Structural diversity and dynamics of microtubules and polymorphic tubulin assemblies

Structure of the γ-tubulin ring complex-capped microtubule

Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the long axis of the filament. We report that the human ~2.3 MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryogenic electron microscopy reconstructions of γ-TuRC-capped microtubule minus ends reveal the extensive intra-domain and inter-domain motions of γ-TuRC subunits that accommodate luminal bridge components and establish lateral and longitudinal interactions between γ-tubulins and α-tubulins. Our structures suggest that γ-TuRC, an inefficient nucleation template owing to its splayed conformation, can transform into a compacted cap at the microtubule minus end and set the lattice architecture of cellular microtubules.

Doublet microtubule inner junction protein FAP20 recruits tubulin to the microtubule lattice

Doublet microtubules of eukaryotic cilia and flagella are made up of a complete A- and an incomplete B-tubule that are fused together. Of the two fusion points, the outer junction is made of tripartite tubulin connections, while the inner junction contains non-tubulin elements. The latter includes flagellar-associated protein 20 (FAP20) and Parkin co-regulated gene protein (PACRG) that together link the A- and B-tubule at the inner junction. While structures of doublet microtubules reveal molecular details, their assembly is poorly understood. In this study, we purified recombinant FAP20 and characterized its effects on microtubule dynamics. We use in vitro reconstitution and cryo-electron microscopy to show that FAP20 recruits free tubulin to the existing microtubule lattice. Our cryo-electron microscopy reconstruction of microtubule:FAP20:tubulin complex reveals the mode of tubulin recruitment by FAP20 onto microtubules, providing insights into assembly steps of B-tubule closure during doublet microtubule formation.

Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers

Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.

Structure of the γ-tubulin ring complex-capped microtubule

Microtubules are composed of α/β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the filament's long-axis. We report that the human ∼2.3MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryo-EM reconstructions of γ-TuRC-capped microtubule minus-ends reveal the extensive intra- and inter-domain motions of γ-TuRC subunits that accommodate its actin-containing luminal bridge and establish lateral and longitudinal interactions between γ- and α-tubulins. Our structures reveal how free γ-TuRC, an inefficient nucleation template due to its splayed conformation, transforms into a stable cap that blocks addition or loss of α/β-tubulins from minus-ends and sets the lattice architecture of cellular microtubules.

One Sentence Summary

Structural insights into how the γ-tubulin ring complex nucleates and caps a 13-protofilament microtubule.

TUBB3 and KIF21A in neurodevelopment and disease

Neuronal migration and axon growth and guidance require precise control of microtubule dynamics and microtubule-based cargo transport. TUBB3 encodes the neuronal-specific β-tubulin isotype III, TUBB3, a component of neuronal microtubules expressed throughout the life of central and peripheral neurons. Human pathogenic TUBB3 missense variants result in altered TUBB3 function and cause errors either in the growth and guidance of cranial and, to a lesser extent, central axons, or in cortical neuronal migration and organization, and rarely in both. Moreover, human pathogenic missense variants in KIF21A, which encodes an anterograde kinesin motor protein that interacts directly with microtubules, alter KIF21A function and cause errors in cranial axon growth and guidance that can phenocopy TUBB3 variants. Here, we review reported TUBB3 and KIF21A variants, resulting phenotypes, and corresponding functional studies of both wildtype and mutant proteins. We summarize the evidence that, in vitro and in mouse models, loss-of-function and missense variants can alter microtubule dynamics and microtubule-kinesin interactions. Lastly, we highlight additional studies that might contribute to our understanding of the relationship between specific tubulin isotypes and specific kinesin motor proteins in health and disease.

Computational Investigation of the Ordered Water System Around Microtubules: Implications for Protein Interactions

The existence of an exclusion zone in which particles of a colloidal suspension in water are repelled from hydrophilic surfaces has been experimentally demonstrated in numerous studies, especially in the case of Nafion surfaces. Various explanations have been proposed for the origin of this phenomenon, which is not completely understood yet. In particular, the existence of a fourth phase of water has been proposed by G. Pollack and if this theory is proven correct, its implications on our understanding of the properties of water, especially in biological systems, would be profound and could give rise to new medical therapies. Here, a simple approach based on the linearized Poisson-Boltzmann equation is developed in order to study the repulsive forces mediated by ordered water and involving the following interacting biomolecules: 1) microtubule and a tubulin dimer, 2) two tubulin dimers and 3) a tubulin sheet and a tubulin dimer. The choice of microtubules in this study is motivated because they could be a good candidate for the generation of an exclusion zone in the cell and these models could be a starting point for detailed experimental investigations of this phenomenon.

A cryo-ET survey of microtubules and intracellular compartments in mammalian axons

The neuronal axon is packed with cytoskeletal filaments, membranes, and organelles, many of which move between the cell body and axon tip. Here, we used cryo-electron tomography to survey the internal components of mammalian sensory axons. We determined the polarity of the axonal microtubules (MTs) by combining subtomogram classification and visual inspection, finding MT plus and minus ends are structurally similar. Subtomogram averaging of globular densities in the MT lumen suggests they have a defined structure, which is surprising given they likely contain the disordered protein MAP6. We found the endoplasmic reticulum in axons is tethered to MTs through multiple short linkers. We surveyed membrane-bound cargos and describe unexpected internal features such as granules and broken membranes. In addition, we detected proteinaceous compartments, including numerous virus-like capsid particles. Our observations outline novel features of axonal cargos and MTs, providing a platform for identification of their constituents.

Hierarchical Assembly Pathways of Spermine-Induced Tubulin Conical-Spiral Architectures

Tubulin, an essential cytoskeletal protein, assembles into various morphologies by interacting with an array of cellular factors. One of these factors is the endogenous polyamine spermine, which may promote and stabilize tubulin assemblies. Nevertheless, the assembled structures and their formation pathways are poorly known. Here we show that spermine induced the in vitro assembly of tubulin into several hierarchical architectures based on a tubulin conical-spiral subunit. Using solution X-ray scattering and cryo-TEM, we found that with progressive increase of spermine concentration tubulin dimers assembled into conical-frustum-spirals of increasing length, containing up to three helical turns. The subunits with three helical turns were then assembled into tubules through base-to-top packing and formed antiparallel bundles of tubulin conical-spiral tubules in a distorted hexagonal symmetry. Further increase of the spermine concentration led to inverted tubulin tubules assembled in hexagonal bundles. Time-resolved experiments revealed that tubulin assemblies formed at higher spermine concentrations assembled from intermediates, similar to those formed at low spermine concentrations. These results are distinct from the classical transition between twisted ribbons, helical, and tubular assemblies, and provide insight into the versatile morphologies that tubulin can form. Furthermore, they may contribute to our understanding of the interactions that control the composition and construction of protein-based biomaterials.

Novel colchicine conjugate with unusual effect on the microtubules of cancer cells

Colchicine derivative bearing substituted bispidine moiety, namely N-{7-(3,7-Di-(tert-butoxycarbonyl)-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonan-9-yl)-oxy-7-oxoheptanoyl}-N-deacetylcolchicine, was synthesized and tested for its effect on the net of microtubules (MT) in lung cancer cells A549. The compound induced not only MT depolymerization but stimulated the formation of small tubulin aggregates and long tubulin fibrils localized mainly around nuclei. The assemblies were morphologically different from tubulin clusters induced by structurally related anticancer agent tubuloclustin. The biotests data demonstrate that the depolymerization takes place for both pure tubulin and tubulin in cellulo, while fibrils are formed only in the cells. The research data of structure–activity relationship for several similar colchicine derivatives synthesized in the work give evidence for the proposition that the initial conjugate may interact not only with tubulin and MT in the cells, but also with MT-associated proteins, involved in the process of tubulin polymerization. The ability to affect simultaneously MAP – tubulin interactions opens attractive prospects in the design of novel anticancer agents.

Helical organization of microtubules occurs in a minority of tunneling membrane nanotubes in normal and cancer urothelial cells

Tunneling membrane nanotubes (TnTs) are membrane protrusions connecting nearby or distant cells in vitro and in vivo. Functions of TnTs in cellular processes are various and rely on TnT structure, which also depends on cytoskeletal composition. In the present study, we focused on the organization of microtubules (MTs) and intermediate filaments (IFs) in TnTs of urothelial cells. We analysed TnTs of normal porcine urothelial cells, which morphologically and physiologically closely resemble normal human urothelial cells, and of cancer cells derived from invasive human urothelial neoplasm. Wide-field fluorescence, confocal and super-resolution microscopy techniques, together with image analyses and 3D reconstructions enlightened specific MT-IF organization in TnTs, and for the first time revealed that MTs and IFs co-occur in the majority of normal and cancer urothelial cell TnTs. Our findings show that in the initiation segment of TnTs, MTs are cross-linked with each other into filamentous network, however in the middle and the attaching segment of TnT, MTs can helically enwrap IFs, the phenomenon that has not been shown before within the TnTs. In this study, we assess MT-IF co-occurrence in TnTs and present evidence that such helical organization of MTs enwrapping IFs is only occurring in a minority of the TnTs. We also discuss the possible cell-biological and physiological reasons for helical organization of MTs in TnTs.

The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth

The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth.

Separating the effects of nucleotide and EB binding on microtubule structure

We report three high-resolution structures of microtubules in different nucleotide states—GMPCPP, GDP, and GTPγS—in the absence of any binding proteins, allowing us to separate the effects of nucleotide- and microtubule (MT)-associated protein (MAPs) binding on MT structure. End-binding (EB) proteins can bind and induce partial lattice compaction of a preformed GMPCPP-bound MT, a lattice type that is far from EBs’ ideal binding platform. We propose a model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs. These global lattice rearrangements in turn affect the affinity of other MT partners and result in the exquisite regulation of the MT dynamics.

Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.

Elastic, dipole-dipole interaction and viscosity impact on vibrational properties of anisotropic hexagonal microtubule lattice

The paper investigates microtubules lattice properties taking into consideration elastic, dipole-dipole interaction of tubulins and viscosity. A microtubule is modeled as a system of bound tubulins, forming a skewed hexagonal two-dimensional lattice. Wave frequencies and group velocities have been calculated. Calculations have been performed for various directions of wave front propagation: helix, along the protofilament, and anti-helix. Three different wave polarization directions have been considered. It has been shown that the direction of the wave polarization influences the frequency and wave group velocity values in the lattice considerably. The impact of dipole-dipole interaction greatly depends on the direction of the wave polarization; thus, it is only moderate for the longitudinally (LA) polarized waves while it is sufficient for the transversely (TA), and out-of-plane (ZA) polarized waves. Moreover dipole-dipole interaction may result in the waves which are able to cause the rupture of microtubules. With viscosity considered, lattice oscillations become harmonically damped only over a certain wavelength range when longitudinal polarization occurs. Out of this range as well as for the other polarization directions, lattice deviations from equilibrium are dampened exponentially. Taking viscosity into consideration also results in a noticeable decrease in frequency and increase in the group wave velocity when the waves are longitudinally polarized. Reverse wave domains which may be associated with a possible phenomenon of negative refraction have been determined for hexagonal microtubule lattice.

A microtubule bestiary: structural diversity in tubulin polymers

Microtubules are long, slender polymers of αβ-tubulin found in all eukaryotic cells. Tubulins associate longitudinally to form protofilaments, and adjacent protofilaments associate laterally to form the microtubule. In the textbook view, microtubules are 1) composed of 13 protofilaments, 2) arranged in a radial array by the centrosome, and 3) built into the 9+2 axoneme. Although these canonical structures predominate in eukaryotes, microtubules with divergent protofilament numbers and higher-order microtubule assemblies have been discovered throughout the last century. Here we survey these noncanonical structures, from the 4-protofilament microtubules of Prosthecobacter to the 40-protofilament accessory microtubules of mantidfly sperm. We review the variety of protofilament numbers observed in different species, in different cells within the same species, and in different stages within the same cell. We describe the determinants of protofilament number, namely nucleation factors, tubulin isoforms, and posttranslational modifications. Finally, we speculate on the functional significance of these diverse polymers. Equipped with novel tubulin-purification tools, the field is now prepared to tackle the long-standing question of the evolutionary basis of microtubule structure.

Measuring Microtubule Supertwist and Defects by Three-Dimensional-Force-Clamp Tracking of Single Kinesin-1 Motors

Three-dimensional (3D) nanometer tracking of single biomolecules provides important information about their biological function. However, existing microscopy approaches often have only limited spatial or temporal precision and do not allow the application of defined loads. Here, we developed and applied a high-precision 3D-optical-tweezers force clamp to track in vitro the 3D motion of single kinesin-1 motor proteins along microtubules. To provide the motors with unimpeded access to the whole microtubule lattice, we mounted the microtubules on topographic surface features generated by UV-nanoimprint lithography. Because kinesin-1 motors processively move along individual protofilaments, we could determine the number of protofilaments the microtubules were composed of by measuring the helical pitches of motor movement on supertwisted microtubules. Moreover, we were able to identify defects in microtubules, most likely arising from local changes in the protofilament number. While it is hypothesized that microtubule supertwist and defects can severely influence the function of motors and other microtubule-associated proteins, the presented method allows for the first time to fully map the microtubule lattice in situ. This mapping allows the correlation of motor-filament interactions with the microtubule fine-structure. With the additional ability to apply loads, we expect our 3D-optical-tweezers force clamp to become a valuable tool for obtaining a wide range of information from other biological systems, inaccessible by two-dimensional and/or ensemble measurements.

The Roles of β-Tubulin Mutations and Isotype Expression in Acquired Drug Resistance

The antitumor drug paclitaxel stabilizes microtubules and reduces their dynamicity, promoting mitotic arrest and eventually apoptosis. Upon assembly of the α/β-tubulin heterodimer, GTP becomes bound to both the α and β-tubulin monomers. During microtubule assembly, the GTP bound to β-tubulin is hydrolyzed to GDP, eventually reaching steady-state equilibrium between free tubulin dimers and those polymerized into microtubules. Tubulin-binding drugs such as paclitaxel interact with β-tubulin, resulting in the disruption of this equilibrium. In spite of several crystal structures of tubulin, there is little biochemical insight into the mechanism by which anti-tubulin drugs target microtubules and alter their normal behavior. The mechanism of drug action is further complicated, as the description of altered β-tubulin isotype expression and/or mutations in tubulin genes may lead to drug resistance as has been described in the literature. Because of the relationship between β-tubulin isotype expression and mutations within β-tubulin, both leading to resistance, we examined the properties of altered residues within the taxane, colchicine and Vinca binding sites. The amount of data now available, allows us to investigate common patterns that lead to microtubule disruption and may provide a guide to the rational design of novel compounds that can inhibit microtubule dynamics for specific tubulin isotypes or, indeed resistant cell lines. Because of the vast amount of data published to date, we will only provide a broad overview of the mutational results and how these correlate with differences between tubulin isotypes. We also note that clinical studies describe a number of predictive factors for the response to anti-tubulin drugs and attempt to develop an understanding of the features within tubulin that may help explain how they may affect both microtubule assembly and stability.

Live visualizations of single isolated tubulin protein self-assembly via tunneling current: effect of electromagnetic pumping during spontaneous growth of microtubule

As we bring tubulin protein molecules one by one into the vicinity, they self-assemble and entire event we capture live via quantum tunneling. We observe how these molecules form a linear chain and then chains self-assemble into 2D sheet, an essential for microtubule, —fundamental nano-tube in a cellular life form. Even without using GTP, or any chemical reaction, but applying particular ac signal using specially designed antenna around atomic sharp tip we could carry out the self-assembly, however, if there is no electromagnetic pumping, no self-assembly is observed. In order to verify this atomic scale observation, we have built an artificial cell-like environment with nano-scale engineering and repeated spontaneous growth of tubulin protein to its complex with and without electromagnetic signal. We used 64 combinations of plant, animal and fungi tubulins and several doping molecules used as drug, and repeatedly observed that the long reported common frequency region where protein folds mechanically and its structures vibrate electromagnetically. Under pumping, the growth process exhibits a unique organized behavior unprecedented otherwise. Thus, “common frequency point” is proposed as a tool to regulate protein complex related diseases in the future.

Giant spermatozoa and a huge spermatheca: a case of coevolution of male and female reproductive organs in the ground louse Zorotypus impolitus (Insecta, Zoraptera)

The male and female genital apparatus of the recently discovered ground louse Zorotypus impolitus were examined using light and electron microscopy. The rounded testes and a large seminal vesicle are connected with a complex of four accessory glands by a long tapering ejaculatory duct. Two accessory glands have the same whitish coloration, whereas the third one is pale blue, and the elongated and cylindrical fourth one translucent. The sperm are the largest known in Hexapoda, 3mm long and 3μm wide, with a volume of ca. 21,000μm(3); the ratio between the diameter of the axoneme and the width of the main body of the sperm ranges between 1:10 and 1:13. The exceptional width of the spermatozoa is due to an extreme enlargement of the mitochondrial derivatives and accessory bodies. A single sperm is contained in a small globular spermatophore (100μm). The highly unusual external transfer correlates with an atypical mating behavior. The male produces several to many spermatophores during the mating process. As in other zorapterans the ovaries are panoistic and the eggs bear two micropyles. An exceptionally large apical spermathecal receptacle is present; it is connected with the vagina by a long spermathecal duct, which varies structurally along its course. A correlation between the sperm size and the size of the spermatheca is likely. Ultrastructural features of different species support two strikingly different models of male and female reproductive apparatus in the small order Zoraptera. This is in stark contrast to the extreme uniformity of their external morphology. It is likely that sexual selection played a decisive role in the evolution of the reproductive system.

Posttranslational acetylation of α-tubulin constrains protofilament number in native microtubules

BACKGROUND

Microtubules are built from linear polymers of α-β tubulin dimers (protofilaments) that form a tubular quinary structure. Microtubules assembled from purified tubulin in vitro contain between 10 and 16 protofilaments; however, such structural polymorphisms are not found in cells. This discrepancy implies that factors other than tubulin constrain microtubule protofilament number, but the nature of these constraints is unknown.

RESULTS

Here, we show that acetylation of MEC-12 α-tubulin constrains protofilament number in C. elegans touch receptor neurons (TRNs). Whereas the sensory dendrite of wild-type TRNs is packed with a cross-linked bundle of long, 15-protofilament microtubules, mec-17;atat-2 mutants lacking α-tubulin acetyltransferase activity have short microtubules, rampant lattice defects, and variable protofilament number both between and within microtubules. All-atom molecular dynamics simulations suggest a model in which acetylation of lysine 40 promotes the formation of interprotofilament salt bridges, stabilizing lateral interactions between protofilaments and constraining quinary structure to produce stable, structurally uniform microtubules in vivo.

CONCLUSIONS

Acetylation of α-tubulin is an essential constraint on protofilament number in vivo. We propose a structural model in which this posttranslational modification promotes the formation of lateral salt bridges that fine-tune the association between adjacent protofilaments and enable the formation of uniform microtubule populations in vivo.

The zinc dyshomeostasis hypothesis of Alzheimer's disease

Alzheimer's disease (AD) is the most common form of dementia in the elderly. Hallmark AD neuropathology includes extracellular amyloid plaques composed largely of the amyloid-β protein (Aβ), intracellular neurofibrillary tangles (NFTs) composed of hyper-phosphorylated microtubule-associated protein tau (MAP-tau), and microtubule destabilization. Early-onset autosomal dominant AD genes are associated with excessive Aβ accumulation, however cognitive impairment best correlates with NFTs and disrupted microtubules. The mechanisms linking Aβ and NFT pathologies in AD are unknown. Here, we propose that sequestration of zinc by Aβ-amyloid deposits (Aβ oligomers and plaques) not only drives Aβ aggregation, but also disrupts zinc homeostasis in zinc-enriched brain regions important for memory and vulnerable to AD pathology, resulting in intra-neuronal zinc levels, which are either too low, or excessively high. To evaluate this hypothesis, we 1) used molecular modeling of zinc binding to the microtubule component protein tubulin, identifying specific, high-affinity zinc binding sites that influence side-to-side tubulin interaction, the sensitive link in microtubule polymerization and stability. We also 2) performed kinetic modeling showing zinc distribution in extra-neuronal Aβ deposits can reduce intra-neuronal zinc binding to microtubules, destabilizing microtubules. Finally, we 3) used metallomic imaging mass spectrometry (MIMS) to show anatomically-localized and age-dependent zinc dyshomeostasis in specific brain regions of Tg2576 transgenic, mice, a model for AD. We found excess zinc in brain regions associated with memory processing and NFT pathology. Overall, we present a theoretical framework and support for a new theory of AD linking extra-neuronal Aβ amyloid to intra-neuronal NFTs and cognitive dysfunction. The connection, we propose, is based on β-amyloid-induced alterations in zinc ion concentration inside neurons affecting stability of polymerized microtubules, their binding to MAP-tau, and molecular dynamics involved in cognition. Further, our theory supports novel AD therapeutic strategies targeting intra-neuronal zinc homeostasis and microtubule dynamics to prevent neurodegeneration and cognitive decline.

MOLECULAR DYNAMIC SIMULATIONS ON THE FOLDING AND CONFORMATIONAL INSIGHTS OF THE TRUNCATED PEPTIDES

A total of 120 ns molecular dynamics simulations was used to study the folding and conformational aspects of six peptides with different lengths (Pep19–25, Pep15–25, Pep1–25, Pep15–39, Pep1–40, and Pep1–50) truncated from the αβ-tubulin dimer. These truncated peptides were found to undergo distinct structural transitions, with Pep1–25 and Pep1–50 folding into their respective stable conformations whereas on the contrary for the others. All the six truncated peptides are more or less compact than the corresponding segments in the αβ-tubulin dimer. The most striking contraction was observed in Pep1–25, which folds in a similar manner of β-hairpin. Pep1–50 has the least contraction and its folded conformation is the closest to that in the αβ-tubulin dimer. Moreover, the same conversions of β12–β23 from helices to hydrogen-bonded turns were witnessed in both Pep1–50 and the αβ-tubulin dimer. The structural instabilities of Pep19–25, Pep15–25, Pep15–39, and Pep1–40 were caused by the lack of long-distance interactions or/and the absence of key residues, with the details given in the discussions. The folding and conformational divergences of six truncated peptides were also observed in their active peptide segments ( Ap 15–25). Ap 15–25 in Pep1–50 achieves the best agreements with the αβ-tubulin dimer, implying that the local structure of Ap 15–25 in the αβ-tubulin dimer can be well reserved in Pep1–50 rather than in the other truncated peptides. The long-distance interactions, especially the key residues (e.g. β48-Arg), play a crucial role in the correct folding of Ap 15–25. The correct folding into the stable conformations is a prerequisite for the peptides to implement their catalytic actions, and therefore the present results are helpful to the future designs of active peptides.

Disturbance of reactive oxygen species homeostasis induces atypical tubulin polymer formation and affects mitosis in root-tip cells of Triticum turgidum and Arabidopsis thaliana

In this study, the effects of disturbance of the reactive oxygen species (ROS) homeostasis on the organization of tubulin cytoskeleton in interphase and mitotic root-tip cells of Triticum turgidum and Arabidopsis thaliana were investigated. Reduced ROS levels were obtained by treatment with diphenylene iodonium (DPI) and N-acetyl-cysteine, whereas menadione was applied to achieve ROS overproduction. Both increased and low ROS levels induced: (a) Macrotubule formation in cells with low ROS levels and tubulin paracrystals under oxidative stress. The protein MAP65-1 was detected in treated cells, exhibiting a conformation comparable to that of the atypical tubulin polymers. (b) Disappearance of microtubules (MTs). (c) Inhibition of preprophase band formation. (d) Delay of the nuclear envelope breakdown at prometaphase. (e) Prevention of perinuclear tubulin polymer assembly in prophase cells. (f) Loss of bipolarity of prophase, metaphase and anaphase spindles. Interestingly, examination of the A. thaliana rhd2/At respiratory burst oxidase homolog C (rbohc) NADPH oxidase mutant, lacking RHD2/AtRBOHC, gave comparable results. Similarly to DPI, the decreased ROS levels in rhd2 root-tip cells, interfered with MT organization and induced macrotubule assembly. These data indicate, for first time in plants, that ROS are definitely implicated in: (a) mechanisms controlling the assembly/disassembly of interphase, preprophase and mitotic MT systems and (b) mitotic spindle function. The probable mechanisms, by which ROS affect these processes, are discussed.

Viscous drag effect in the flexural rigidity and cantilever stiffness of bio- and nano-filaments measured with the shooting-bead method

The so-called shooting-bead method is a fast and easy experimental technique for evaluating cantilever stiffness and flexural rigidity of semiflexible to semirigid rodlike biological and nano-filaments based on the measurement of just two distances. In this paper we have derived the shooting-bead formula for cantilever stiffness and flexural rigidity taking into account the effects of the viscous drag force exerted on the filament itself. To this end, we have defined a key variable, called the filament energy-loss factor (or filament drag factor), which accounts for all the energy-loss effects. It has been shown that due to the logarithmic dependence of the filament energy-loss factor on the radius and the length of the filament, inclusion of this factor in the formula for the flexural rigidity has a very noticeable effect on the result even for very thin or long filaments. It has also been shown that the effect due to the consideration of filament energy-loss factor on calculation of the flexural rigidity increases with increasing the flexibility of the filament. We have also considered various sources of experimental error and estimated their effects.

Toxicological housekeeping genes: do they really keep the house?

It is assumed that the expression of housekeeping genes is constant regardless of experimental conditions. In toxicology, this assumption has indeed become a misconception of reasonable concern, as these so-called housekeeping genes vary considerably across different experimental conditions and thereby lead to an erroneous interpretation of the expression profile of a target gene. Given that the choice of reference gene will ultimately influence statistical interpretation of toxicological data, it is essential to validate potential reference genes prior to their use, to establish their suitability for a specific experimental purpose. Therefore, the aim of this study is to quantitatively evaluate the most commonly used housekeeping genes in toxicology research for their suitability as reference endpoints, and thus provide toxicology researchers who have little experience in molecular biology but find themselves interested or involved with gene expression analysis with a summary of information necessary for re-evaluating their procedures. We show that the expression pattern of beta-actin, beta-tubulin, 18S ribosomal RNA (18S rRNA), and elongation factor-lalpha (EF-lalpha), representing commonly used housekeeping genes in toxicology, was modulated on the basis of random exposure condition and time, in both in vivo and in vitro test systems of Atlantic salmon (Salmo salar). Based on the data presented herein and several other reports by other researchers, there are very few biological justifications to refer to anything as a housekeeping gene in real-time PCR assays for toxicological research. However, given the absolute need for normalization genes to correct for sample-to-sample variations, the choice of internal control gene should be determined empirically on the basis of the individual exposure condition and by the individual researcher.

The potential of a new stable ultrasound contrast agent for site-specific targeting. An in vitro experiment

Microbubble-based ultrasound contrast agents can be used for specific site targeting, but demonstrate time-limited opacification. We have previously demonstrated the potential of gold-bound microtubules to provide a stable ultrasound contrast effect. Aim of the present study was to test the feasibility of gold-bound microtubules specifically to bind to human thrombi and to inflammatory activated human umbilical vein endothelial cells (HUVEC) in vitro. HUVEC were incubated with tumor necrosis factor, to induce expression of adhesion molecules. Human clots and HUVEC were incubated with biotinylated monoclonal antifibrin and anti-E-selectin antibodies, respectively. Probes were incubated with excess avidin followed by biotinylated gold-bound microtubules and by secondary Cy3-anti-beta-tubulin antibody and processed for immune fluorescence microscopy. Clots were transferred in copolymer foils filled with buffer and were ultrasonographically imaged before and after their treatment with the antifibrin antibody and with biotinylated microtubules, using a broadband harmonic transducer, transmitting and receiving at a mean frequency of 1.7 MHz and 3.2 MHz. The feasibility of specific gold-bound microtubules conjugation to antibody treated clots and HUVEC was confirmed using immune fluorescence analysis. Contrast intensities of the clots significantly increased after their treatment with antifibrin antibody and incubation with gold-bound microtubules (39 +/- 2 dB versus 26 +/- 2 dB, p < 0.001) and remained high after 20 min of ultrasound exposure (37 +/- 2 dB versus 39 +/- 2 dB, p = NS). Thus, gold-bound microtubules can specifically bind to human thrombi and to endothelial cells, providing a significant contrast effect which remains stable in the ultrasound field. This may be a promising approach to target thrombi and inflammatory active atherosclerotic plaques.

Elastic response, buckling, and instability of microtubules under radial indentation

We tested the mechanical properties of single microtubules by lateral indentation with the tip of an atomic force microscope. Indentations up to approximately 3.6 nm, i.e., 15% of the microtubule diameter, resulted in an approximately linear elastic response, and indentations were reversible without hysteresis. At an indentation force of around 0.3 nN we observed an instability corresponding to an approximately 1-nm indentation step in the taxol-stabilized microtubules, which could be due to partial or complete rupture of a relatively small number of lateral or axial tubulin-tubulin bonds. These indentations were reversible with hysteresis when the tip was retracted and no trace of damage was observed in subsequent high-resolution images. Higher forces caused substantial damage to the microtubules, which either led to depolymerization or, occasionally, to slowly reannealing holes in the microtubule wall. We modeled the experimental results using finite-element methods and find that the simple assumption of a homogeneous isotropic material, albeit structured with the characteristic protofilament corrugations, is sufficient to explain the linear elastic response of microtubules.

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Giant sperm cells with accessory macrotubules in a neuropteran insect

The flagellar axoneme of the atypical spermatozoa (paraspermatozoa) of Mantispa perla (Neuroptera, Planipennia) contains accessory microtubules or rather macrotubules that are 55 nm in diameter and that has a wall consisting of about 40 protofilaments. The sperm tail further contains two giant mitochondrial derivatives, which during spermiogenesis store an electron dense material. The mature spermatozoon has a flattened acrosome and a elliptical nucleus. These giant spermatozoa may furnish nutrients to the functional spermatozoa (euspermatozoa) when they reach the female genital tracts or/and they function in sperm competition filling the spermatheca.

Elastic vibrations in seamless microtubules

Parameters characterizing elastic properties of microtubules, measured in several recent experiments, reflect an anisotropic character. We describe the microscopic dynamical properties of microtubules using a discrete model based on an appropriate lattice of dimers. Adopting a harmonic approximation for the dimer-dimer interactions and estimating the lattice elastic constants, we make predictions regarding vibration dispersion relations and vibration propagation velocities. Vibration frequencies and velocities are expressed as functions of the elastic constants and of the geometrical characteristics of the microtubules. We show that vibrations which propagate along the protofilament do so significantly faster than those along the helix.

Readout of protein microarrays using intrinsic time resolved UV fluorescence for label-free detection

Detecting protein-protein interactions other than those of antibody-antigen pairs still represents a demanding and tedious task. In the present work, a novel method as an alternative to current molecular biology-based detection procedures is established. It solely relies on the change of fluorescence decay times of the protein's intrinsic fluorophores tryptophan and tyrosine due to protein-protein interaction. Unlike previously utilized related methods, no labelling of the binding partners is required. This opens the possibility to detect proteins and their natural interactions without perturbation due to chemical alteration. The technique uses immobilization of one of the protein partners onto solid supports, which allows performance of protein binding studies in the microarray format. Fluorescence lifetime experiments of proteins in their different binding states have been applied to protease/protease-substrate pairs, as well as to the tubulin/kinesin system. Different binding behavior of proteins in solution towards protein partners immobilized on protein microarrays was detected with regard to binding specificity and protein amount. This label-free method for analyzing protein microarrays offers broad applicability ranging from principal investigations of protein interactions to applications in molecular biology and medicine.

Interaction of metal salts with cytoskeletal motor protein systems

Interactions of chemicals with the microtubular network of cells may lead to genotoxicity. Micronuclei (MN) might be caused by interaction of metals with tubulin and/or kinesin. The genotoxic effects of inorganic lead and mercury salts were studied using the MN assay and the CREST analysis in V79 Chinese hamster fibroblasts. Effects on the functional activity of motor protein systems were examined by measurement of tubulin assembly and kinesin-driven motility. Lead and mercury salts induced MN dose-dependently. The no-effect-concentration for MN induction was 1.1 microM PbCl(2), 0.05 microM Pb(OAc)(2) and 0.01 microM HgCl(2). The in vitro results obtained for PbCl(2) correspond to reported MN induction in workers occupationally exposed to lead, starting at 1.2 microM Hg(II) (Vaglenov et al., 2001, Environ. Health Perspect. 109, 295-298). The CREST Analysis indicate aneugenic effects of Pb(II) and aneugenic and additionally clastogenic effects of Hg(II). Lead (chloride, acetate, and nitrate) and mercury (chloride and nitrate) interfered dose-dependently with tubulin assembly in vitro. The no-effect-concentration for lead salts in this assay was 10 microM. Inhibition of tubulin assembly by mercury started at 2 microM. The gliding velocity of microtubules along immobilised kinesin molecules was affected by 25 microM Pb(NO(3))(2) and 0.1 microM HgCl(2) in a dose-dependent manner. Our data support the hypothesis that lead and mercury genotoxicity may result, at least in part, via disturbance of chromosome segregation via interaction with cytoskeletal proteins.

Use of small-angle neutron scattering to study tubulin polymers

Small-angle neutron scattering has been used to examine taxol-stabilized microtubules and other tubulin samples in both H(2)O and D(2)O buffers. Measurements were made at pH/pD values between 6.0 and 7.8, and observed scattered intensities, I(Q), have been interpreted in terms of multicomponent models of microtubules and related tubulin polymers. A semiquantitative curve fitting procedure has been used to estimate the relative amounts of the supramolecular components of the samples. At both pH and pD 7.0 and above, the tubulin polymers are seen to be predominantly microtubules. Although in H(2)O buffer the polymer distribution is little changed as the pH varies, when pD is lowered the samples appear to contain an appreciable amount of sheetlike structures and the average microtubule protofilament number increases from ca. 12.5 at pD > or = approximately 7.0 to ca. 14 at pD approximately 6.0. Such structural change indicates that analysis of microtubule solutions based on H(2)O/D(2)O contrast variation must be performed with caution, especially at lower pH/pD.

The cryptophycin-tubulin ring structure indicates two points of curvature in the tubulin dimer

Cryptophycin-1 is the parent compound of a group of cyclic peptides with potent antineoplastic activity. Cryptophycins are thought to function by modulating the dynamic instability of spindle microtubules, and in vitro are known to bind in an equimolar ratio to the beta-tubulin subunit and to induce the formation of ring-like complexes. However, the detailed mechanisms whereby the cryptophycins interact with tubulin are not known. We have investigated the origin of the conformational changes in tubulin both biochemically and by electron microscopy and image analysis. Cryptophycin was found to protect both alpha- and beta-tubulin against proteolysis by trypsin, indicating conformational changes in specific regions of both subunits. The ring mass was determined to be approximately 0.81 MDa by sedimentation velocity combined with dynamic light scattering and by STEM, indicating a complex of eight alphabeta dimers. Statistical analysis of rings imaged by cryoelectron microscopy revealed 16-fold symmetry, corresponding to eight dimers. Computational averaging based on this symmetry yielded an image of a 24 nm diameter ring, at 2.6 nm resolution, that clearly distinguishes intradimer contacts from interdimer contacts, and allows discrimination of alpha-subunits from beta-subunits. Fitting of the tubulin dimer crystal structure into this projected density map indicates two points of curvature: a 13 degrees intradimer bend and a 32 degrees interdimer bend. We conclude that drug binding to one subunit (beta) results in two bends per dimer, affecting both subunits.

Brain-specific p25 protein binds to tubulin and microtubules and induces aberrant microtubule assemblies at substoichiometric concentrations

Previously, we have demonstrated the presence of a protein factor [tubulin polymerization perturbing protein (TPPP)] in brain and neuroblastoma cell but not in muscle extract that uniquely influences the microtubule assembly. Here we describe a procedure for isolation of this protein from the cytosolic fraction of bovine brain and present evidence that this protein is a target of both tubulin and microtubules in vitro. The crucial step of the purification is the cationic exchange chromatography; the bound TPPP is eluted at high salt concentrations, indicating the basic character of the protein. By IDA-nanoLC-MS analysis of the peptides extracted from the gel-digested purified TPPP, we show the presence of a single protein in the purified fraction that corresponds to p25, a brain-specific protein the function of which has not been identified. Circular dichroism data have revealed that, on one hand, the alpha-helix content of p25 is very low (4%) with respect to the predicted values (30-43%), and its binding to tubulin induces remarkable alteration in the secondary structure of the protein(s). As shown by turbidimetry, pelleting experiments, and electron microscopy, p25 binds to paclitaxel-stabilized microtubules and bundles them. p25 induces formation of unusual (mainly double-walled) microtubules from tubulin in the absence of paclitaxel. The amount of aberrant tubules formed depends on the p25 concentration, and the process occurs at substoichiometric concentrations. Our in vitro data suggest that p25 could act as a unique MAP in vivo.

Potential of gold-bound microtubules as a new ultrasound contrast agent

Contrast agents based on gas-filled microspheres share the problem of time limited opacification due to low stability of microbubbles. The aim of this study was to test if gold-bound microtubules provide backscattering that allows microtubules to be potentially useful as an ultrasound (US) contrast agent. Gold colloids were immobilized on protein microtubule walls. Latex balloons were filled with gold-bound microtubules or conventional left heart contrast agent and were ultrasonographically imaged in fundamental and harmonic modes. Feasibility of anti-beta-tubulin antibody conjugation to gold-bound microtubules was confirmed using immune fluorescence analysis. Gold particles were successfully bound to microtubules. Contrast intensities in latex balloons filled with gold-bound microtubules (141 +/- 35) were comparable to those with Levovist (180 +/- 35) and did not decrease significantly during continuous US imaging for 20 min (135 +/- 34 vs. Levovist 5.0 +/- 2.0). Anti-beta-tubulin antibodies were successfully conjugated to gold-bound microtubules. Gold-bound microtubules provide a persistent contrast effect, suggesting their use as an ultrasonic contrast agent with the feasibility of antibody conjugation.

Analysis of the migration behaviour of single microtubules in electric fields

By video contrast microscopy, individual microtubules formed from pure tubulin in the presence of taxol were studied in constant electric fields. At nearly physiological conditions, i.e., in a buffer at pH 6.8 and 120 mM ionic strength, suspended microtubules moved towards the anode with an electrophoretic mobility of approximately 2.6 x 10(-4) cm(2)/V s, corresponding to an unbalanced negative charge of 0.19 electron charges per tubulin dimer. Strikingly, this value is lower by a factor of at least 50 than that calculated from crystallographic data for the non-assembled tubulin dimer. Moreover, the taxol-stabilized microtubules had an isoelectric point of about pH 4.2 which is significantly lower than that known for the tubulin monomers. This indicates that microtubule formation is accompanied by substantial changes of charge distribution within the tubulin subunits. Constant electric fields were shown to affect also the orientation of microtubules gliding across a kinesin-coated surface at pH 6.8.

Altered patterns of tubulin polymerization in dividing leaf cells of Chlorophyton comosum after a hyperosmotic treatment

•  Microtubule organization and tubulin polymerization in meristematic leaf cells of Chlorophyton comosum treated with an aqueous solution of 1 M mannitol, inducing plasmolysis, were examined with immunofluorescence and transmission electron microscopy. •  Hyperosmotic treatment induced disintegration of the interphase microtubule systems. Free tubulin, either liberated from the depolymerized microtubules or pre-existing as a nonassembled pool, was incorporated into a network of paracrystals. In most of the dividing cells, mitotic and cytokinetic microtubule systems were replaced by atypical spindle-like structures displaying bipolarity and atypical phragmoplasts, respectively. These atypical mitotic and cytokinetic structures consisted of large densely packed bundles of macrotubules (32 nm diameter) or macrotubules and paracrystals. Tubulin paracrystals also occurred in ectopic positions in plasmolysed mitotic and cytokinetic cells. Dividing cells displaying paracrystals only did not form atypical mitotic and cytokinetic apparatuses. •  Short hyperosmotic stress causes disintegration of all microtubule arrays in dividing cells of C. comosum. Free tubulin is incorporated into macrotubules and tubulin paracrystals. The latter exhibit definite periodicity and characteristic fine structure.

Viscoelastic properties of f-actin, microtubules, f-actin/alpha-actinin, and f-actin/hexokinase determined in microliter volumes with a novel nondestructive method

A nondestructive method to determine viscoelastic properties of gels and fluids involves an oscillating glass fiber serving as a sensor for the viscosity of the surrounding fluid. Extremely small displacements (typically 1-100 nm) are caused by the glass rod oscillating at its resonance frequency. These displacements are analyzed using a phase-sensitive acoustic microscope. Alterations of the elastic modulus of a fluid or gel change the propagation speed of a longitudinal acoustic wave. The system allows to study quantities as small as 10 microliters with temporal resolution >1 Hz. For 2-100 microM f-actin gels a final viscosity of 1.3-9.4 mPa s and a final elastic modulus of 2.229-2.254 GPa (corresponding to 1493-1501 m/s sound velocity) have been determined. For 10- to 100-microM microtubule gels (native, without stabilization by taxol), a final viscosity of 1.5-124 mPa s and a final elastic modulus of 2.288-2. 547 GPa (approximately 1513-1596 m/s) have been determined. During polymerization the sound velocity in low-concentration actin solutions increased up to +1.3 m/s (approximately 1.69 kPa) and decreased up to -7 m/s (approximately 49 kPa) at high actin concentrations. On polymerization of tubulin a concentration-dependent decrease of sound velocity was observed, too (+48 to -12 m/s approximately 2.3-0.1 MPa, for 10- to 100-microM tubulin). This decrease was interpreted by a nematic phase transition of the actin filaments and microtubules with increasing concentration. 2 mM ATP (when compared to 0.2 mM ATP) increased polymerization rate, final viscosity and elastic modulus of f-actin (17 microM). The actin-binding glycolytic enzyme hexokinase also accelerated the polymerization rate and final viscosity but elastic modulus (2.26 GPa) was less than for f-actin polymerized in presence of 0.2 mM ATP (2.28 GPa).

Characterization of microtubule-phosphofructokinase complex: specific effects of MgATP and vinblastine

Phosphofructokinase interacts with both microtubules and microtubules containing microtubule-associated proteins to produce bundling and periodical cross-bridging of tubules. Immunoelectron microscopy using anti-phosphofructokinase antibodies provided direct evidence that the kinase molecules are responsible for the cross-bridging of microtubules. Limited proteolysis by subtilisin, a procedure that cleaves the N-terminal segment of the free enzyme as well as the C-terminal "tails" of tubulin subunits exposed on microtubules, showed that while phosphofructokinase becomes resistant, tubulin retains sensitivity against proteolysis within the heterologous complex. These data suggest that the N-terminal segment of the enzyme, but not the C-terminal "tail" of tubulin subunits, is involved in the interaction between the microtubule and the kinase. The phosphorylation of phosphofructokinase or microtubules containing microtubule-associated proteins by the cAMP-dependent protein kinase did not interfere with the heterologous complex formation. MgATP prevents phosphofructokinase binding to the microtubules, and it can displace the enzyme from the single microtubules. However, the bundled microtubules are apparently resistant to the MgATP dissociation effect. Modelling of the assembly process suggests that the tubulin-kinase complex is able to polymerize as the free tubulin. Vinblastine, an anti-mitotic agent, inhibits tubulin assembly; however, its inhibitory effect is partially suppressed in the presence of phosphofructokinase. Fluorescence anisotropy measurements indicated that kinase and vinblastine compete for tubulin binding with no evidence for ternary complex formation. This competitive mechanism and the ability of the tubulin-enzyme complex to polymerize into microtubules may result in the resistance of the tubulin-enzyme complex against the inhibition of assembly induced by vinblastine. Microtubules formed in the presence of vinblastine plus phosphofructokinase can be visualized by electron microscopy. A molecular model is suggested that summarizes the effects of MgATP and vinblastine on the multiple equilibria in the tubulin/microtubules/phosphofructokinase system.