Dynein structure and power stroke

Self-assembly of coiled coils in synthetic biology: inspiration and progress

Biological self-assembly is very complex and results in highly functional materials. In effect, it takes a bottom-up approach using biomolecular building blocks of precisely defined shape, size, hydrophobicity, and spatial distribution of functionality. Inspired by, and drawing lessons from self-assembly processes in nature, scientists are learning how to control the balance of many small forces to increase the complexity and functionality of self-assembled nanomaterials. The coiled-coil motif, a multipurpose building block commonly found in nature, has great potential in synthetic biology. In this review we examine the roles that the coiled-coil peptide motif plays in self-assembly in nature, and then summarize the advances that this has inspired in the creation of functional units, assemblies, and systems.

Bending of the "9+2" axoneme analyzed by the finite element method

Many data demonstrate that the regulation of the bending polarity of the "9+2" axoneme is supported by the curvature itself, making the internal constraints central in this process, adjusting either the physical characteristics of the machinery or the activity of the enzymes involved in different pathways. Among them, the very integrated Geometric Clutch model founds this regulation on the convenient adjustments of the probability of interaction between the dynein arms and the beta-tubulin monomers of the outer doublet pairs on which they walk. Taking into consideration (i) the deviated bending of the outer doublets pairs (Cibert, C., Heck, J.-V., 2004. Cell Motil. Cytoskeleton 59, 153-168), (ii) the internal tensions of the radial spokes and the tangential links (nexin links, dynein arms), (iii) a theoretical 5 microm long proximal segment of the axoneme and (iv) the short proximal segment of the axoneme, we have reevaluated the adjustments of these intervals using a finite element approach. The movements we have calculated within the axonemal cylinder are consistent with the basic hypothesis that found the Geometric Clutch model, except that the axonemal side where the dynein arms are active increases the intervals between the two neighbor outer doublet pairs. This result allows us to propose a mechanism of bending reversion of the axoneme, involving the concerted ignition of the molecular engines along the two opposite sides of the axoneme delineated by the bending plane.

Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis

Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, our lack of knowledge in situ has precluded an understanding of the bending mechanism. Here we reveal nucleotide-induced global structural changes of the outer and inner dynein arms of Chlamydomonas reinhardtii flagella in situ using electron cryotomography. The ATPase domains of the dynein heavy chains move toward the distal end, and the N-terminal tail bends sharply during product release. This motion could drive the adjacent microtubule to cause a sliding motion. In contrast to in vitro results, in the presence of nucleotides, outer dynein arms coexist as clusters of apo or nucleotide-bound forms in situ. This implies a cooperative switching, which may be related to the mechanism of bending.

Flagellar and ciliary beating: the proven and the possible

The working mechanism of the eukaryotic flagellar axoneme remains one of nature's most enduring puzzles. The basic mechanical operation of the axoneme is now a story that is fairly complete; however, the mechanism for coordinating the action of the dynein motor proteins to produce beating is still controversial. Although a full grasp of the dynein switching mechanism remains elusive, recent experimental reports provide new insights that might finally disclose the secrets of the beating mechanism: the special role of the inner dynein arms, especially dynein I1 and the dynein regulatory complex, the importance of the dynein microtubule-binding affinity at the stalk, and the role of bending in the selection of the active dynein group have all been implicated by major new evidence. This Commentary considers this new evidence in the context of various hypotheses of how axonemal dynein coordination might work.

Communication between the AAA+ ring and microtubule-binding domain of dynein

Dyneins are microtubule motors, the core of which consists of a ring of AAA+ domains. ATP-driven conformational changes of the AAA+ ring are used to drive the movement of a mechanical element (termed the linker domain) that provides the motor's powerstroke and to change the affinity of the motor for microtubules (strong binding during the power stroke and weak binding to allow stepping and recocking of the linker domain). Dynein's microtubule-binding domain (MTBD) is located at the end of a 10 nm long anti-parallel coiled coil (the stalk) and conformational changes that alter the affinity for microtubules must propagate through this coiled coil. A recent crystal structure of dynein's MTBD sheds new light on how this long-range communication along a coiled coil might occur.

LIS1 and NudE induce a persistent dynein force-producing state

Cytoplasmic dynein is responsible for many aspects of cellular and subcellular movement. LIS1, NudE, and NudEL are dynein interactors initially implicated in brain developmental disease but now known to be required in cell migration, nuclear, centrosomal, and microtubule transport, mitosis, and growth cone motility. Identification of a specific role for these proteins in cytoplasmic dynein motor regulation has remained elusive. We find that NudE stably recruits LIS1 to the dynein holoenzyme molecule, where LIS1 interacts with the motor domain during the prepowerstroke state of the dynein crossbridge cycle. NudE abrogates dynein force production, whereas LIS1 alone or with NudE induces a persistent-force dynein state that improves ensemble function of multiple dyneins for transport under high-load conditions. These results likely explain the requirement for LIS1 and NudE in the transport of nuclei, centrosomes, chromosomes, and the microtubule cytoskeleton as well as the particular sensitivity of migrating neurons to reduced LIS1 expression.

A low affinity ground state conformation for the Dynein microtubule binding domain

Dynein interacts with microtubules through a dedicated binding domain that is dynamically controlled to achieve high or low affinity, depending on the state of nucleotide bound in a distant catalytic pocket. The active sites for microtubule binding and ATP hydrolysis communicate via conformational changes transduced through a approximately 10-nm length antiparallel coiled-coil stalk, which connects the binding domain to the roughly 300-kDa motor core. Recently, an x-ray structure of the murine cytoplasmic dynein microtubule binding domain (MTBD) in a weak affinity conformation was published, containing a covalently constrained beta(+) registry for the coiled-coil stalk segment (Carter, A. P., Garbarino, J. E., Wilson-Kubalek, E. M., Shipley, W. E., Cho, C., Milligan, R. A., Vale, R. D., and Gibbons, I. R. (2008) Science 322, 1691-1695). We here present an NMR analysis of the isolated MTBD from Dictyostelium discoideum that demonstrates the coiled-coil beta(+) registry corresponds to the low energy conformation for this functional region of dynein. Addition of sequence encoding roughly half of the coiled-coil stalk proximal to the binding tip results in a decreased affinity of the MTBD for microtubules. In contrast, addition of the complete coiled-coil sequence drives the MTBD to the conformationally unstable, high affinity binding state. These results suggest a thermodynamic coupling between conformational free energy differences in the alpha and beta(+) registries of the coiled-coil stalk that acts as a switch between high and low affinity conformations of the MTBD. A balancing of opposing conformations in the stalk and MTBD enables potentially modest long-range interactions arising from ATP binding in the motor core to induce a relaxation of the MTBD into the stable low affinity state.

Regulators of the cytoplasmic dynein motor

Eukaryotic cells use cytoskeletal motor proteins to transport many different intracellular cargos. Numerous kinesins and myosins have evolved to cope with the various transport needs that have arisen during eukaryotic evolution. Surprisingly, a single cytoplasmic dynein (a minus end-directed microtubule motor) carries out similarly diverse transport activities as the many different types of kinesin. How is dynein coupled to its wide range of cargos and how is it spatially and temporally regulated? The answer could lie in the several multifunctional adaptors, including dynactin, lissencephaly 1, nuclear distribution protein E (NUDE) and NUDE-like, Bicaudal D, Rod-ZW10-Zwilch and Spindly, that regulate dynein function and localization.

Protein engineering approaches to study the dynein mechanism using a Dictyostelium expression system

Dyneins are microtubule-based motor complexes that power a wide variety of motile processes within eukaryotic cells, including the beating of cilia and flagella and intracellular trafficking along microtubules. Mechanistic studies on dynein have been hampered by their enormous size (molecular masses of 0.5-3MDa) and molecular complexity. However, the recent establishment of recombinant expression systems for cytoplasmic dynein, together with structural and functional analyses, has advanced our understanding of the molecular mechanisms of dynein motility. Here, we describe several protocols for protein engineering approaches to the dynein mechanism using a Dictyostelium discoideum expression system. We first describe the design and preparation of recombinant dynein suitable for mechanistic studies. We then discuss two distinct functional assays that take advantage of the recombinant dynein. One is for detection of dynein's conformational changes during the ATPase cycle. Another is an in vitro motility assay at multiple- and single-molecule levels for examination of the dynamic behavior of dynein moving on a microtubule.

The dynein stalk contains an antiparallel coiled coil with region-specific stability

The dynein motor proteins interact with microtubules at the distal end of an unusual 12-15 nm stalk, which communicates with the sites for nucleotide hydrolysis and microtubule binding in a cyclical, bidirectional manner. Here, we report that the stalk shaft of rat cytoplasmic dynein is an antiparallel alpha-helical coiled coil, the stability of which is markedly altered by changes at its proximal and distal ends, consistent with a structure capable of rapid, cyclical rearrangement during the dynein cross-bridge cycle.

Dynein light intermediate chain in Aspergillus nidulans is essential for the interaction between heavy and intermediate chains

Cytoplasmic dynein is a complex containing heavy chains (HCs), intermediate chains (ICs), light intermediate chains (LICs), and light chains (LCs). The HCs are responsible for motor activity. The ICs at the tail region of the motor interact with dynactin, which is essential for dynein function. However, functions of other subunits and how they contribute to the assembly of the core complex are not clearly defined. Here, we analyzed in the filamentous fungus Aspergillus nidulans functions of the only LIC and two LCs, RobA (Roadblock/LC7) and TctexA (Tctex1) in dynein-mediated nuclear distribution (nud). Whereas the deletion mutant of tctexA did not exhibit an apparent nud mutant phenotype, the deletion mutant of robA exhibited a nud phenotype at an elevated temperature, which is similar to the previously characterized nudG (LC8) deletion mutant. Remarkably, in contrast to the single mutants, the robA and nudG double deletion mutant exhibits a severe nud phenotype at various temperatures. Thus, functions of these two LC classes overlap to some extent, but the presence of both becomes important under specific conditions. The single LIC, however, is essential for dynein function in nuclear distribution. This is evidenced by the identification of the nudN gene as the LIC coding gene, and by the nud phenotype exhibited by the LIC down-regulating mutant, alcA-LIC. Without a functional LIC, the HC-IC association is significantly weakened, and the HCs could no longer accumulate at the microtubule plus end. Thus, the LIC is essential for the assembly of the core complex of dynein in Aspergillus.

Multivalency in the assembly of intrinsically disordered Dynein intermediate chain

Dynein light chains are thought to increase binding efficiency of dynein intermediate chain to both dynein heavy chain and dynactin, but their exact role is not clear. Isothermal titration calorimetry and x-ray crystallography reported herein indicate that multivalency effects underlie efficient dynein assembly and regulation. For a ternary complex of a 60-amino acid segment of dynein intermediate chain (IC) bound to two homodimeric dynein light chains Tctex1 and LC8, there is a 50-fold affinity enhancement for the second light chain binding. For a designed IC construct containing two LC8 sites, observed the 1000-fold enhancement reflects a remarkably pure entropic chelate effect of a magnitude commensurate with theoretical predictions. The lower enhancement in wild-type IC is attributed to unfavorable free energy changes associated with incremental interactions of IC with Tctex1. Our results show assembled dynein IC as an elongated, flexible polybivalent duplex, and suggest that polybivalency is an important general mechanism for constructing stable yet reversible and functionally versatile complexes.

An outer arm dynein light chain acts in a conformational switch for flagellar motility

A system distinct from the central pair-radial spoke complex was proposed to control outer arm dynein function in response to alterations in the mechanical state of the flagellum. In this study, we examine the role of a Chlamydomonas reinhardtii outer arm dynein light chain that associates with the motor domain of the gamma heavy chain (HC). We demonstrate that expression of mutant forms of LC1 yield dominant-negative effects on swimming velocity, as the flagella continually beat out of phase and stall near or at the power/recovery stroke switchpoint. Furthermore, we observed that LC1 interacts directly with tubulin in a nucleotide-independent manner and tethers this motor unit to the A-tubule of the outer doublet microtubules within the axoneme. Therefore, this dynein HC is attached to the same microtubule by two sites: via both the N-terminal region and the motor domain. We propose that this gamma HC-LC1-microtubule ternary complex functions as a conformational switch to control outer arm activity.

The advent of near-atomic resolution in single-particle electron microscopy

Single-particle electron microscopy (EM) can provide structural information for a large variety of biological molecules, ranging from small proteins to large macromolecular assemblies, without the need to produce crystals. The year 2008 has become a landmark year for single-particle EM as for the first time density maps have been produced at a resolution that made it possible to trace protein backbones or even to build atomic models. In this review, we highlight some of the recent successes achieved by single-particle EM and describe the individual steps involved in producing a density map by this technique. We also discuss some of the remaining challenges and areas, in which further advances would have a great impact on the results that can be achieved by single-particle EM.

Multiscale approaches for studying energy transduction in dynein

Cytoplasmic dynein is an important motor that drives all minus-end directed movement along microtubules. Dynein is a complex motor whose processive motion is driven by ATP-hydrolysis. Dynein's run length has been measured to be several millimetres with typical velocities in the order of a few nanometres per second. Therefore, the average time between steps is a fraction of a second. When this time scale is compared with typical time scales for protein side chain and backbone movements (approximately 10(-9) s and approximately 10(-5) s, respectively), it becomes clear that a multi-timescale modelling approach is required to understand energy transduction in this protein. Here, we review recent efforts to use computational and mathematical modelling to understand various aspects of dynein's chemomechanical cycle. First, we describe a structural model of dynein's motor unit showing a heptameric organization of the motor subunits. Second, we describe our molecular dynamics simulations of the motor unit that are used to investigate the dynamics of the various motor domains. Third, we present a kinetic model of the coordination between the two dynein heads. Lastly, we investigate the various potential geometries of the dimer during its hydrolytic and stepping cycle.

Mechanical design of translocating motor proteins

Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature's design strategy for these molecular engines.

Kinetic models for the coordinated stepping of cytoplasmic dynein

To generate processive motion along a polymer track requires that motor proteins couple their ATP hydrolysis cycle with conformational changes in their structural subunits. Numerous experimental and theoretical efforts have been devoted to establishing how this chemomechanical coupling occurs. However, most processive motors function as dimers. Therefore a full understanding of the motor's performance also requires knowledge of the coordination between the chemomechanical cycles of the two heads. We consider a general two-headed model for cytoplasmic dynein that is built from experimental measurements on the chemomechanical states of monomeric dynein. We explore different possible scenarios of coordination that simultaneously satisfy two main requirements of the dimeric protein: high processivity (long run length) and high motor velocity (fast ATP turnover). To demonstrate the interplay between these requirements and the necessity for coordination, we first develop and analyze a simple mechanical model for the force-induced stepping in the absence of ATP. Next we use a simplified model of dimeric dynein's chemomechanical cycle to establish the kinetic rules that must be satisfied for the model to be consistent with recent data for the motor's performance from single molecule experiments. Finally, we use the results of these investigations to develop a full model for dimeric dynein's chemomechanical cycle and analyze this model to make experimentally testable predictions.

Helix sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding

Coupling between ATPase and track binding sites is essential for molecular motors to move along cytoskeletal tracks. In dynein, these sites are separated by a long coiled coil stalk that must mediate communication between them, but the underlying mechanism remains unclear. Here we show that changes in registration between the two helices of the coiled coil can perform this function. We locked the coiled coil at three specific registrations using oxidation to disulfides of paired cysteine residues introduced into the two helices. These trapped ATPase activity either in a microtubule-independent high or low state, and microtubule binding activity either in an ATP-insensitive strong or weak state, depending on the registry of the coiled coil. Our results provide direct evidence that dynein uses sliding between the two helices of the stalk to couple ATPase and microtubule binding activities during its mechanochemical cycle.

AAA+ Ring and linker swing mechanism in the dynein motor

Dynein ATPases power diverse microtubule-based motilities. Each dynein motor domain comprises a ring-like head containing six AAA+ modules and N- and C-terminal regions, together with a stalk that binds microtubules. How these subdomains are arranged and generate force remains poorly understood. Here, using electron microscopy and image processing of tagged and truncated Dictyostelium cytoplasmic dynein constructs, we show that the heart of the motor is a hexameric ring of AAA+ modules, with the stalk emerging opposite the primary ATPase site (AAA1). The C-terminal region is not an integral part of the ring but spans between AAA6 and near the stalk base. The N-terminal region includes a lever-like linker whose N terminus swings by ∼17 nm during the ATPase cycle between AAA2 and the stalk base. Together with evidence of stalk tilting, which may communicate changes in microtubule binding affinity, these findings suggest a model for dynein's structure and mechanism.

Walking the walk: how kinesin and dynein coordinate their steps

Molecular motors drive key biological processes such as cell division, intracellular organelle transport, and sperm propulsion and defects in motor function can give rise to various human diseases. Two dimeric microtubule-based motor proteins, kinesin-1 and cytoplasmic dynein can take over one hundred steps without detaching from the track. In this review, we discuss how these processive motors coordinate the activities of their two identical motor domains so that they can walk along microtubules.

Structure and functional role of dynein's microtubule-binding domain

Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.

Dynein pulls microtubules without rotating its stalk

Dynein is a microtubule motor that powers motility of cilia and flagella. There is evidence that the relative sliding of the doublet microtubules is due to a conformational change in the motor domain that moves a microtubule bound to the end of an extension known as the stalk. A predominant model for the movement involves a rotation of the head domain, with its stalk, toward the microtubule plus end. However, stalks bound to microtubules have been difficult to observe. Here, we present the clearest views so far of stalks in action, by observing sea urchin, outer arm dynein molecules bound to microtubules, with a new method, "cryo-positive stain" electron microscopy. The dynein molecules in the complex were shown to be active in in vitro motility assays. Analysis of the electron micrographs shows that the stalk angles relative to microtubules do not change significantly between the ADP.vanadate and no-nucleotide states, but the heads, together with their stalks, shift with respect to their A-tubule attachments. Our results disagree with models in which the stalk acts as a lever arm to amplify structural changes. The observed movement of the head and stalk relative to the tail indicates a new plausible mechanism, in which dynein uses its stalk as a grappling hook, catching a tubulin subunit 8 nm ahead and pulling on it by retracting a part of the tail (linker).

Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella

The inner dynein arm regulates axonemal bending motion in eukaryotes. We used cryo-electron tomography to reconstruct the three-dimensional structure of inner dynein arms from Chlamydomonas reinhardtii. All the eight different heavy chains were identified in one 96-nm periodic repeat, as expected from previous biochemical studies. Based on mutants, we identified the positions of the AAA rings and the N-terminal tails of all the eight heavy chains. The dynein f dimer is located close to the surface of the A-microtubule, whereas the other six heavy chain rings are roughly colinear at a larger distance to form three dyads. Each dyad consists of two heavy chains and has a corresponding radial spoke or a similar feature. In each of the six heavy chains (dynein a, b, c, d, e, and g), the N-terminal tail extends from the distal side of the ring. To interact with the B-microtubule through stalks, the inner-arm dyneins must have either different handedness or, more probably, the opposite orientation of the AAA rings compared with the outer-arm dyneins.

Life as a nanoscale phenomenon

The nanoscale is not just the middle ground between molecular and macroscopic but a dimension that is specifically geared to the gathering, processing, and transmission of chemical-based information. Herein we consider the living cell as an integrated self-regulating complex chemical system run principally by nanoscale miniaturization, and propose that this specific level of dimensional constraint is critical for the emergence and sustainability of cellular life in its minimal form. We address key aspects of the structure and function of the cell interface and internal metabolic processing that are coextensive with the up-scaling of molecular components to globular nanoobjects (integral membrane proteins, enzymes, and receptors, etc) and higher-order architectures such as microtubules, ribosomes, and molecular motors. Future developments in nanoscience could provide the basis for artificial life.

Regulatory ATPase sites of cytoplasmic dynein affect processivity and force generation

The heavy chain of cytoplasmic dynein contains four nucleotide-binding domains referred to as AAA1–AAA4, with the first domain (AAA1) being the main ATP hydrolytic site. Although previous studies have proposed regulatory roles for AAA3 and AAA4, the role of ATP hydrolysis at these sites remains elusive. Here, we have analyzed the single molecule motility properties of yeast cytoplasmic dynein mutants bearing mutations that prevent ATP hydrolysis at AAA3 or AAA4. Both mutants remain processive, but the AAA4 mutant exhibits a surprising increase in processivity due to its tighter affinity for microtubules. In addition to changes in motility characteristics, AAA3 and AAA4 mutants produce less maximal force than wild-type dynein. These results indicate that the nucleotide binding state at AAA3 and AAA4 can allosterically modulate microtubule binding affinity and affect dynein processivity and force production.

HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence

The toxicity and inefficacy of actual organic drugs against Leishmaniosis justify research projects to find new molecular targets in Leishmania species including Leishmania infantum (L. infantum) and Leishmaniamajor (L. major), both important pathogens. In this sense, quantitative structure-activity relationship (QSAR) methods, which are very useful in Bioorganic and Medicinal Chemistry to discover small-sized drugs, may help to identify not only new drugs but also new drug targets, if we apply them to proteins. Dyneins are important proteins of these parasites governing fundamental processes such as cilia and flagella motion, nuclear migration, organization of the mitotic splinde, and chromosome separation during mitosis. However, despite the interest for them as potential drug targets, so far there has been no report whatsoever on dyneins with QSAR techniques. To the best of our knowledge, we report here the first QSAR for dynein proteins. We used as input the Spectral Moments of a Markov matrix associated to the HP-Lattice Network of the protein sequence. The data contain 411 protein sequences of different species selected by ClustalX to develop a QSAR that correctly discriminates on average between 92.75% and 92.51% of dyneins and other proteins in four different train and cross-validation datasets. We also report a combined experimental and theoretic study of a new dynein sequence in order to illustrate the utility of the model to search for potential drug targets with a practical example. First, we carried out a 2D-electrophoresis analysis of L. infantum biological samples. Next, we excised from 2D-E gels one spot of interest belonging to an unknown protein or protein fragment in the region M<20,200 and pI<4. We used MASCOT search engine to find proteins in the L. major data base with the highest similarity score to the MS of the protein isolated from L. infantum. We used the QSAR model to predict the new sequence as dynein with probability of 99.99% without relying upon alignment. In order to confirm the previous function annotation we predicted the sequences as dynein with BLAST and the omniBLAST tools (96% alignment similarity to dyneins of other species). Using this combined strategy, we have successfully identified L. infantum protein containing dynein heavy chain, and illustrated the potential use of the QSAR model as a complement to alignment tools.

Proton-sponge coated quantum dots for siRNA delivery and intracellular imaging

We report the rational design of multifunctional nanoparticles for short-interfering RNA (siRNA) delivery and imaging based on the use of semiconductor quantum dots (QDs) and proton-absorbing polymeric coatings (proton sponges). With a balanced composition of tertiary amine and carboxylic acid groups, these nanoparticles are specifically designed to address longstanding barriers in siRNA delivery such as cellular penetration, endosomal release, carrier unpacking, and intracellular transport. The results demonstrate dramatic improvement in gene silencing efficiency by 10-20-fold and simultaneous reduction in cellular toxicity by 5-6-fold, when compared directly with existing transfection agents for MDA-MB-231 cells. The QD-siRNA nanoparticles are also dual-modality optical and electron-microscopy probes, allowing real-time tracking and ultrastructural localization of QDs during delivery and transfection. These new insights and capabilities represent a major step toward nanoparticle engineering for imaging and therapeutic applications.

Three-dimensional reconstruction of axonemal outer dynein arms in situ by electron tomography

We present here for the first time a 3D reconstruction of in situ axonemal outer dynein arms. This reconstruction has been obtained by electron tomography applied to a series of tilted images collected from metal replicas of rapidly frozen, cryofractured, and metal-replicated sperm axonemes of the cecidomid dipteran Monarthropalpus flavus. This peculiar axonemal model consists of several microtubular laminae that proved to be particularly suitable for this type of analysis. These laminae are sufficiently planar to allow the visualization of many dynein molecules within the same fracture face, allowing us to recover a significant number of equivalent objects and to improve the signal-to-noise ratio of the reconstruction by applying advanced averaging protocols. The 3D model we obtained showed the following interesting structural features: First, each dynein arm has two head domains that are almost parallel and are obliquely oriented with respect to the longitudinal axis of microtubules. The two heads are therefore positioned at different distances from the surface of the A-tubule. Second, each head domain consists of a series of globular subdomains that are positioned on the same plane. Third, a stalk domain originates as a conical region from the proximal head and ends with a small globular domain that contacts the B-tubule. Fourth, the stem region comprises several globular subdomains and presents two distinct points of anchorage to the surface of the A-tubule. Finally, and most importantly, contrary to what has been observed in isolated dynein molecules adsorbed to flat surfaces, the stalk and the stem domains are not in the same plane as the head.

The dynein stalk head, the microtubule binding-domain of dynein: NMR assignment and ligand binding

Dynein is a motor ATPase, and the C-terminal two-thirds of its heavy chain form a ring structure. One of protrudings from this ring structure is a stalk whose tip, the dynein stalk head (DSH), is thought to be the microtubule-binding domain. As a first step toward elucidating the functional mechanisms of DSH, we aimed at the NMR structural analysis of an isolated DSH from mouse cytoplasmic dynein. The DSH expressed in bacteria and purified was coprecipitated with microtubules, suggesting its proper folding. Chemical shifts of the DSH were obtained from NMR measurements, and backbone assignment identified 94% of the main-chain N-H signals. Secondary structural prediction programs showed that about 60% of the residues formed alpha-helices. A region with cationic residues K58 and R61 (and possibly R66 as well), and another with R86, K88, K90, and K91, were found to form alpha-helices. Both of these regions may be important in the formation of the DSH-binding site to a microtubule that has a low pI with a number of acidic residues. Two synthetic peptides containing the sequence of the alpha-helix 12 of beta-tubulin, considered to be important in binding to DSH, were investigated. Of these two peptides, the one with higher helix-formation propensity appeared to bind to DSH, since it precipitated with DSH in a nearly stoichiometric manner. This suggested that the alpha-helicity of this region would be important in its binding to DSH.

Model for the unidirectional motion of a dynein molecule

Cytoplasmic dyneins transport cellular organelles by moving on a microtubule filament. It has been found recently that depending on the applied force and the concentration of the adenosine triphosphate molecules, dynein's step size varies. Based on these studies, we propose a simple model for dynein's unidirectional motion taking into account the variations in its step size. We study how the average velocity and the relative dispersion in the displacement vary with the applied load. The model is amenable to further extensions by inclusion of details associated with the structure and the processivity of the molecule.

Arp11 affects dynein-dynactin interaction and is essential for dynein function in Aspergillus nidulans

The dynactin complex contains proteins including p150 that interacts with cytoplasmic dynein and an actin-related protein Arp1 that forms a minifilament. Proteins including Arp11 and p62 locate at the pointed end of the Arp1 filament, but their biochemical functions are unclear (Schroer TA. Dynactin. Annu Rev Cell Dev Biol 2004;20:759-779). In Aspergillus nidulans, loss of Arp11 or p62 causes the same nuclear distribution (nud) defect displayed by dynein mutants, indicating that these pointed-end proteins are essential for dynein function. We constructed a strain with S-tagged p150 of dynactin that allows us to pull down components of the dynactin and dynein complexes. Surprisingly, while the ratio of pulled-down Arp1 to S-p150 in Arp11-depleted cells is clearly lower than that in wild-type cells, the ratio of pulled-down dynein to S-p150 is significantly higher. We further show that the enhanced dynein-dynactin interaction in Arp11-depleted cells is also present in the soluble fraction and therefore is not dependent upon the affinity of these proteins to the membrane. We suggest that loss of the pointed-end proteins alters the Arp1 filament in a way that affects the conformation of p150 required for its proper interaction with the dynein motor.

Tuning microtubule-based transport through filamentous MAPs: the problem of dynein

We recently proposed that regulating the single-to-multiple motor transition was a likely strategy for regulating kinesin-based transport in vivo. In this study, we use an in vitro bead assay coupled with an optical trap to investigate how this proposed regulatory mechanism affects dynein-based transport. We show that tau's regulation of kinesin function can proceed without interfering with dynein-based transport. Surprisingly, at extremely high tau levels--where kinesin cannot bind microtubules (MTs)--dynein can still contact MTs. The difference between tau's effects on kinesin- and dynein-based motility suggests that tau can be used to tune relative amounts of plus-end and minus-end-directed transport. As in the case of kinesin, we find that the 3RS isoform of tau is a more potent inhibitor of dynein binding to MTs. We show that this isoform-specific effect is not because of steric interference of tau's projection domains but rather because of tau's interactions with the motor at the MT surface. Nonetheless, we do observe a modest steric interference effect of tau away from the MT and discuss the potential implications of this for molecular motor structure.

Molecular mechanism of force generation by dynein, a molecular motor belonging to the AAA+ family

Dynein is an AAA+ (ATPase associated with various cellular activities)-type motor complex that utilizes ATP hydrolysis to actively drive microtubule sliding. The dynein heavy chain (molecular mass >500 kDa) contains six tandemly linked AAA+ modules and exhibits full motor activities. Detailed molecular dissection of this motor with unique architecture was hampered by the lack of an expression system for the recombinant heavy chain, as a result of its large size. However, the recent success of recombinant protein expression with full motor activities has provided a method for advances in structure-function studies in order to elucidate the molecular mechanism of force generation.

Molecular motors: not quite like clockwork

Models commonly used to explain the mechanism of myosin motors typically include a power stroke that is attributed to a conformational change in the motor domain and amplified by a long lever arm that connects the motor domain to the cargo. Similar models have proved less enlightening in the case of microtubule motors, for which it may be more helpful to consider models involving thermally driven mechanisms.

Force-induced bidirectional stepping of cytoplasmic dynein

Cytoplasmic dynein is a minus-end-directed microtubule motor whose mechanism of movement remains poorly understood. Here, we use optical tweezers to examine the force-dependent stepping behavior of yeast cytoplasmic dynein. We find that dynein primarily advances in 8 nm increments but takes other sized steps (4-24 nm) as well. An opposing force induces more frequent backward stepping by dynein, and the motor walks backward toward the microtubule plus end at loads above its stall force of 7 pN. Remarkably, in the absence of ATP, dynein steps processively along microtubules under an external load, with less force required for minus-end- than for plus-end-directed movement. This nucleotide-independent walking reveals that force alone can drive repetitive microtubule detachment-attachment cycles of dynein's motor domains. These results suggest a model for how dynein's two motor domains coordinate their activities during normal processive motility and provide new clues for understanding dynein-based motility in living cells.

Kinesin and dynein-dynactin at intersecting microtubules: motor density affects dynein function

Kinesin and cytoplasmic dynein are microtubule-based motor proteins that actively transport material throughout the cell. Microtubules can intersect at a variety of angles both near the nucleus and at the cell periphery, and the behavior of molecular motors at these intersections has implications for long-range transport efficiency and accuracy. To test motor function at microtubule intersections, crossovers were arranged in vitro using flow to orient successive layers of filaments. Single kinesin and cytoplasmic dynein-dynactin molecules fused with green-fluorescent protein, and artificial bead cargos decorated with multiple motors, were observed while they encountered intersections. Single kinesins tend to cross intersecting microtubules, whereas single dynein-dynactins have a more varied response. For bead cargos, kinesin motion is independent of motor number. Dynein beads with high motor numbers pause, but their actions become more varied as the motor number decreases. These results suggest that regulating the number of active dynein molecules could change a motile cargo into one that is anchored at an intersection, consistent with dynein's proposed transport and tethering functions in the cell.

New insights into the cell biology of insect axonemes

Insects do not possess ciliated epithelia, and cilia/flagella are present in the sperm tail and--as modified cilia--in mechano- and chemosensory neurons. The core cytoskeletal component of these organelles, the axoneme, is a microtubule-based structure that has been conserved throughout evolution. However, in insects the sperm axoneme exhibits distinctive structural features; moreover, several insect groups are characterized by an unusual sperm axoneme variability. Besides the abundance of morphological data on insect sperm flagella, most of the available molecular information on the insect axoneme comes from genetic studies on Drosophila spermatogenesis, and only recently other insect species have been proposed as useful models. Here, we review the current knowledge on the cell biology of insect axoneme, including contributions from both Drosophila and other model insects.