Mobility of taxol in microtubule bundles

Getting around the cell: physical transport in the intracellular world

Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.

C12, a combretastatin-A4 analog, exerts anticancer activity by targeting microtubules

Combretastatin A4 and its analogs are undergoing various clinical trials for the treatment of different cancers. This study illustrated the molecular mechanism and antitumor activity of C12, (5-Quinolin-3-yl and 4-(3,4,5-trimethoxyphenyl) substituted imidazol-2-amine), a synthetic analog of CA-4. C12 reduced the tumor volume of MCF-7 xenograft in NOD-SCID mice without affecting the bodyweight of the mice. Further, C12 inhibited the proliferation of several types of cancer cells more efficiently than their noncancerous counterparts. Using GFP-EB1 imaging, the effects of C12 on the interphase microtubule dynamics were determined in live HeLa cells. C12 (10 nM, half-maximal proliferation inhibitory concentration) reduced the growth rate of microtubules by 52% and increased the pause time of microtubules by 68%. In addition, fluorescence recovery after photobleaching analysis demonstrated that 10 nM C12 strongly suppressed spindle microtubule dynamics in HeLa cells. C12 treatment reduced the interpolar distance between the two spindle poles, increased the chromosome congression index, inhibited chromosome movement, and increased the level of mitotic checkpoint complex proteins BubR1 and Mad2. The evidence presented here indicated that C12 could induce different modes of cell death, depending on the extent of microtubule depolymerization. Since C12 targets both the mitotic and non-mitotic cells and showed a stronger activity against cancerous cells than non-cancerous cells, it may have an advantage in cancer chemotherapy. The results significantly enhance our understanding of the antitumor mechanism of the microtubule-depolymerizing agents.

Self-organization of spindle-like microtubule structures

Microtubule self-organization is an essential physical process underlying several essential cellular functions, including cell division. In cell division, the dominant arrangement is the mitotic spindle, a football-shaped microtubule-based machine responsible for separating the chromosomes. We are interested in the underlying fundamental principles behind the self-organization of the spindle shape. Prior biological works have hypothesized that motor proteins control the proper formation of the spindle. Many of these motor proteins are also microtubule-crosslinkers, so it is unclear if the critical aspect is the motor activity or the crosslinking. In this study, we seek to address this question by examining the self-organization of microtubules using crosslinkers alone. We use a minimal system composed of tubulin, an antiparallel microtubule-crosslinking protein, and a crowding agent to explore the phase space of organizations as a function of tubulin and crosslinker concentration. We find that the concentration of the antiparallel crosslinker, MAP65, has a significant effect on the organization and resulted in spindle-like arrangements at relatively low concentration without the need for motor activity. Surprisingly, the length of the microtubules only moderately affects the equilibrium phase. We characterize both the shape and dynamics of these spindle-like organizations. We find that they are birefringent homogeneous tactoids. The microtubules have slow mobility, but the crosslinkers have fast mobility within the tactoids. These structures represent a first step in the recapitulation of self-organized spindles of microtubules that can be used as initial structures for further biophysical and active matter studies relevant to the biological process of cell division.

Mechanical properties of doubly stabilized microtubule filaments

Microtubules are cytoskeletal filaments responsible for cell morphology and intracellular organization. Their dynamical and mechanical properties are regulated through the nucleotide state of the tubulin dimers and the binding of drugs and/or microtubule-associated proteins. Interestingly, microtubule-stabilizing factors have differential effects on microtubule mechanics, but whether stabilizers have cumulative effects on mechanics or whether one effect dominates another is not clear. This is especially important for the chemotherapeutic drug Taxol, an important anticancer agent and the only known stabilizer that reduces the rigidity of microtubules. First, we ask whether Taxol will combine additively with another stabilizer or whether one stabilizer will dominate another. We call microtubules in the presence of Taxol and another stabilizer, doubly stabilized. Second, since Taxol is often added to a number of cell types for therapeutic purposes, it is important from a biomedical perspective to understand how Taxol added to these systems affects the mechanical properties in treated cells. To address these questions, we use the method of freely fluctuating filaments with our recently developed analysis technique of bootstrapping to determine the distribution of persistence lengths of a large population of microtubules treated with different stabilizers, including Taxol, guanosine-5' [(α, β)-methyleno] triphosphate, guanosine-5'-O-(3-thiotriphosphate), tau, and MAP4. We find that combinations of these stabilizers have novel effects on the mechanical properties of microtubules.

Paclitaxel-conjugated PAMAM dendrimers adversely affect microtubule structure through two independent modes of action

Paclitaxel (Taxol) is an anticancer drug that induces mitotic arrest via microtubule hyperstabilization but causes side effects due to its hydrophobicity and cellular promiscuity. The targeted cytotoxicity of hydrophilic paclitaxel-conjugated polyamidoamine (PAMAM) dendrimers has been demonstrated in cultured cancer cells. Mechanisms of action responsible for this cytotoxicity are unknown, that is, whether the cytotoxicity is due to paclitaxel stabilization of microtubules, as is whether paclitaxel is released intracellularly from the dendrimer. To determine whether the conjugated paclitaxel can bind microtubules, we used a combination of ensemble and single microtubule imaging techniques in vitro. We demonstrate that these conjugates adversely affect microtubules by (1) promoting the polymerization and stabilization of microtubules in a paclitaxel-dependent manner, and (2) bundling preformed microtubules in a paclitaxel-independent manner, potentially due to protonation of tertiary amines in the dendrimer interior. Our results provide mechanistic insights into the cytotoxicity of paclitaxel-conjugated PAMAM dendrimers and uncover unexpected risks of using such conjugates therapeutically.

Synthesis and Biological Evaluation of a Biotinylated Paclitaxel With an Extra-Long Chain Spacer Arm

A biotinylated paclitaxel derivative with an extra-long-chain (LC-LC-Biotin) spacer arm was synthesized using an improved synthetic reaction sequence. The biotinylated paclitaxel analogue retained excellent microtubule stabilizing activity in vitro. Furthermore, it was shown that this analogue can simultaneously engage streptavidin and the binding site on microtubules, making it suitable for localization studies or for the attachment of paclitaxel to solid substrates via a streptavidin linkage.

Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin

PURPOSE

To explore possible ways in which yew tree tubulin is naturally resistant to paclitaxel. While the yew produces a potent cytotoxin, paclitaxel, it is immune to paclitaxel's cytotoxic action.

METHODS

Tubulin sequence data for plant species were obtained from Alberta 1000 Plants Initiative. Sequences were assembled with Trinity de novo assembly program and tubulin identified. Homology modeling using MODELLER software was done to generate structures for yew tubulin. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann calculations were performed with the Amber package to determine binding affinity of paclitaxel to yew tubulin. ClustalW2 program and PHYLIP package were used to perform phylogenetic analysis on plant tubulin sequences.

RESULTS

We specifically analyzed several important regions in tubulin structure: the high-affinity paclitaxel binding site, as well as the intermediate binding site and microtubule nanopores. Our analysis indicates that the high-affinity binding site contains several substitutions compared to human tubulin, all of which reduce the binding energy of paclitaxel.

CONCLUSIONS

The yew has achieved a significant reduction of paclitaxel's affinity for its tubulin by utilizing several specific residue changes in the binding pocket for paclitaxel.

Loop formation of microtubules during gliding at high density

The microtubule cytoskeleton, including the associated proteins, forms a complex network essential to multiple cellular processes. Microtubule-associated motor proteins, such as kinesin-1, travel on microtubules to transport membrane bound vesicles across the crowded cell. Other motors, such as cytoplasmic dynein and kinesin-5, are used to organize the cytoskeleton during mitosis. In order to understand the self-organization processes of motors on microtubules, we performed filament-gliding assays with kinesin-1 motors bound to the cover glass with a high density of microtubules on the surface. To observe microtubule organization, 3% of the microtubules were fluorescently labeled to serve as tracers. We find that microtubules in these assays are not confined to two dimensions and can cross one other. This causes microtubules to align locally with a relatively short correlation length. At high density, this local alignment is enough to create 'intersections' of perpendicularly oriented groups of microtubules. These intersections create vortices that cause microtubules to form loops. We characterize the radius of curvature and time duration of the loops. These different behaviors give insight into how crowded conditions, such as those in the cell, might affect motor behavior and cytoskeleton organization.

Escaping the flatlands: new approaches for studying the dynamic assembly and activation of GPCR signaling complexes

Despite significant recent advances in molecular and structural studies of G protein-coupled receptors (GPCRs), an understanding of transmembrane signal transduction with chemical precision requires new approaches. Simple binary receptor-ligand or receptor-G protein complex models cannot adequately describe the relevant macromolecular signaling machineries. GPCR signalosomes undergo complex dynamic assembly-disassembly reactions to create allosteric signaling conduits whose properties cannot necessarily be predicted from individual elements alone. The combinatorial possibilities inherent in a system with hundreds of potential components suggest that high-content miniaturized experimental platforms and computational approaches will be required. To study allosteric effects involved in signalosome reaction pathways, a bottom-up approach using multicolor single-molecule detection fluorescence experiments in biochemically defined systems and complemented by molecular dynamics models of macromolecular complexes is proposed. In bridging the gap between molecular and systems biology, this synthetic approach suggests a way forward from the flatlands to multi-dimensional data collection.

Model of ionic currents through microtubule nanopores and the lumen

It has been suggested that microtubules and other cytoskeletal filaments may act as electrical transmission lines. An electrical circuit model of the microtubule is constructed incorporating features of its cylindrical structure with nanopores in its walls. This model is used to study how ionic conductance along the lumen is affected by flux through the nanopores, both with and without an external potential applied across its two ends. Based on the results of Brownian dynamics simulations, the nanopores were found to have asymmetric inner and outer conductances, manifested as nonlinear IV curves. Our simulations indicate that a combination of this asymmetry and an internal voltage source arising from the motion of the C-terminal tails causes cations to be pumped across the microtubule wall and propagate in both directions down the microtubule through the lumen, returning to the bulk solution through its open ends. This effect is demonstrated to add directly to the longitudinal current through the lumen resulting from an external voltage source applied across the two ends of the microtubule. The predicted persistent currents directed through the microtubule wall and along the lumen could be significant in directing the dissipation of weak, endogenous potential gradients toward one end of the microtubule within the cellular environment.

TTLL3 Is a tubulin glycine ligase that regulates the assembly of cilia

In most ciliated cell types, tubulin is modified by glycylation, a posttranslational modification of unknown function. We show that the TTLL3 proteins act as tubulin glycine ligases with chain-initiating activity. In Tetrahymena, deletion of TTLL3 shortened axonemes and increased their resistance to paclitaxel-mediated microtubule stabilization. In zebrafish, depletion of TTLL3 led to either shortening or loss of cilia in several organs, including the Kupffer's vesicle and olfactory placode. We also show that, in vivo, glutamic acid and glycine ligases oppose each other, likely by competing for shared modification sites on tubulin. We propose that tubulin glycylation regulates the assembly and dynamics of axonemal microtubules and acts either directly or indirectly by inhibiting tubulin glutamylation.

Identification and characterization of an intermediate taxol binding site within microtubule nanopores and a mechanism for tubulin isotype binding selectivity

Tubulin, the primary subunit of microtubules, is remarkable for the variety of small molecules to which it binds. Many of these are very useful or promising agents in cancer chemotherapy. One of the most useful of these is paclitaxel. The tubulin molecule is itself an alpha/beta heterodimer, both alpha- and beta-tubulin monomers existing as multiple isotypes. Despite the success of paclitaxel as an anticancer drug, resistance often occurs in cancer cells and has been associated with variations in tubulin isotype expression, most notably with the increased expression of betaIII-tubulin. Paclitaxel is thought to reach its binding site on beta-tubulin by diffusion through nanopores in the microtubule wall. It has been suggested that a transitional step in this process may be the binding of paclitaxel to an intermediate site within a nanopore, from which it moves directly to its binding site in the microtubule interior facing the lumen. To test this hypothesis, we have computationally docked paclitaxel within a microtubule nanopore and simulated its passage to the intermediate binding site. Targeted molecular dynamics was then used to test the hypothesis that paclitaxel utilizes the H6/H7 loop as a hinge to move directly from this intermediate binding site to its final position in the luminal binding site. We observed that this motion appears to be stabilized by the formation of a hydrogen bond involving serine 275 in beta-tubulin isotypes I, IIa, IIb, IVa, IVb, V, VII, and VIII. Interestingly, this residue is replaced by alanine in the betaIII and VI isotypes. This observation raises the possibility that the observed isotype difference in paclitaxel binding may be a kinetic effect arising from the isotype difference at this residue. We are now able to suggest derivatives of paclitaxel that may reverse the isotype-specificity or lead to an alternate stabilizing hydrogen-bond interaction with tubulin, thus increasing the rate of passage to the luminal binding site and hopefully offering a therapeutic advantage in paclitaxel resistant cases.

Diffusion and binding of finite-size particles in confined geometries

Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the particle dimensions, steric interactions between particles, as well as particle-wall interactions, will play a crucial role in determining transport properties. To elucidate the effects of these interactions on particle transport, we consider the diffusion and binding of finite-size particles within a channel whose diameter is comparable to the size of the particles. Using a simple lattice model of this process, we calculate the steady-state current and density profiles of both bound and free particles in the channel. We show that the system can exhibit qualitatively different behavior depending on the ratio of the channel width to the particle size. We also perform simulations of this system and find excellent agreement with our analytic results.

Supported phospholipid bilayers as a platform for neural progenitor cell culture

Supported phospholipid bilayers constitute a biomimetic platform for cell behavior studies and a new approach to the design of cell culture substrates. Phosphocholine bilayers are resistant to cell attachment, but can be functionalized with bioactive molecules to promote specific cell interactions. Here, we explore phosphocholine bilayers, functionalized with the laminin-derived IKVAV pentamer, as substrates for attachment, growth, and differentiation of neural progenitor cells (AHPs). By varying peptide concentration (0-10%), we discovered a strongly nonlinear relationship between cell attachment and IKVAV concentration, with a threshold of 1% IKVAV required for attachment, and saturation in cell binding at 3% IKVAV. This behavior, together with the 10-fold reduction in cell attachment when using a jumbled peptide sequence, gives evidence for a specific interaction between IKVAV and its AHP cell-surface receptor. After 8 days in culture, the peptide-functionalized bilayers promoted a high degree of cell cluster formation. This is in contrast to the predominant monolayer growth, observed for these cells on the standard laminin coated growth substrates. The peptide-functionalized bilayer did not induce differentiation levels over those observed for the laminin coated substrates. These results are promising in that peptide-functionalized bilayers can allow attachment and growth of stem cells without induction of differentiation.

Lateral mobility of tethered vesicle-DNA assemblies

Supported lipid membranes are particularly attractive for use in biochemical assays because of their resistance to nonspecific adsorption and their unique ability to host transmembrane proteins. Although ideal for use in many surface-based detection techniques, supported bilayers can make the incorporation of proteins problematic due to the steric constraints of the underlying substrate. A recently developed strategy overcomes this obstacle by tethering liposomes to supported lipid bilayers via cholesterol-tagged DNA. Due to the fluidity of the bilayer, the vesicle assemblies exhibited significant lateral mobility. The corresponding diffusion coefficients were then investigated using fluorescence recovery after photobleaching (FRAP). The diffusivity was neither sensitive to the size of the vesicles nor to the length of the DNA tether. However, changing from single cholesterol tethers to double cholesterol tethers caused a decrease in the diffusivity of the assemblies by a factor of 3. Perhaps even more notable was the fact that single cholesterol-DNA without vesicles diffused 6 times faster than the corresponding assemblies. Double cholesterol-DNA diffused 11 times faster. This discrepancy is believed to arise from the fact that each vesicle is tethered to the bilayer by multiple DNA pairs.

Local controlled drug delivery to the brain: mathematical modeling of the underlying mass transport mechanisms

The mass transport mechanisms involved in the controlled delivery of drugs to living brain tissue are complex and yet not fully understood. Often the drug is embedded within a polymeric or lipidic matrix, which is directly administered into the brain tissue, that is, intracranially. Different types of systems, including microparticles and disc- or rod-shaped implants are used to control the release rate and, thus, to optimize the drug concentrations at the site of action in the brain over prolonged periods of time. Most of these dosage forms are biodegradable to avoid the need for the removal of empty remnants after drug exhaustion. Various physical and chemical processes are involved in the control of drug release from these systems, including water penetration, drug dissolution, degradation of the matrix and drug diffusion. Once the drug has been released from the delivery system, it has to be transported through the living brain tissue to the target site(s). Again, a variety of phenomena, including diffusion, drug metabolism and degradation, passive or active uptake into CNS tissue and convection can be of importance for the fate of the drug. An overview is given of the current knowledge of the nature of barriers to free access of drug to tumour sites within the brain and the state of the art of: (i) mathematical modeling approaches describing the physical transport processes and chemical reactions which can occur in different types of intracranially administered drug delivery systems, and of (ii) theories quantifying the mass transport phenomena occurring after drug release in the living tissue. Both, simplified as well as complex mathematical models are presented and their major advantages and shortcomings discussed. Interestingly, there is a significant lack of mechanistically realistic, comprehensive theories describing both parts in detail, namely, drug transport in the dosage form and in the living brain tissue. High quality experimental data on drug concentrations in the brain tissue are difficult to obtain, hence this is itself an issue in testing mathematical approaches. As a future perspective, the potential benefits and limitations of these mathematical theories aiming to facilitate the design of advanced intracranial drug delivery systems and to improve the efficiency of the respective pharmacotherapies are discussed.

Systematic evaluation of FRAP experiments performed in a confocal laser scanning microscope

The diffusion coefficient as well as the dimensionality of the diffusion process can be determined by straightforward and facile data analysis, when fluorescence recovery after photobleaching (FRAP) is measured as a function of time and space by means of confocal laser scanning microscopy. Experiments representing one-dimensional diffusion from a plane source or two-dimensional diffusion from a line source are readily realized. In the data analysis, the deviations of the actual initial conditions from ideal models are consistently taken into account, so that no calibration measurements are needed. The method is applied to FRAP experiments on solutions of Rhodamine B in glycerol and aqueous suspensions of polymethyl methacrylate microspheres.

[Ca2+]i signaling between mitochondria and endoplasmic reticulum in neurons is regulated by microtubules. From mitochondrial permeability transition pore to Ca2+-induced Ca2+ release

The positioning and dynamics of organelles depend on membrane-cytoskeleton interactions. Mitochondria relocate along microtubules (MT), but it is not clear whether MT have direct effects on mitochondrial function. Using two-photon microscopy and the mitochondrial fluorescent dyes rhodamine 123 and Rhod-2, we showed that Taxol and nocodazole, which correspondingly stabilize and disrupt MT, decreased potential and Ca(2+) in the mitochondria of brain stem pre-Botzinger complex neurons. Without changing basal cytoplasmic Ca(2+) ([Ca(2+)](i)), Taxol promoted the generation of [Ca(2+)](i) spikes in dendrites. These spikes were abolished after blockade of Ca(2+) influx and after depletion of internal Ca(2+) stores, indicating the involvement of Ca(2+)-induced Ca(2+) release. Nocodazole decreased mitochondrial potential and [Ca(2+)](m) and produced a long lasting increase in [Ca(2+)](i). MT-acting drugs depolarized single immobilized mitochondria and released previously stored Ca(2+). All of these effects were inhibited by pretreatment with blockers of mitochondrial permeability transition pore (mPTP), cyclosporin A, and 2-aminoethoxydiphenyl borate. Induction of mPTP by Taxol and nocodazole was confirmed by using a calcein/Co(2+) imaging technique. Electron and optical microscopy revealed tubulin bound to mitochondria. Mitochondria, MT, and endoplasmic reticulum (ER) showed strong co-localization, the degree of which decreased after MT were disrupted. We propose that changes in the structure of MT by Taxol and nocodazole promote the induction of mPTP. Subsequent Ca(2+) efflux stimulates the Ca(2+) release from the ER that drives spontaneous [Ca(2+)](i) transients. Thus, close positioning of mitochondria to the ER as determined by MT can be essential for the local [Ca](i) signaling in neurons.

Tau induces cooperative Taxol binding to microtubules

Taxol and tau are two ligands that stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds beta tubulin in the MT interior. Tau is a MT-associated protein that binds both alpha and beta tubulin on the MT exterior. Both Taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts to bundle, stiffen, and space MTs. A structural study recently suggested that Taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces Taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau, yields the equilibrium dissociation constant of approximately 2 microM, and determines the escape rate of Taxol through one pore to be 1.7 x 10(3) (M x s)(-1). Extension of the model yields a measure of Taxol cooperativity with a Hill coefficient of at least 15 when tau is present at a 1:1 molar ratio with tubulin.