Takashi Naka

Topological analysis of MAPK cascade for kinetic ErbB signaling.

Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins. Earlier experimental research indicated that cells expressing both EGFR (epidermal growth factor receptor) and the ErbB4 receptor (E1/4 cells) induced E1/4 cell-specific B-Raf activation and higher extracellular signal-regulated kinase (ERK) activation, followed by cellular transformation, than cells solely expressing EGFR (E1 cells) in Chinese hamster ovary (CHO) cells. Since our experimental data revealed the presence of positive feedback by ERK on upstream pathways, it was estimated that the cross-talk/feedback pathway structure of the Raf-MEK-ERK cascade might affect ERK activation dynamics in our cell system. To uncover the regulatory mechanism concerning the ERK dynamics, we used topological models and performed parameter estimation for all candidate structures that possessed ERK-mediated positive feedback regulation of Raf. The structure that reliably reproduced a series of experimental data regarding signal amplitude and duration of the signaling molecules was selected as a solution. We found that the pathway structure is characterized by ERK-mediated positive feedback regulation of B-Raf and B-Raf-mediated negative regulation of Raf-1. Steady-state analysis of the estimated structure indicated that the amplitude of Ras activity might critically affect ERK activity through ERK-B-Raf positive feedback coordination with sustained B-Raf activation in E1/4 cells. However, Rap1 that positively regulates B-Raf activity might be less effective concerning ERK and B-Raf activity. Furthermore, we investigated how such Ras activity in E1/4 cells can be regulated by EGFR/ErbB4 heterodimer-mediated signaling. From a sensitivity analysis of the detailed upstream model for Ras activation, we concluded that Ras activation dynamics is dominated by heterodimer-mediated signaling coordination with a large initial speed of dimerization when the concentration of the ErbB4 receptor is considerably high. Such characteristics of the signaling cause the preferential binding of the Grb2-SOS complex to heterodimer-mediated signaling molecules.

Phase Transition and Spin Dynamics in LiVO2

The phase transition and the spin dynamics in a triangular lattice compound LiVO 2 have been studied through magnetic susceptibility and NMR measurements. It has been found that the quadrupole effect and the anisotropy of the Knight shift of the 51 V nuclei are appreciably induced due to the distortion of the local symmetry at the V ions below the nonmagnetic-magnetic transition temperatures which are about 500 K on heating and 440 K on cooling. The electronic state and the spin dynamics of V ions above the transition have been explained by the localized spin model with the spin number S =1. It has also been suggested that the dynamics from the transition to about 140 K may be described by the thermally excited spin whose ground state is possibly spin-singlet due to the trimerization of V 3+ ions.

OBIYagns: a grid-based biochemical simulator with a parameter estimator

UNLABELLED OBIYagns (yet another gene network simulator) is a biochemical system simulator that comprises a multiple-user Web-based graphical interface, an ordinary differential equation solver and a parameter estimators distributed over an open bioinformatics grid (OBIGrid). This grid-based biochemical simulation system can achieve high performance and provide a secure simulation environment for estimating kinetic parameters in an acceptable time period. OBIYagns can be applied to larger system biology-oriented simulation projects. AVAILABILITY OBIYagns example models, methods and user guide are available at https://access.obigrid.org/yagns/ SUPPLEMENTARY INFORMATION Please refer to Bioinformatics online.

Kinetics of membrane-bound enzymes: Validity of quasi-steady-state approximation for a Michaelis-Menten-type reaction

Abstract The dynamic behavior of a reaction-diffusion system with a Michaelis-Menten-type enzyme immobilized at a uniform concentration in a membrane is analyzed to examine the validity of the quasi-steady-state approximation at nonsteady state in a heterogeneous and open system. The conditions for validity are evaluated for the well-known S - v relationship (Michaelis equation) in the membrane-bound enzyme system by comparison with the actual reaction velocity determined from computer simulation. The analysis of the responses of the system to stepwise changes in substrate influx rate infers that the validity is governed rather by the ratios of the Michaelis constant to the total enzyme concentration ( K m / E T and to the maximum velocity ( K m / V max ) than by the individual rate constants. Throughouts the course of the responses, the Michaelis equation is reliable, with an error below 1% when the ratio K m / E T is higher than 100. This same accuracy cannot be attained when the ratio K m / E T is less than 1. In the case the ratio K m / E T is approx. 10 the error exceeds 1% only for the very early phase of the responses. The ratio of K m / E max is related to the characteristics of the dynamic behavior of the system, affecting the time for the maximum error to occur in the Michaelis equation during the response.

A two-dimensional compartment model for the reaction-diffusion system of acetylcholine in the synaptic cleft at the neuromuscular junction

A minimal compartment model of the reaction-diffusion system (RD system) of a neurotransmitter in a two-dimensional space of axis-symmetrical disc is proposed to represent the chemical transmission process of a quantum of acetylcholine (ACh) in the synaptic cleft at the neuromuscular junction. The behavior of the RD system for ACh is expressed by a two-dimensional diffusion equation with nonlinear reaction terms due to the rate processes for ACh receptor and acetylcholinesterase. The simulation analysis of the RD system reveals that the radial diffusion process of ACh has more distinctive effects on spontaneous generation of the miniature endplate current (MEPC) than the transverse process. The anisotropic diffusion is effective in the RD system since the diffusion coefficient of ACh in the radial direction is evaluated to be about 1.0 x 10(-6) cm2 sec-1 for appropriate characterization of the MEPC, on which the diffusion coefficient in the transverse direction larger than 2.0 x 10(-6) cm2 sec-1 has virtually no effects. The compartment model is thus appropriately constructed to comprise three elements on the transverse coordinate and ten elements on the radial coordinate in the disc with 500 nm of radius and 50 nm of height.

Silence on the relevant literature and errors in implementation

node j have changed, but other indirectly affected nodes also change because the initial perturbation has propagated through the network. MRA has solved the problem of finding local, direct links between components through the global responses for networks of any size and complexity 2. The development and application of methods that are conceptually similar to MRA (e.g., regulatory strength analysis 8 and maximum likelihood-based MRA 9,10) has reinforced the validity of using MRA-type methods to reconstruct network connections 11–16. The Barzel & Barabási study 1 uses the same concept and strikingly similar terminologies to reconstruct networks by deriving the local connection coefficients from the global response coefficients. Key equations (3) and (4) in their silencing method 1 express the local coefficients in terms of the global coefficients and are a subset of the published MRA equations 2,9,10,17–19 with a formal replacement of the diagonal elements of the local response matrix by zeros instead of minus ones (Supplementary Note 1). Another formal difference is that the variant of the global response matrix used by Barzel & Barabási 1 considers the global change in each node that results To the Editor: In the August 2013 issue of this journal, Barzel & Barabási reported a method for reconstructing network topologies 1. Here we show that the Barzel & Barabási method is a variant of a previously published method, modular response analysis (MRA) 2. We also demonstrate that the implementation of their algorithm using statistical similarity measures as a proxy for global network responses to perturbations is erroneous and its performance is overestimated. The reconstruction of network connections from data remains a fundamental problem in biology. It is not immediately obvious how to capture direct links between individual network nodes from experimental data because a perturbation to a component propagates through a network, causing widespread (global) changes, thereby masking direct (local) connections between nodes. This question has been previously studied in >100 publications, collectively representing MRA (reviewed in refs. 3–7). MRA quantifies direct interactions between network nodes (i and j) using the local response coefficients (also known as connection coefficients), which describe direct effects of a small change in node j on node i, while keeping the remaining nodes unchanged to prevent the spread of the perturbation. The local responses cannot be directly assessed, whereas the global responses can be measured; when following a perturbation to node j, the entire network relaxes to a …

Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity

BackgroundEpidermal growth factor receptor (EGFR) signaling plays an important role in the regulation of cell proliferation, survival, metastasis, and invasion in various tumors. Earlier studies showed that the EGFR is frequently overexpressed in non-small-cell lung cancer (NSCLC) and EGFR mutations at specific amino acid residues in the kinase domain induce altered responsiveness to gefitinib, a small molecule EGFR tyrosine kinase inhibitor. However, the mechanism underlying the drug response modulated by EGFR mutation is still largely unknown. To elucidate drug response in EGFR signal transduction pathway in which complex dynamics of multiple molecules involved, a systematic approach is necessary. In this paper, we performed experimental and computational analyses to clarify the underlying mechanism of EGFR signaling and cell-specific gefitinib responsiveness in three H1299-derived NSCLC cell lines; H1299 wild type (H1299WT), H1299 with an overexpressed wild type EGFR (H1299EGFR-WT), and H1299 with an overexpressed mutant EGFR L858R (H1299L858R; gefitinib sensitive mutant).ResultsWe predicted and experimentally verified that Mig6, which is a known negative regulator of EGFR and specifically expressed in H1299L858R cells, synergized with gefitinib to suppress cellular growth. Computational analyses indicated that this inhibitory effect is amplified at the phosphorylation/dephosphorylation steps of MEK and ERK.ConclusionsThus, we showed that L858R receptor mutation in combination with expression of its negative regulator, Mig6, alters signaling outcomes and results in variable drug sensitivity.

Simulation analysis of the effects of the simultaneous release of quanta of acetylcholine on the endplate current at the neuromuscular junction

Arrival of an action potential to a nerve terminal at the neuromuscular junction induces the release of a few hundred quanta of acetylcholine (ACh) into the synaptic cleft, resulting in depolarization of the muscle cell which is observed as the endplate current (EPC). The release of each quantum of ACh invokes the miniature endplate current (MEPC), so that an EPC could be generated by summation of the MEPCs both in time during evolution of the EPC and in space for a certain area of the post-synaptic membrane. In this study, a mathematical model for EPC generation is developed as a reaction-diffusion system (RD system) which represents the dynamic behavior of ACh in the chemical transmission process with the simultaneous quantum release of ACh. The RD system for ACh is mathematically expressed by a two-dimensional diffusion equation with nonlinear reaction terms due to the rate processes for acetylcholinesterase (AChE) and ACh receptor (AChR). Numerical solution of the governing equation with the method of lines and the Gear method yields temporal changes in relative concentrations of the open channel form of AChR which is assumed to be equivalent to the EPC. Analysis of the behavior of the RD system with respect to the various distances between the release sites of ACh on the pre-synaptic membrane demonstrates that the amplitude of EPC is quite sensitive to the distances around 0.5 µm, but independent of the values of the diffusion coefficient of ACh in the synaptic cleft.

Evaluation of characteristic parameters for the neurotransmitter release mechanisms at the neuromuscular junction.

The process of neurotransmitter release at the neuromuscular junction needs to be represented appropriately in modeling of the synaptic chemical transmission as a reaction-diffusion system. The release mechanisms of the expanding pore and the acceleration are analyzed by the computer simulation with respect to the effects of the characteristic parameters in the mechanisms on spontaneous generation of the miniature endplate current (MEPC), leading to the following evaluation. In the expanding pore mechanism the expanding rate of the pore more than 10 nm ms(-1) and the diffusion coefficient of acetylcholine in the synaptic cleft (D(c)) of about 1.0 x 10(-6) cm2 s(-1) yield the maximum amplitude, the rise time and the decay time constant of the MEPC in agreement with the empirical data. In the active release mechanism the 10-fold acceleration of the natural diffusion and a similar value of D(c) are required to suit for the empirical MEPC.

Validity of transfer-function representation of input-output relation in allosteric models☆

A transfer-function representation of reaction velocity is devised to describe analytically and approximately an input-output response of allosteric enzyme around a steady state. The transfer function is derived on assuming an exponential change in reaction velocity for the indicial response to substrate influx rate. The validity of the representation with variation in the kinetic parameters and flow rates is examined for the response of Koshland-Nemethy-Filmer (KNF) and Monod-Wyman-Changeux (MWC) dimeric models by comparing with the exact response obtained from the computer simulation, that is, by numerical integration of the rate equation. The representation has a wider valid region with a decrease in influx rate than with an increase. For the KNF model the representation is valid for negative cooperativity, but invalid for positive cooperativity. For the MWC model the validity decreases with stronger cooperativity. With the transfer functions valid for the Michaelis-Menten and allosteric reactions, we may derive the transfer-function representation for many metabolic pathways.