exhibited by flagellar beat frequency parallels that seen in the calculated proportion of the both-detached enzyme species and is interpreted as a requirement for a molecule of substrate to bind to each active site in a multimeric dynein in order to produce oscillatory motion. Furthermore, the proportion of the both-detached enzyme species correlates with experimentally observed changes in beat frequency with a nucleotide analog and with product inhibition.

Phosphorothioate analogs of ATP as the substrates of dynein and ciliary or flagellar movement

The phosphorothioate analog of ATP has a sulfur atom replacing a non-bridging oxygen atom of the triphosphate moiety of ATP. Due to the tetrahedral nature of the phosphorus atom, stereoisomers are known to exist, designated as the Sp and Rp isomers. We have reported [Shimizu & Furusawa (1986) Biochemistry 25, 5787] on the hydrolytic activity of the 22S dynein from Tetrahymena cilia towards the phosphorothioate analogs of ATP. In this paper, we extend our study and report on the microtubule-dynein dissociation by these analogs and on their ability to support sea urchin flagellar dynein enzymatic activity as well as ciliary or flagellar motility. It has been shown that the microtubule--22S-dynein complex is dissociated by the binding of ATP to the dynein enzymatic sites [Porter & Johnson (1983) J. Biol. Chem. 258, 6575]. We studied the dissociation by adenosine 5'-[alpha-thio]triphosphate (ATP[alpha S]), Sp or Rp, by light-scattering stopped-flow methods. The dissociation by (Sp)ATP[alpha S] was rapid and the rate of the light-scattering change by (Sp)ATP[alpha S] was a hyperbolic function of the nucleotide concentration, indicating that dissociation was a two-step process. On the other hand, (Rp)ATP[alpha S] up to 2 mM induced only slow and partial dissociation of the complex, while, in the presence of vanadate, it induced complete dissociation with a slightly higher rate (0.5 s-1). The adenosine 5'-[beta-thio]triphosphate (ATP[beta S]) isomers did not induce dissociation. The hydrolytic activity of the outer arm dynein from sea urchin sperm flagella towards these analogs was similar to that of 22S dynein. The ratios of Vmax (nmol.mg protein-1.min-1)/apparent Km (microM) of this dynein were 400-720, 53, 9.7, 0.62 and 0.028 for ATP, ATP[alpha S] (Sp or Rp), ATP[beta S] (Sp or Rp), respectively, in the presence of Mg2+ as the supporting cation. This dynein exhibited the same stereospecificity at beta phosphate as the 22S dynein or myosin. The detergent models of Tetrahymena or sea urchin spermatozoa were reactivated only by ATP or (Sp)ATP[alpha S] while other analogs were ineffective. The maximal beat frequency of the cilia or flagella reactivated by (Sp)ATP[alpha S] was one-quarter to one-half of that produced by ATP reactivation.

The mechanochemistry of kinesin. A review

The mechanochemical protein kinesin is believed to play an important role in intracellular vesicle movements, including the anterograde motion of axoplasmic transport. This article reviews some of the pharmacological and biochemical information about kinesin, particularly with respect to the properties of nucleotide-dependent microtubule binding, microtubule-activated ATPase activity, and kinesin-driven microtubule translocation. The implications of this information on the mechanochemical mechanisms of kinesin are discussed and a brief comparison of kinesin with two other mechanochemical proteins, myosin and dynein, is also given.

One-dimensional diffusion of microtubules bound to flagellar dynein

Dynein is a multisubunit ATPase that powers microtubule-based motility. We find that a dissociated dynein particle containing the beta heavy chain subunit translocates microtubules unidirectionally over a glass surface in the presence of ATP. However, after nucleotide hydrolysis is inhibited by vanadate, unidirectional translocation ceases, and microtubules instead undergo irregular back-and-forth motion along their longitudinal axes. Quantitative analysis reveals that this motion is due to thermal-driven diffusion, but, unlike a particle undergoing Brownian motion, the diffusion is restricted to one dimension. The properties of the diffusional movement indicate that dynein can interact with microtubules in a way that permits the latter to diffuse only along their longitudinal axes. This weak binding interaction may constitute an important intermediate state in dynein's force-generating cycle.

Adenosine 5'-O-(3-thiotriphosphate) hydrolysis by dynein

The interaction of dynein with ATP gamma S, a phosphorothioate analogue of ATP, has been investigated in depth. The hydrolyses of ATP gamma S and of ATP were shown to be mutually competitive. ATP gamma S induced complete dissociation of the microtubule-dynein complex such that the time course of dissociation monitored by stopped-flow light-scattering methods followed a single exponential. The ATP gamma S concentration dependence of the rate of dissociation was hyperbolic, indicating that the dissociation is at least a two-step process: M.D + ATP gamma S in equilibrium M.D.ATP gamma S----M + D.ATP gamma S. The fit to the hyperbola gives an apparent Kd = 0.5 mM for the binding of ATP gamma S to the microtubule-dynein complex, and the maximal rate of 45 s-1 defines the rate of dissociation of the ternary M.D.ATP gamma S complex. Rapid quench-flow experiments demonstrated that the hydrolysis of ATP gamma S by dynein exhibited an initial burst of product formation. The size of the burst was 1.2 mol/10(6) g of dynein, comparable to that in the case of ATP hydrolysis. The steady-state rate of ATP gamma S turnover by dynein was activated by MAP-free microtubules. Because the rate of ATP gamma S turnover is severalfold (4-8) slower than ATP turnover, the rate-limiting step must be release of thiophosphate, not ADP. Thus, microtubules can activate the rate of thiophosphate release. The stereochemical course of phosphoric residue transfer was determined by using ATP gamma S stereospecifically labeled in the gamma position with 18O.(ABSTRACT TRUNCATED AT 250 WORDS)

Activation of the dynein adenosinetriphosphatase by cross-linking to microtubules

The microtubule-dynein complex consisting of 22S dynein from Tetrahymena cilia and MAP-free microtubules was subjected to treatment with various concentrations of 1-ethyl-3-[3-(dimethylamino)-propyl]carbodiimide (EDC), a zero-length cross-linker, at 28 degrees C for 1 h. Following cross-linking of the microtubule-dynein complex, nearly all of the ATPase activity cosedimented with the microtubules in the presence of ATP. Electron microscopic observation by negative staining revealed that, following treatment with 1 mM EDC, the complex did not dissociate in the presence of ATP, although the dynein decoration pattern was disordered. The complex treated with 3 mM EDC exhibited normal microtubule-dynein patterns even after the addition of ATP. The ATPase activity of the microtubule-dynein complex was enhanced about 30-fold by the treatment with 1-3 mM EDC. These results indicate that the ATPase activation was caused by the close proximity of the dynein ATPase sites to the microtubules and provide further support for the functional interaction of all three dynein heads with the microtubule. The maximal specific activity was 12 mumol min-1 (mg of dynein)-1, corresponding to a turnover rate of 150 s-1, which may be the rate-limiting step at infinite microtubule concentration and may represent the maximum rate of force production in the axoneme.

Microtubules accelerate ADP release by dynein

The effects of microtubules on the phosphate-water oxygen exchange reactions catalyzed by dynein were examined in order to determine the mechanism by which microtubules activate the ATPase. Microtubules inhibited the rate of medium exchange observed during net ATP hydrolysis. Inhibition of the exchange reaction was proportional to the extent of microtubule activation of ATP turnover with no effect on the partition coefficient. These data argue that microtubules do not increase the rate of release of phosphate from dynein; rather, they increase the rate of ADP release. Microtubules markedly inhibited medium phosphate-water exchange reactions observed in the presence of ADP and Pi. With increasing concentrations of ADP, the rate of exchange increased in parallel to the dissociation of dynein from the microtubules, suggesting that only free dynein and not the microtubule-dynein complex catalyzes the exchange reaction. The rates of dynein binding to microtubules in the absence and presence of saturating ADP were 1.6 X 10(6) and 9.8 X 10(5) M-1 s-1, respectively. ADP inhibited the rate of the ATP-induced dissociation of the microtubule-dynein complex with an apparent Kd = 0.37 mM for the binding of ADP to the microtubule-dynein complex. However, the rate of dissociation of ADP from the M.D.ADP complex was quite fast (approximately 1000 s-1). These data support the postulate of a high-energy dynein-ADP intermediate and indicate that microtubules activate the dynein ATPase by enhancing the rate of ADP release.

High-frequency nanometre-scale vibration in 'quiescent' flagellar axonemes

The movement of cilia and flagella is based on the interaction between dynein arms and microtubules coupled with ATP hydrolysis. Although it is established that dynein arms cause adjacent microtubules to slide, little is known about the elementary process underlying the force production. To look more closely at the mechano-chemical conversion mechanism, we recently developed an optical method for measuring a nanometre-scale displacement with a time-resolution better than 1 ms. We now report the detection of high frequency (approximately 300 Hz) vibration of sub-nanometre amplitude in non-beating flagellar axonemes. This vibration could reflect the movement of individual activated dynein arms.