Browsing by Author "Tuszynski, Jack A."
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- ItemA continuous model for microtubule dynamics with catastrophe, rescue and nucleation processes(2009) Hinow, Peter; Rezania, Vahid; Tuszynski, Jack A.Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo referred to as dynamic instability. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in the polymerization of microtubules from tubulin dimers. Our model is an extension of various mathematical models developed earlier formulated in order to capture and unify the various aspects of tubulin polymerization. While attempting to use a minimal number of adjustable parameters, the proposed model covers a broad range of behaviors and has predictive features discussed in the paper. We have analyzed the range of resultant dynamical behavior of the microtubules by changing each of the parameter values at a time and observing the emergence of various dynamical regimes, that agree well with the previously reported experimental data. observing the emergence of various dynamical regimes, that agree well with reported experimental behavior.
- ItemA nanometric probe of the local proton concentration in microtubule-based biophysical systems(2022) Kalra, Aarat P.; Eakins, Boden B.; Vagin, Sergei I.; Wang, Hui; Patel, Sahil D.; Winter, Philip; Aminpour, Maral; Lewis, John D.; Rezania, Vahid; Shankar, Karthik; Scholes, Gregory D.; Tuszynski, Jack A.; Rieger, Bernhard; Meldrum, AlkiviathesWe show a double-functional fluorescence sensing paradigm that can retrieve nanometric pH information on biological structures. We use this method to measure the extent of protonic condensation around microtubules, which are protein polymers that play many roles crucial to cell function. While microtubules are believed to have a profound impact on the local cytoplasmic pH, this has been hard to show experimentally due to the limitations of conventional sensing techniques. We show that subtle changes in the local electrochemical surroundings cause a double-functional sensor to transform its spectrum, thus allowing a direct measurement of the protonic concentration at the microtubule surface. Microtubules concentrate protons by as much as one unit on the pH scale, indicating a charge storage role within the cell via the localized ionic condensation. These results confirm the bioelectrical significance of microtubules and reveal a sensing concept that can deliver localized biochemical information on intracellular structures.
- ItemA new method for protein characterization and classification using geometrical features for 3D face analysis: an example of tubulin structures(2021) Di Grazia, Luca; Aminpour, Maral; Vezzetti, Enrico; Rezania, Vahid; Marcolin, Federica; Tuszynski, Jack A.This article reports on the results of research aimed to translate biometric 3D face recognition concepts and algorithms into the field of protein biophysics in order to precisely and rapidly classify morphological features of protein surfaces. Both human faces and protein surfaces are free-forms and some descriptors used in differential geometry can be used to describe them applying the principles of feature extraction developed for computer vision and pattern recognition. The first part of this study focused on building the protein dataset using a simulation tool and performing feature extraction using novel geometrical descriptors. The second part tested the method on two examples, first involved a classification of tubulin isotypes and the second compared tubulin with the FtsZ protein, which is its bacterial analog. An additional test involved several unrelated proteins. Different classification methodologies have been used: a classic approach with a support vector machine (SVM) classifier and an unsupervised learning with a k-means approach. The best result was obtained with SVM and the radial basis function kernel. The results are significant and competitive with the state-of-the-art protein classification methods. This leads to a new methodological direction in protein structure analysis.
- ItemA physiologically-based flow network model for hepatic drug elimination I: regular lattice lobule model(2013) Rezania, Vahid; Marsh, Rebeccah; Coombe, Dennis; Tuszynski, Jack A.We develop a physiologically-based lattice model for the transport and metabolism of drugs in the functional unit of the liver, called the lobule. In contrast to earlier studies, we have emphasized the dominant role of convection in well-vascularized tissue with a given structure. Estimates of convective, diffusive and reaction contributions are given. We have compared drug concentration levels observed exiting the lobule with their predicted detailed distribution inside the lobule, assuming that most often the former is accessible information while the latter is not.
- ItemA physiologically-based flow network model for hepatic drug elimination II: variable lattice lobule models(2013) Rezania, Vahid; Marsh, Rebeccah; Coombe, Dennis; Tuszynski, Jack A.We extend a physiologically-based lattice model for the transport and metabolism of drugs in the liver lobule (liver functional unit) to consider structural and spatial variability. We compare predicted drug concentration levels observed exiting the lobule with their detailed distribution inside the lobule, and indicate the role that structural variation has on these results. Liver zonation and its role on drug metabolism represent another aspect of structural inhomogeneity that we consider here. Since various liver diseases can be thought to produce such structural variations, our analysis gives insight into the role of disease on liver function and performance. These conclusions are based on the dominant role of convection in well-vascularized tissue with a given structure.
- ItemAll wired up: an exploration of the electrical properties of microtubules and tubulin(2020) Kalra, Aarat P.; Eakins, Boden B.; Patel, Sahil D.; Ciniero, Gloria; Rezania, Vahid; Shankar, Karthik; Tuszynski, Jack A.Microtubules are hollow, cylindrical polymers of the protein α, β tubulin, that interact mechanochemically with a variety of macromolecules. Due to their mechanically robust nature, microtubules have gained attention as tracks for precisely directed transport of nanomaterials within lab-on-a-chip devices. Primarily due to the unusually negative tail-like C-termini of tubulin, recent work demonstrates that these biopolymers are also involved in a broad spectrum of intracellular electrical signaling. Microtubules and their electrostatic properties are discussed in this Review, followed by an evaluation of how these biopolymers respond mechanically to electrical stimuli, through microtubule migration, electrorotation and C-termini conformation changes. Literature focusing on how microtubules act as nanowires capable of intracellular ionic transport, charge storage, and ionic signal amplification is reviewed, illustrating how these biopolymers attenuate ionic movement in response to electrical stimuli. The Review ends with a discussion on the important questions, challenges, and future opportunities for intracellular microtubule-based electrical signaling.
- ItemBuilding a 3D virtual liver: methods for simulating blood flow and hepatic clearance on 3D structures(2016) White, Diana; Coombe, Dennis; Rezania, Vahid; Tuszynski, Jack A.In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver.
- ItemCell death and survival due to cytotoxic exposure modelled as a two-state Ising system(2020) Moghadam, Arbabi S.; Rezania, Vahid; Tuszynski, Jack A.Cancer chemotherapy agents are assessed for their therapeutic utility primarily by their ability to cause apoptosis of cancer cells and their potency is given by an IC50 value. Chemotherapy uses both target-specific and systemic-action drugs and drug combinations to treat cancer. It is important to judiciously choose a drug type, its dosage and schedule for optimized drug selection and administration. Consequently, the precise mathematical formulation of cancer cells' response to chemotherapy may assist in the selection process. In this paper, we propose a mathematical description of the cancer cell response to chemotherapeutic agent exposure based on a time-tested physical model of two-state multiple-component systems near criticality. We describe the Ising model methodology and apply it to a diverse panel of cytotoxic drugs administered against numerous cancer cell lines in a dose–response manner. The analysed dataset was generated by the Netherlands Translational Research Center B.V. (Oncolines). This approach allows for an accurate and consistent analysis of cytotoxic agents' effects on cancer cell lines and reveals the presence or absence of the bystander effect through the interaction constant. By calculating the susceptibility function, we see the value of IC50 coinciding with the peak of this measure of the system's sensitivity to external perturbations.
- ItemFrom a quantum mechanical description of the assembly processes in microtubules to their semiclassical nonlinear dynamics(2007) Rezania, Vahid; Tuszynski, Jack A.In this paper a quantum mechanical description of the assembly/disassembly process for microtubules is proposed. We introduce creation and annihilation operators that raise or lower the microtubule length by a tubulin layer. Following that, the Hamiltonian and corresponding equations of motion are derived that describe the dynamics of microtubules. These Heisenberg-type equations are then transformed to semi-classical equations using the method of coherent structures. The latter equations are very similar to the phenomenological equations that describe dynamic instability of microtubules in a tubulin solution.
- ItemInvestigation of the electrical properties of microtubule ensembles under cell-like conditions(2020) Aarat, Kalra P.; Patel, Sahil D.; Bhuiyan, Asadullah; Preto, Jordane; Scheuer, Kyle G.; Mohammed, Usman; Lewis, John D.; Rezania, Vahid; Shankar, Karthik; Tuszynski, Jack A.Microtubules (MTs) are cylindrical polymers composed of the heterodimers of protein α, β- tubulin that play a variety of well-recognised intracellular roles, such as maintaining the shape and rigidity of the cell, aiding in positioning and stabilisation of the mitotic spindle for allowing chromosomal segregation, acting as ‘rails’ for macromolecular transport and forming cilia and flagella for cell movement. Since the tubulin dimer possesses a high negative electric charge of ~23e and a large intrinsic high dipole moment of approximately 1750 D [1,2], MTs have been implicated in electrically-mediated biological roles [3,4,5,6]. They have been modelled as nanowires capable of enhancing ionic transport [7,8], and simulated to receive and attenuate electrical oscillations [4,9,10,11]. In solution, MTs have been shown to align with applied electric fields [2,12,13,14,15,16]. Recently, MTs have also been modelled as the primary cellular targets for low-intensity (1–2 V), intermediate-frequency (100–300 kHz) electric fields termed TTFields (tumour-treating electric fields) that inhibit cancer cell proliferation, in particular glioma [17,18,19]. Indeed, MTs have been reported to decrease buffer solution resistance [12,13], leading to a conductance peak at frequencies close to the TTField regime . While these studies show that MTs are highly sensitive to external electric fields, answers to the questions ‘How do MTs effect a solution’s capacitance?’ and ‘What is the capacitance of a single MT?’ are still elusive and crucial to the determination of the dielectric properties of living cells. The tubulin concentration in mammalian cells varies in the micromolar range (~10–25 μM) [21,22]. In vitro, polymerizing tubulin at such high concentrations can lead to the formation of entangled networks, confounding quantification of the individual MT response to electric fields. Electro-rotation, di-electrophoresis and impedance spectroscopy are thus performed using low concentrations of tubulin, in the nanomolar regime, to enable robust observation of individual MTs.
- ItemLiver bioreactor design issues of fluid flow and zonation, fibrosis, and mechanics: a computational perspective(2020) Rezania, Vahid; Coombe, Dennis; Tuszynski, Jack A.Tissue engineering, with the goal of repairing or replacing damaged tissue and organs, has continued to make dramatic science-based advances since its origins in the late 1980’s and early 1990’s. Such advances are always multi-disciplinary in nature, from basic biology and chemistry through physics and mathematics to various engineering and computer fields. This review will focus its attention on two topics critical for tissue engineering liver development: (a) fluid flow, zonation, and drug screening, and (b) biomechanics, tissue stiffness, and fibrosis, all within the context of 3D structures. First, a general overview of various bioreactor designs developed to investigate fluid transport and tissue biomechanics is given. This includes a mention of computational fluid dynamic methods used to optimize and validate these designs. Thereafter, the perspective provided by computer simulations of flow, reactive transport, and biomechanics responses at the scale of the liver lobule and liver tissue is outlined, in addition to how bioreactor-measured properties can be utilized in these models. Here, the fundamental issues of tortuosity and upscaling are highlighted, as well as the role of disease and fibrosis in these issues. Some idealized simulations of the effects of fibrosis on lobule drug transport and mechanics responses are provided to further illustrate these concepts. This review concludes with an outline of some practical applications of tissue engineering advances and how efficient computational upscaling techniques, such as dual continuum modeling, might be used to quantify the transition of bioreactor results to the full liver scale.
- ItemMicrotubule assembly of isotypically purified tubulin and its mixtures(2008) Rezania, Vahid; Azarenko, Olga; Jordan, Mary Ann; Bolterauer, Hannes; Huzil, J. Torin; Tuszynski, Jack A.; Luduena, Richard F.Numerous isotypes of the structural protein tubulin have now been characterized in various organisms and their expression offers a plausible explanation for observed differences affecting microtubule function in vivo. While this is an attractive hypothesis, there are only a handful of studies demonstrating a direct influence of tubulin isotype composition on the dynamic properties of microtubules. Here, we present the results of experimental assays on the assembly of microtubules from bovine brain tubulin using purified isotypes at various controlled relative concentrations. A novel data analysis is developed using recursive maps which are shown to be related to the master equation formalism. We have found striking similarities between the three isotypes of bovine tubulin studied in regard to their dynamic instability properties, except for subtle differences in their catastrophe frequencies. When mixtures of tubulin isotypes are analyzed, their nonlinear concentration dependence is modeled and interpreted in terms of lower affinities of tubulin dimers belonging to the same isotype than those that represent different isotypes indicating hitherto unsuspected influences of tubulin dimers on each other within a microtubule. Finally, we investigate the fluctuations in microtubule assembly and disassembly rates and conclude that the inherent rate variability may signify differences in the guanosine-59-triphosphate composition of the growing and shortening microtubule tips. It is the main objective of this article to develop a quantitative model of tubulin polymerization for individual isotypes and their mixtures. The possible biological significance of the observed differences is addressed.
- ItemModel of ionic currents through microtubule nanopores and the lumen(2010) Freedman, Holly; Rezania, Vahid; Priel, Avner; Carpenter, Eric; Noskov, Sergei Y.; Tuszynski, Jack A.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 when an external potential is 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 a net current to be pumped across the microtubule wall and propagate down the microtubule through the lumen. This effect is demonstrated to enhance and add directly to the longitudinal current through the lumen resulting from an external voltage source, and could be significant in amplifying low-intensity endogenous currents within the cellular environment or as a nano-bioelectronic device.
- ItemModeling the effects of drug binding on the dynamic instability of microtubules(2011) Hinow, Peter; Rezania, Vahid; Lopus, Manu; Jordan, Mary Ann; Tuszynski, Jack A.We propose a stochastic model that accounts for the growth, catastrophe and rescue processes of steady state microtubules assembled from MAP-free tubulin in the possible presence of a microtubule associated drug. As an example for the latter, we both experimentally and theoretically study the perturbation of microtubule dynamic instability by S-methyl-D-DM1, a synthetic derivative of the microtubule-targeted agent maytansine and a potential anticancer agent. Our model predicts that among drugs that act locally at the microtubule tip, primary inhibition of the loss of GDP tubulin results in stronger damping of microtubule dynamics than inhibition of GTP tubulin addition. On the other hand, drugs whose action occurs in the interior of the microtubule need to be present in much higher concentrations to have visible effects.
- ItemMultifractality nature of microtubule dynamic instability process(2021) Rezania, Vahid; Sudirga, Ferry C.; Tuszynski, Jack A.The irregularity of growing and shortening patterns observed experimentally in microtubules and their ensembles reflects a dynamical system that fluctuates stochastically between assembly and disassembly phases. The observed time series of microtubule lengths have been extensively analyzed to shed light on structural and dynamical properties of microtubules. Here, for the first time, Multifractal Detrended Fluctuation analysis (MFDFA) has been employed to investigate the multifractal and topological properties of both experimental and simulated microtubule time series. We find that the time dependence of microtubule length possesses true multifractal characteristics and cannot be described by mono-fractal distributions. Based on the multifractal spectrum profile, a set of multifractal indices have been calculated that can be related to the level of dynamical processes in microtubules. We also show that the resulting multifractal spectra for the simulated data might not be comparable with experimental data.
- ItemOn the classical vibrational coherence of carbonyl groups in the selectivity filter backbone of the KcsA ion channel(2015) Salari, Vahid; Sajadi, Maryam; Bassereh, Hassan; Rezania, Vahid; Alaei, Mojtaba; Tuszynski, Jack A.It has been suggested that quantum coherence in the selectivity filter of ion channel may play a key role in fast conduction and selectivity of ions. However, it has not been clearly elucidated yet why classical coherence is not sufficient for this purpose. In this paper, we investigate the classical vibrational coherence between carbonyl groups oscillations in the selectivity filter of KcsA ion channels based on the data obtained from molecular dynamics simulations. Our results show that classical coherence plays no effective role in fast ionic conduction.
- ItemOxygen distribution in the liver lobule: three dimensional computational models(2015) Rezania, Vahid; Coombe, Dennis; Tuszynski, Jack A.We develop a computational model for the transport and metabolism of drugs as well as oxygen in the functional unit of the liver called the lobule. The functional unit of an organ is the smallest structural unit that can independently serve all of the organ’s functions.
- ItemResponse to alternating electric fields of tubulin dimers and microtubule ensembles in electrolytic solutions(2017) Santelices, Iara B.; Friesen, Douglas E.; Bell, Clayton; Hough, Cameron M.; Xiao, Jack; Kalra, Aarat P.; Kar, Piyush; Freedman, Holly; Rezania, Vahid; Lewis, John D.; Shankar, Karthik; Tuszynski, Jack A.Microtubules (MTs), which are cylindrical protein filaments that play crucial roles in eukaryotic cell functions, have been implicated in electrical signalling as biological nanowires. We report on the small-signal AC (“alternating current”) conductance of electrolytic solutions containing MTs and tubulin dimers, using a microelectrode system. We find that MTs (212 nM tubulin) in a 20-fold diluted BRB80 electrolyte increase solution conductance by 23% at 100 kHz, and this effect is directly proportional to the concentration of MTs in solution. The frequency response of MT-containing electrolytes exhibits a concentration-independent peak in the conductance spectrum at 111 kHz (503 kHz FWHM that decreases linearly with MT concentration), which appears to be an intrinsic property of MT ensembles in aqueous environments. Conversely, tubulin dimers (42 nM) decrease solution conductance by 5% at 100 kHz under similar conditions. We attribute these effects primarily to changes in the mobility of ionic species due to counter-ion condensation effects, and changes in the solvent structure and solvation dynamics. These results provide insight into MTs’ ability to modulate the conductance of aqueous electrolytes, which in turn, has significant implications for biological information processing, especially in neurons, and for intracellular electrical communication in general.
- ItemRevealing and attenuating the electrostatic properties of tubulin and its polymers(2021) Kalra, Aarat P.; Patel, Sahil D.; Eakins, Boden B.; Riddell, Saralyn; Kumar, Pawan; Winter, Philip; Preto, Jordane; Carlson, Kris W.; Lewis, John D.; Rezania, Vahid; Tuszynski, Jack A.; Shankar, KarthikTubulin is an electrostatically negative protein that forms cylindrical polymers termed microtubules, which are crucial for a variety of intracellular roles. Exploiting the electrostatic behavior of tubulin and microtubules within functional microfluidic and optoelectronic devices is limited due to the lack of understanding of tubulin behavior as a function of solvent composition. This work displays the tunability of tubulin surface charge using dimethyl sulfoxide (DMSO) for the first time. Increasing the DMSO volume fractions leads to the lowering of tubulin's negative surface charge, eventually causing it to become positive in solutions >80% DMSO. As determined by electrophoretic mobility measurements, this change in surface charge is directionally reversible, i.e., permitting control between −1.5 and + 0.2 cm2 (V s)−1. When usually negative microtubules are exposed to these conditions, the positively charged tubulin forms tubulin sheets and aggregates, as revealed by an electrophoretic transport assay. Fluorescence-based experiments also indicate that tubulin sheets and aggregates colocalize with negatively charged g-C3N4 sheets while microtubules do not, further verifying the presence of a positive surface charge. This study illustrates that tubulin and its polymers, in addition to being mechanically robust, are also electrically tunable.
- ItemRevealing and attenuating the electrostatic properties of tubulin and microtubules(2020) Kalra, Aarat P.; Patel, Sahil D.; Winter, Philip; Wang, Hui; Carlson, Kris W.; Rezania, Vahid; Lewis, John; Meldrum, Al; Shankar, Karthik; Tuszynski, Jack A.Cancer treatment modalities such as chemotherapy and radiation therapy involve several side effects including an increased risk of getting cancer a second time. TTField (Tumour-treating field) therapy is a novel cancer-treatment modality that has attained U.S FDA approval for treatment of Glioblastoma Multiforme. TTFields are low intensity (1-2 V/cm), intermediate frequency (100-300 kHz) electric fields that have been shown to drastically lower tumor growth. While the only side-effects of TTField exposure are mild skin rashes, the exact mechanism of how TTFields act is not well understood. Models of TTFields posit that they target α, β- tubulin, a highly negatively charged (−50e), high dipole moment (∼1750 D) protein. Tubulin forms hollow cylindrical polymers termed microtubules, which form bundles that are crucial for mitosis and macromolecular transport. When exposed to TTFields, tubulin is expected to re-align and spatially relocate in response, inhibiting microtubule growth and interfering with mitosis. Using photolithography for microelectrode fabrication, we exposed unpolymerized tubulin containing solutions to AC electric fields and measured solution conductance. Interestingly, while we found that the presence of microtubules increased solution ionic conductance with a peak at TTField-like frequencies, the presence of unpolymerized tubulin reduced ionic conductance. Next, we used a parallel-plate electrode setup to compare the capacitance of solutions containing unpolymerized tubulin to those containing microtubules at identical physiological tubulin concentrations and ionic strengths. We found that while the presence of microtubules increased solution capacitance appreciably, the presence of unpolymerized tubulin did not. We are presently quantifying the chemical nature of the counterionic cloud around tubulin using a pH-sensitive fluorophore and Dynamic Light Scattering. Our results, in addition to displaying the significance of the tubulin polymerization state on the solution’ dielectric properties, also indicate that TTFields may target ion-tubulin interactions to inhibit tumour growth.