Jack A Tuszynski

Publications of Jack A Tuszynski

• Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?

  Authors: Travis J A Craddock, Jack A Tuszynski, Stuart Hameroff

  PLoS computational biology. 03/2012; 8(3):e1002421.

  Memory is attributed to strengthened synaptic connections among particular brain neurons, yet synaptic membrane components are transient, whereas memories can endure. This suggests synapticMemory is attributed to strengthened synaptic connections among particular brain neurons, yet synaptic membrane components are transient, whereas memories can endure. This suggests synaptic information is encoded and 'hard-wired' elsewhere, e.g. at molecular levels within the post-synaptic neuron. In long-term potentiation (LTP), a cellular and molecular model for memory, post-synaptic calcium ion (Ca(2+)) flux activates the hexagonal Ca(2+)-calmodulin dependent kinase II (CaMKII), a dodacameric holoenzyme containing 2 hexagonal sets of 6 kinase domains. Each kinase domain can either phosphorylate substrate proteins, or not (i.e. encoding one bit). Thus each set of extended CaMKII kinases can potentially encode synaptic Ca(2+) information via phosphorylation as ordered arrays of binary 'bits'. Candidate sites for CaMKII phosphorylation-encoded molecular memory include microtubules (MTs), cylindrical organelles whose surfaces represent a regular lattice with a pattern of hexagonal polymers of the protein tubulin. Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively, e.g. conveying synaptic information as ordered arrays of six "bits", and thus "bytes", with 64 to 5,281 possible bit states per CaMKII-MT byte. Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.

• An investigation of the plausibility of stochastic resonance in tubulin dimers.

  Authors: Aditya A Saha, Travis J A Craddock, Jack A Tuszynski

  Bio Systems. 02/2012; 107(2):81-7.

  This paper considers the possibility of stochastic resonance (SR) in tubulin dimers. A formula for the signal-to-noise ratio (SNR) of tubulin as a function of temperature is derived. The effectiveThis paper considers the possibility of stochastic resonance (SR) in tubulin dimers. A formula for the signal-to-noise ratio (SNR) of tubulin as a function of temperature is derived. The effective potential experienced by a delocalized electron in such a dimer is postulated to be a symmetric bimodal well. Inter-well and intra-well motions are described by Kramers rate theory and the Langevin formalism respectively. The frequency-dependent expression for the SNR shows that the response of the electron-tubulin dimer system is enhanced by ambient dipolar oscillations in specific frequency regimes. This is a characteristic of SR. Biophysical implications of this property such as the relevance to 8.085 MHz microtubule resonance and the clocking mechanism are detailed.

• A Physiologically-Based Flow Network Model for Hepatic Drug Elimination I: Regular Lattice Lobule Model

  Authors: Vahid Rezania, Rebeccah E Marsh, Dennis Coombe, Jack A Tuszynski

  11/2011;

  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 emphasizedWe 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.

• Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface.

  Authors: Holly Freedman, Tyler Luchko, Richard F Luduena, Jack A Tuszynski

  Proteins. 10/2011; 79(10):2968-82.

  Tubulin, an α/β heterodimer, has had most of its 3D structure analyzed; however, the carboxy (C)-termini remain elusive. Importantly, the C-termini play critical roles in regulating microtubuleTubulin, an α/β heterodimer, has had most of its 3D structure analyzed; however, the carboxy (C)-termini remain elusive. Importantly, the C-termini play critical roles in regulating microtubule structure and function. They are sites of most of the post-translational modifications of tubulin and interaction sites with molecular motors and microtubule-associated proteins. Simulated annealing was used in our molecular dynamics modeling to predict the interactions of the C-terminal tails with the tubulin dimer. We examined differences in their flexibility, interactions with the body of tubulin, and the existence of structural motifs. We found that the α-tubulin tail interacts with the H11 helix of β-tubulin, and the β-tubulin tail interacts with the H11 helix of α-tubulin. Tail domains and H10/B9 loops interact with each other and compete for interactions with positively-charged residues of the H11 helix on the neighboring monomer. In a simulation in which α-tubulin's H10/B9 loop switches on sub-nanosecond intervals between interactions with the C-terminal tail of α-tubulin and the H11 helix of β-tubulin, the intermediate domain of α-tubulin showed more fluctuations compared to those in the other simulations, indicating that tail domains may cause shifts in the position of this domain. This suggests that C-termini may affect the conformation of the tubulin dimer which may explain their essential function in microtubule formation and effects on ligand binding to microtubules. Our modeling also provides evidence for a disordered-helical/helical double-state system of the T3/H3 region of the microtubule, which could be linked to depolymerization following GTP hydrolysis.

• QM and QM/MD simulations of the Vinca alkaloids docked to tubulin.

  Authors: Evan B Kelly, Jack A Tuszynski, M Klobukowski

  Journal of molecular graphics & modelling. 07/2011; 30:54-66.

  The Vinca alkaloids are a class of pharmaceutically relevant binary indole-indoline alkaloids based on and including natural extracts of the periwinkle plant, Catharanthus rosea. Two naturalThe Vinca alkaloids are a class of pharmaceutically relevant binary indole-indoline alkaloids based on and including natural extracts of the periwinkle plant, Catharanthus rosea. Two natural products, vinblastine and vincristine, have been in clinical use as important chemotherapy agents for over four decades. Two semi-synthetic Vinca alkaloids, vindesine and vinorelbine, are currently in investigational chemotherapy programs, and a third semi-synthetic, vinflunine, is in advanced clinical trials. In addition to these five compounds studied in the present work, there are hundreds of other natural and semi-synthetic Vinca alkaloids known, although most are not clinically advantageous. The Vinca alkaloids are anti-mitotic agents that affect the cellular protein tubulin and bind to a specific site known as the Vinca domain located on β-tubulin. While the Vinca domain is well established, the specific binding mode of each drug is not. However, there is much insight into the binding mode and this has provided a strong base of information to begin simulations and to make comparisons against. Complicating the issue, however, is the large size of the Vinca alkaloids and their complex molecular structure, including a rotatable single bond joining the indole and indoline portions of each compound. The differential geometric and tubulin-binding properties of the drugs are not fully known. In the present work, the projection of the potential energy surface on the major torsional angle was calculated at the semi-empirical AM1 level, through in vacuo geometry optimizations. QM/MD simulations were performed, with the drugs at the AM1 level, of each Vinca alkaloid free in TIP3P water, and also bound to β-tubulin. A single equilibrium structure, resembling a known crystallographic vinblastine structure, for the free drugs was found. Further, the 1Z2B crystal structure of vinblastine bound to tubulin appears to be a valid starting point for simulations of all five Vinca alkaloids studied here.

• Entropic fragment-based approach to aptamer design.

  Authors: Chih-Yuan Tseng, Md Ashrafuzzaman, Jonathan Y Mane, Janice Kapty, John R Mercer, Jack A Tuszynski

  Chemical biology & drug design. 07/2011; 78(1):1-13.

  Aptamers are short RNA/DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers haveAptamers are short RNA/DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA/DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.

• Vibrational dynamics of bio- and nano-filaments in viscous solution subjected to ultrasound: implications for microtubules.

  Authors: Abdorreza Samarbakhsh, Jack A Tuszynski

  European biophysics journal : EBJ. 05/2011; 40(8):937-46.

  In this paper, using a new analytical method, we solved the beam equation for a uniform bio- and nano-filament in a viscous solution. The filament is assumed to be attached at its two ends and drivenIn this paper, using a new analytical method, we solved the beam equation for a uniform bio- and nano-filament in a viscous solution. The filament is assumed to be attached at its two ends and driven by ultrasound plane waves. To obtain analytical solutions, we converted the beam equation to an equation that allows us the use of the method of separation of variables. We then reconstructed the solution of the original beam equation from the solution of the converted equation. Subsequently, we have used the parametric equations derived in this paper to investigate the resonance condition for a microtubule (MT) in an aqueous solution. We show that by using ultrasound plane waves, one cannot satisfy a resonance condition for MTs treated as rigid rods. In order to achieve resonance, a single mode of the MT vibration must be excited with a harmonic number larger than a threshold value found here. Single mode excitation not only helps to transfer a minimum amount of energy to the surrounding medium compared with multi-mode excitation, but it also allows for a simultaneous high amplitude and high mode quality that is impossible using plane waves. In order to overcome this difficulty, we propose to use an ultrasound generation device as a potential technical solution characterized by both frequency control and optimized energy transfer to the MT. Finally, the minimum required intensity of the ultrasound at the location of the MT in order to break it is shown to be on the order of 10(5) W/m(2), which corresponds to 170 dB.

• A model of competing saturable kinetic processes with application to the pharmacokinetics of the anticancer drug paclitaxel.

  Authors: Rebeccah E Marsh, Jack A Tuszyński, Michael Sawyer, Kenneth J E Vos

  Mathematical biosciences and engineering : MBE. 04/2011; 8(2):325-54.

  A saturable multi-compartment pharmacokinetic model for the anti-cancer drug paclitaxel is proposed based on a meta-analysis of pharmacokinetic data published over the last two decades. We presentA saturable multi-compartment pharmacokinetic model for the anti-cancer drug paclitaxel is proposed based on a meta-analysis of pharmacokinetic data published over the last two decades. We present and classify the results of time series for the drug concentration in the body to uncover the underlying power laws. Two dominant fractional power law exponents were found to characterize the tails of paclitaxel concentration-time curves. Short infusion times led to a power exponent of -1.57 ± 0.14, while long infusion times resulted in tails with roughly twice the exponent. Curves following intermediate infusion times were characterized by two power laws. An initial segment with the larger slope was followed by a long-time tail characterized by the smaller exponent. The area under the curve and the maximum concentration exhibited a power law dependence on dose, both with compatible fractional power exponents. Computer simulations using the proposed model revealed that a two-compartment model with both saturable distribution and elimination can reproduce both the single and crossover power laws. Also, the nonlinear dose-dependence is correlated with the empirical power law tails. The longer the infusion time the better the drug delivery to the tumor compartment is a clinical recommendation we propose.

• Computer assisted design of second-generation colchicine derivatives.

  Authors: J Torin Huzil, Jonathan Mane, Jack A Tuszynski

  Interdisciplinary sciences, computational life sciences. 06/2010; 2(2):169-74.

  Cytoskeletal proteins, such as tubulin, are a primary target for many successful anti-cancer drugs. The expression of several beta-tubulin isotypes in normal and cancerous cells provides a platformCytoskeletal proteins, such as tubulin, are a primary target for many successful anti-cancer drugs. The expression of several beta-tubulin isotypes in normal and cancerous cells provides a platform upon which to construct chemotherapeutic agents capable of differentiating between them. To test this hypothesis, we have previously designed several colchicine derivatives and computationally probed them for affinity to the beta-tubulin isotypes. Subsequent synthesis and cytotoxicity assays produced a small set of promising compounds exhibiting IC(50) values approximately 30 fold lower than values previously reported for colchicine. Here we describe the creation and testing of these first-generation colchicine derivatives and discuss the subsequent design and preliminary computational screening of a novel set of second-generation derivatives using the most promising first-generation derivatives as scaffolds.

• Computational design and biological testing of highly cytotoxic colchicine ring A modifications.

  Authors: John Torin Huzil, Philip Winter, Lorelei Johnson, Alexander L Weis, Tamas Bakos, Asok Banerjee, Richard F Luduena, Sambasivarao Damaraju, Jack A Tuszynski

  Chemical biology & drug design. 06/2010; 75(6):541-50.

  Microtubules are the primary target for many anti-cancer drugs, the majority of which bind specifically to beta-tubulin. The existence of several beta-tubulin isotypes, coupled with their variedMicrotubules are the primary target for many anti-cancer drugs, the majority of which bind specifically to beta-tubulin. The existence of several beta-tubulin isotypes, coupled with their varied expression in normal and cancerous cells provides a platform upon which to construct selective chemotherapeutic agents. We have examined five prevalent human beta-tubulin isotypes and identified the colchicine-binding site as the most promising for drug design based on specificity. Using this binding site as a template, we have designed several colchicine derivatives and computationally probed them for affinity to the beta-tubulin isotypes. These compounds were synthesized and subjected to cytotoxicity assays to determine their effectiveness against several cancerous cell lines. We observed a correlation between computational-binding predictions and experimentally determined IC(50) values, demonstrating the utility of computational screening in the design of more effective colchicine derivatives. The most promising derivative exhibited an IC(50) approximately threefold lower than values previously reported for either colchicine or paclitaxel, demonstrating the utility of computational design and assessment of binding to tubulin.

• Microtubule ionic conduction and its implications for higher cognitive functions.

  Authors: Travis J A Craddock, Jack A Tuszynski, Avner Priel, Holly Freedman

  Journal of integrative neuroscience. 06/2010; 9(2):103-22.

  The neuronal cytoskeleton has been hypothesized to play a role in higher cognitive functions including learning, memory and consciousness. Experimental evidence suggests that both microtubules andThe neuronal cytoskeleton has been hypothesized to play a role in higher cognitive functions including learning, memory and consciousness. Experimental evidence suggests that both microtubules and actin filaments act as biological electrical wires that can transmit and amplify electric signals via the flow of condensed ion clouds. The potential transmission of electrical signals via the cytoskeleton is of extreme importance to the electrical activity of neurons in general. In this regard, the unique structure, geometry and electrostatics of microtubules are discussed with the expected impact on their specific functions within the neuron. Electric circuit models of ionic flow along microtubules are discussed in the context of experimental data, and the specific importance of both the tubulin C-terminal tail regions, and the nano-pore openings lining the microtubule wall is elucidated. Overall, these recent results suggest that ions, condensed around the surface of the major filaments of the cytoskeleton, flow along and through microtubules in the presence of potential differences, thus acting as transmission lines propagating intracellular signals in a given cell. The significance of this conductance to the functioning of the electrically active neuron, and to higher cognitive function is also discussed.

• Model of ionic currents through microtubule nanopores and the lumen.

  Authors: Holly Freedman, Vahid Rezania, Avner Priel, Eric Carpenter, Sergei Y Noskov, Jack A Tuszynski

  Physical review. E, Statistical, nonlinear, and soft matter physics. 05/2010; 81(5 Pt 1):051912.

  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 featuresIt 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.

• Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer.

  Authors: Holly Freedman, Linh P Huynh, Ly Le, Thomas E Cheatham, Jack A Tuszynski, Thanh N Truong

  The journal of physical chemistry. B. 02/2010; 114(6):2227-37.

  To provide more accurate computational estimates of binding free energies in solution from molecular dynamics (MD) simulations, a separate solvation contribution for the binding ligand is determinedTo provide more accurate computational estimates of binding free energies in solution from molecular dynamics (MD) simulations, a separate solvation contribution for the binding ligand is determined from a linear response treatment. We use explicit water coordinates for this term and combine with MM-PBSA (molecular mechanics, Poisson-Boltzmann, and surface area contributions) in a new approach (MM-PB/LRA-SA). To assess this method, application to the binding between theophylline and its derivatives to an RNA aptamer was performed and compared with experimental binding affinities. Explicitly solvated MD trajectories were generated with the same parameter set used in the previous work by Gouda et al., who compared the relative binding of these molecules by both the MM-PBSA and thermodynamic integration methods. Substituting the linear response term for the ligand in the MM-PB/LRA-SA approach led to an improvement upon MM-PBSA when compared with experimental and thermodynamic integration results at approximately twice the computational cost. The balance between accuracy and computational expense achieved using this method suggests potential advantages in applying it in the virtual drug-screening process.

• Quantitative analysis of the effect of tubulin isotype expression on sensitivity of cancer cell lines to a set of novel colchicine derivatives.

  Authors: Chih-Yuan Tseng, Jonathan Y Mane, Philip Winter, Lorelei Johnson, Torin Huzil, Elzbieta Izbicka, Richard F Luduena, Jack A Tuszynski

  Molecular cancer. 01/2010; 9:131.

  A maximum entropy approach is proposed to predict the cytotoxic effects of a panel of colchicine derivatives in several human cancer cell lines. Data was obtained from cytotoxicity assays performedA maximum entropy approach is proposed to predict the cytotoxic effects of a panel of colchicine derivatives in several human cancer cell lines. Data was obtained from cytotoxicity assays performed with 21 drug molecules from the same family of colchicine compounds and correlate these results with independent tubulin isoform expression measurements for several cancer cell lines. The maximum entropy method is then used in conjunction with computed relative binding energy values for each of the drug molecules against tubulin isotypes to which these compounds bind with different affinities. We have found by using our analysis that alphabetaI and alphabetaIII tubulin isoforms are the most important isoforms in establishing predictive response of cancer cell sensitivity to colchicine derivatives. However, since alphabetaI tubulin is widely distributed in the human body, targeting it would lead to severe adverse side effects. Consequently, we have identified tubulin isotype alphabetaIII as the most important molecular target for inhibition of microtubule polymerization and hence cancer cell cytotoxicity. Tubulin isotypes alphabetaI and alphabetaII are concluded to be secondary targets. The benefit of being able to correlate expression levels of specific tubulin isotypes and the resultant cell death effect is that it will enable us to better understand the origin of drug resistance and hence design optimal structures for the elimination of cancer cells. The conclusion of the study described herein identifies tubulin isotype alphabetaIII as a target for optimized chemotherapy drug design.

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

  Authors: Abdorreza Samarbakhsh, Jack A Tuszynski

  Physical review. E, Statistical, nonlinear, and soft matter physics. 08/2009; 80(1 Pt 1):011903.

  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 andThe 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.

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

  Authors: Holly Freedman, J Torin Huzil, Tyler Luchko, Richard F Ludueña, Jack A Tuszynski

  Journal of chemical information and modeling. 03/2009; 49(2):424-36.

  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 theTubulin, 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.

• Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests.

  Authors: Travis J. A. Craddock, Catherine Beauchemin, Jack A. Tuszynski

  Biosystems. 01/2009; 97:28-34.

• Electrostatic Contributions to Colchicine Binding within Tubulin Isotypes.

  Authors: John Torin Huzil, Khaled Barakat, Jack A Tuszynski

  Electromagnetic biology and medicine. 01/2009; 28(4):355-64.

  Tubulin, the structural subunit of microtubules, is the target of some highly successful anti-tumor drugs. Most of these drugs bind to the beta-tubulin resulting in the inhibition of microtubuleTubulin, the structural subunit of microtubules, is the target of some highly successful anti-tumor drugs. Most of these drugs bind to the beta-tubulin resulting in the inhibition of microtubule dynamics and eventually cell death. The varied cellular distribution of several human isotypes of beta -tubulin provides a platform upon which to construct novel chemotherapeutic agents that are able to differentiate between these types of cells. To test this hypothesis, we have previously created homology models of the nine most frequently observed human beta -tubulin isotypes and analyzed them for differences in the colchicine-binding site. Here, we describe the electrostatic properties of the colchicine binding site and how this may affect calculated drug binding affinities between the beta -tubulin isotypes.

• Effect of calcium on electrical energy transfer by microtubules.

  Authors: Avner Priel, Arnolt J Ramos, Jack A Tuszynski, Horacio F Cantiello

  Journal of biological physics. 11/2008; 34(5):475-85.

  Microtubules (MTs) are important cytoskeletal superstructures implicated in neuronal morphology and function, which are involved in vesicle trafficking, neurite formation and differentiation andMicrotubules (MTs) are important cytoskeletal superstructures implicated in neuronal morphology and function, which are involved in vesicle trafficking, neurite formation and differentiation and other morphological changes. The structural and functional properties of MTs depend on their high intrinsic charge density and functional regulation by the MT depolymerising properties of changes in Ca(2 + ) concentration. Recently, we reported on remarkable properties of isolated MTs, which behave as biomolecular transistors capable of amplifying electrical signals (Priel et al., Biophys J 90:4639-4643, 2006). Here, we demonstrate that MT-bathing (cytoplasmic) Ca(2 + ) concentrations modulate the electrodynamic properties of MTs. Electrical amplification by MTs was exponentially dependent on the Ca(2 + ) concentration between 10( - 7) and 10( - 2) M. However, the electrical connectivity (coupling) of MTs was optimal at a narrower window of Ca(2 + ) concentrations. We observed that while raising bathing Ca(2 + ) concentration increased electrical amplification by MTs, energy transfer was highest in the presence of ethylene glycol tetraacetic acid (lowest Ca(2 + ) concentration). Our data indicate that Ca(2 + ) is an important modulator of electrical amplification by MTs, supporting the hypothesis that this divalent cation, which adsorbs onto the polymer's surface, plays an important role as a regulator of the electrical properties of MTs. The Ca(2 + )-dependent ability of MTs to modulate and amplify electrical signals may provide a novel means of cell signaling, likely contributing to neuronal function.

• Identification of tubulin drug binding sites and prediction of relative differences in binding affinities to tubulin isotypes using digital signal processing.

  Authors: Ke Chen, J Torin Huzil, Holly Freedman, Parameswaran Ramachandran, Andreas Antoniou, Jack A Tuszynski, Lukasz Kurgan

  Journal of molecular graphics & modelling. 10/2008;

  Microtubules are involved in numerous cellular processes including chromosome segregation during mitosis and, as a result, their constituent protein, tubulin, has become a successful target ofMicrotubules are involved in numerous cellular processes including chromosome segregation during mitosis and, as a result, their constituent protein, tubulin, has become a successful target of several chemotherapeutic drugs. In general, these drugs bind indiscriminately to tubulin within both cancerous and healthy cells, resulting in unwanted side effects. However, differences between beta-tubulin isotypes expressed in a wide range of cell types may aid in the development of anti-tubulin drugs having increased specificity for only certain types of cells. Here, we describe a digital signal processing (DSP) method that is capable of predicting hot spots for the tubulin family of proteins as well as determining relative differences in binding affinities to these hot spots based only on the primary sequence of 10 human tubulin isotypes. Due to the fact that several drug binding sites have already been characterized within beta-tubulin, we are able to correlate hot spots with the binding sites for known chemotherapy drugs. We have also verified the accuracy of this method using the correlation between the binding affinities of characterized drugs and the tubulin isotypes. Additionally, the DSP method enables the rapid estimation of relative differences in binding affinities within the binding sites of tubulin isotypes that are yet to be experimentally determined.