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1.
IET Syst Biol ; 9(2): 41-51, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26672147

RESUMO

NF-κB is a transcription factor regulating expression of more than 500 genes, and its dysfunction leads to the autoimmune and inflammatory diseases. In malignant cancer cells, NF-κB is constitutively activated. Thus the elucidation of mechanisms for NF-κB regulation is important for the establishment of therapeutic treatment caused by incorrect NF-κB responses. Cytoplasmic NF-κB translocates to the nucleus by the application of extracellular stimuli such as cytokines. Nuclear NF-κB is known to oscillate with the cycle of 1.5-4.5 h, and it is thought that the oscillation pattern regulates the expression profiles of genes. In this review, first we briefly describe regulation mechanisms of NF-κB. Next, published computational simulations on the oscillation of NF-κB are summarised. There are at least 60 reports on the computational simulation and analysis of NF-κB oscillation. Third, the importance of a 'space' for the regulation of oscillation pattern of NF-κB is discussed, showing altered oscillation pattern by the change in spatial parameters such as diffusion coefficient, nuclear to cytoplasmic volume ratio (N/C ratio), and transport through nuclear membrane. Finally, simulations in a true intracellular space (TiCS), which is an intracellular 3D space reconstructed in a computer with organelles such as nucleus and mitochondria are discussed.


Assuntos
Relógios Biológicos/fisiologia , Regulação da Expressão Gênica/fisiologia , Modelos Biológicos , NF-kappa B/metabolismo , Transdução de Sinais/fisiologia , Ativação Transcricional/fisiologia , Animais , Simulação por Computador , Redes Reguladoras de Genes/fisiologia , Humanos
2.
PLoS One ; 10(6): e0127633, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26042739

RESUMO

The activated transcription factor NF-κB shuttles between the cytoplasm and the nucleus resulting in the oscillation of nuclear NF-κB (NF-κBn). The oscillation pattern of NF-κBn is implicated in the regulation of gene expression profiles. Using computational models, we previously reported that spatial parameters, such as the diffusion coefficient, nuclear to cytoplasmic volume ratio, transport through the nuclear envelope, and the loci of translation of IκB protein, modified the oscillation pattern of NF-κBn. In a subsequent report, we elucidated the importance of the "reset" of NF-κBn (returning of NF-κB to the original level) and of a "reservoir" of IκB in the cytoplasm. When the diffusion coefficient of IκB was large, IκB stored at a distant location from the nucleus diffused back to the nucleus and "reset" NF-κBn. Herein, we report mechanisms that regulate the persistency and frequency of NF-κBn oscillation by nuclear transport. Among the four parameters of nuclear transport tested in our spatio-temporal computational model, the export of IκB mRNA from the nucleus regulated the persistency of oscillation. The import of IκB to the nucleus regulated the frequency of oscillation. The remaining two parameters, import and export of NF-κB to and from the nucleus, had virtually no effect on the persistency or frequency. Our analyses revealed that lesser export of IκB mRNA allowed NF-κBn to transcript greater amounts of IκB mRNA, which was retained in the nucleus, and was subsequently exported to the cytoplasm, where large amounts of IκB were synthesized to "reset" NF-κBn and drove the persistent oscillation. On the other hand, import of greater amounts of IκB led to an increase in the influx and the efflux of NF-κB to and from the nucleus, resulting in an increase in the oscillation frequency. Our study revealed the importance of nuclear transport in regulating the oscillation pattern of NF-κBn.


Assuntos
Núcleo Celular/metabolismo , NF-kappa B/metabolismo , Transdução de Sinais , Transporte Ativo do Núcleo Celular , Simulação por Computador , Humanos , Proteínas I-kappa B/metabolismo , Transporte Proteico , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
3.
PLoS Comput Biol ; 11(6): e1004326, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26115353

RESUMO

Stress granules (SGs) are non-membranous cytoplasmic aggregates of mRNAs and related proteins, assembled in response to environmental stresses such as heat shock, hypoxia, endoplasmic reticulum (ER) stress, chemicals (e.g. arsenite), and viral infections. SGs are hypothesized as a loci of mRNA triage and/or maintenance of proper translation capacity ratio to the pool of mRNAs. In brain ischemia, hippocampal CA3 neurons, which are resilient to ischemia, assemble SGs. In contrast, CA1 neurons, which are vulnerable to ischemia, do not assemble SGs. These results suggest a critical role SG plays in regards to cell fate decisions. Thus SG assembly along with its dynamics should determine the cell fate. However, the process that exactly determines the SG assembly dynamics is largely unknown. In this paper, analyses of experimental data and computer simulations were used to approach this problem. SGs were assembled as a result of applying arsenite to HeLa cells. The number of SGs increased after a short latent period, reached a maximum, then decreased during the application of arsenite. At the same time, the size of SGs grew larger and became localized at the perinuclear region. A minimal mathematical model was constructed, and stochastic simulations were run to test the modeling. Since SGs are discrete entities as there are only several tens of them in a cell, commonly used deterministic simulations could not be employed. The stochastic simulations replicated observed dynamics of SG assembly. In addition, these stochastic simulations predicted a gamma distribution relative to the size of SGs. This same distribution was also found in our experimental data suggesting the existence of multiple fusion steps in the SG assembly. Furthermore, we found that the initial steps in the SG assembly process and microtubules were critical to the dynamics. Thus our experiments and stochastic simulations presented a possible mechanism regulating SG assembly.


Assuntos
Grânulos Citoplasmáticos/química , Grânulos Citoplasmáticos/metabolismo , Modelos Biológicos , Animais , Arsenitos/farmacologia , Células COS , Chlorocebus aethiops , Biologia Computacional , Simulação por Computador , Grânulos Citoplasmáticos/efeitos dos fármacos , Grânulos Citoplasmáticos/fisiologia , Células HeLa , Humanos , Análise Espaço-Temporal , Estresse Fisiológico/efeitos dos fármacos
4.
PLoS One ; 10(3): e0116637, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25780926

RESUMO

Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10 min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation.


Assuntos
Moléculas de Adesão Celular/metabolismo , Recuperação de Fluorescência Após Fotodegradação , Imunoglobulinas/metabolismo , Proteínas dos Microfilamentos/metabolismo , Proteínas Nucleares/metabolismo , Fatores de Transcrição/metabolismo , Animais , Sítios de Ligação , Adesão Celular , Molécula 1 de Adesão Celular , Cães , Células Epiteliais/citologia , Células Epiteliais/metabolismo , Humanos , Cinética , Células Madin Darby de Rim Canino , Proteínas dos Microfilamentos/química , Movimento , Proteínas Nucleares/química , Estabilidade Proteica , Fatores de Transcrição/química
5.
Math Biosci Eng ; 12(6): 1189-202, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26775856

RESUMO

Invasion and metastasis are the main cause of death in cancer patients. The initial step of invasion is the degradation of extracellular matrix (ECM) by primary cancer cells in a tissue. Membranous metalloproteinase MT1-MMP and soluble metalloproteinase MMP-2 are thought to play an important role in the degradation of ECM. In the previous report, we found that the repetitive insertion of MT1-MMP to invadopodia was crucial for the effective degradation of ECM (Hoshino, D., et al., PLoS Comp. Biol., 2012, e1002479). However, the role of MMP-2 and the effect of inhibitors for these ECM-degrading proteases were still obscure. Here we investigated these two problems by using the same model as in the previous report. First we tested the effect of MMP-2 and found that while MT1-MMP played a major role in the degradation of ECM, MMP-2 played only a marginal effect on the degradation of ECM. Based on these findings, we next tested the effect of a putative inhibitor for MT1-MMP and found that such inhibitor was ineffective in blocking ECM degradation. Then we tested combined strategy including inhibitor for MT1-MMP, reduction of its turnover and its content in vesicles. A synergistic effect of combined strategy was observed in the decrease in the efficacy of ECM degradation. Our simulation study suggests the importance of combined strategy in blocking cancer invasion and metastasis.


Assuntos
Modelos Biológicos , Invasividade Neoplásica/prevenção & controle , Simulação por Computador , Matriz Extracelular/efeitos dos fármacos , Matriz Extracelular/metabolismo , Humanos , Conceitos Matemáticos , Metaloproteinase 14 da Matriz/metabolismo , Metaloproteinase 2 da Matriz/metabolismo , Inibidores de Metaloproteinases de Matriz/farmacologia , Invasividade Neoplásica/fisiopatologia
6.
PLoS One ; 9(10): e109895, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25302804

RESUMO

The transcription factor NF-κB shuttles between the cytoplasm and the nucleus, and nuclear NF-κB is known to oscillate with a cycle of 1.5-2.5 h following the application of external stimuli. Oscillation pattern of NF-κB is implicated in regulation of the gene expression profile. In a previous report, we found that the oscillation pattern of nuclear NF-κB in a computational 3D spherical cell was regulated by spatial parameters such as nuclear to cytoplasmic volume ratio, nuclear transport, locus of protein synthesis, and diffusion coefficient. Here we report analyses and a biological implication for the regulation of oscillation pattern by diffusion coefficient. Our analyses show that the "reset" of nuclear NF-κB, defined as the return of nuclear NF-κB to the initial level or lower, was crucial for the oscillation; this was confirmed by the flux analysis. In addition, we found that the distant cytoplasmic location from the nucleus acted as a "reservoir" for storing newly synthesized IκBα. When the diffusion coefficient of proteins was large (≥ 10-11 m2/s), a larger amount of IκBα was stored in the "reservoir" with a large flux by diffusion. Subsequently, stored IκBα diffused back to the nucleus, where nuclear NF-κB was "reset" to the initial state. This initiated the next oscillation cycle. When the diffusion coefficient was small (≤ 10-13 m2/s), oscillation of nuclear NF-κB was not observed because a smaller amount of IκBα was stored in the "reservoir" and there was incomplete "reset" of nuclear NF-κB. If the diffusion coefficient for IκBα was increased to 10-11 m2/s keeping other proteins at 10-13 m2/s, the oscillation was rescued confirming the "reset" and "reservoir" hypothesis. Finally, we showed altered effective value of diffusion coefficient by diffusion obstacles. Thus, organelle crowding seen in stressed cells possibly changes the oscillation pattern by controlling the effective diffusion coefficient.


Assuntos
Núcleo Celular/metabolismo , Simulação por Computador , Citoplasma/metabolismo , Modelos Biológicos , NF-kappa B/metabolismo , Transporte Biológico , Humanos
8.
Theor Biol Med Model ; 10: 62, 2013 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-24152322

RESUMO

BACKGROUND: One of the most challenging problems in biological image analysis is the quantification of the dynamical mechanism and complexity of the intracellular space. This paper investigates potential spatial chaos and complex behavior of the intracellular space of typical cancer and normal cell images whose structural details are revealed by the combination of scanning electron microscopy and focused ion beam systems. Such numerical quantifications have important implications for computer modeling and simulation of diseases. METHODS: Cancer cell lines derived from a human head and neck squamous cell carcinoma (SCC-61) and normal mouse embryonic fibroblast (MEF) cells produced by focused ion beam scanning electron microscopes were used in this study. Spatial distributions of the organelles of cancer and normal cells can be analyzed at both short range and long range of the bounded dynamical system of the image space, depending on the orientations of the spatial cell. A procedure was designed for calculating the largest Lyapunov exponent, which is an indicator of the potential chaotic behavior in intracellular images. Furthermore, the sample entropy and regularity dimension were applied to measure the complexity of the intracellular images. RESULTS: Positive values of the largest Lyapunov exponents (LLEs) of the intracellular space of the SCC-61 were obtained in different spatial orientations for both long-range and short-range models, suggesting the chaotic behavior of the cell. The MEF has smaller positive values of LLEs in the long range than those of the SCC-61, and zero vales of the LLEs in the short range analysis, suggesting a non-chaotic behavior. The intracellular space of the SCC-61 is found to be more complex than that of the MEF. The degree of complexity measured in the spatial distribution of the intracellular space in the diagonal direction was found to be approximately twice larger than the complexity measured in the horizontal and vertical directions. CONCLUSION: Initial findings are promising for characterizing different types of cells and therefore useful for studying cancer cells in the spatial domain using state-of-the-art imaging technology. The measures of the chaotic behavior and complexity of the spatial cell will help computational biologists gain insights into identifying associations between the oscillation patterns and spatial parameters of cells, and appropriate model for simulating cancer cell signaling networks for cancer treatment and new drug discovery.


Assuntos
Fibroblastos/citologia , Espaço Intracelular/metabolismo , Neoplasias/patologia , Dinâmica não Linear , Animais , Linhagem Celular Tumoral , Embrião de Mamíferos/citologia , Entropia , Fibroblastos/ultraestrutura , Humanos , Camundongos , Modelos Biológicos , Neoplasias/ultraestrutura
10.
PLoS Comput Biol ; 9(5): e1003086, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23737743

RESUMO

Focal degradation of extracellular matrix (ECM) is the first step in the invasion of cancer cells. MT1-MMP is a potent membrane proteinase employed by aggressive cancer cells. In our previous study, we reported that MT1-MMP was preferentially located at membrane protrusions called invadopodia, where MT1-MMP underwent quick turnover. Our computer simulation and experiments showed that this quick turnover was essential for the degradation of ECM at invadopodia (Hoshino, D., et al., (2012) PLoS Comp. Biol., 8: e1002479). Here we report on characterization and analysis of the ECM-degrading activity of MT1-MMP, aiming at elucidating a possible reason for its repetitive insertion in the ECM degradation. First, in our computational model, we found a very narrow transient peak in the activity of MT1-MMP followed by steady state activity. This transient activity was due to the inhibition by TIMP-2, and the steady state activity of MT1-MMP decreased dramatically at higher TIMP-2 concentrations. Second, we evaluated the role of the narrow transient activity in the ECM degradation. When the transient activity was forcibly suppressed in computer simulations, the ECM degradation was heavily suppressed, indicating the essential role of this transient peak in the ECM degradation. Third, we compared continuous and pulsatile turnover of MT1-MMP in the ECM degradation at invadopodia. The pulsatile insertion showed basically consistent results with the continuous insertion in the ECM degradation, and the ECM degrading efficacy depended heavily on the transient activity of MT1-MMP in both models. Unexpectedly, however, low-frequency/high-concentration insertion of MT1-MMP was more effective in ECM degradation than high-frequency/low-concentration pulsatile insertion even if the time-averaged amount of inserted MT1-MMP was the same. The present analysis and characterization of ECM degradation by MT1-MMP together with our previous report indicate a dynamic nature of MT1-MMP at invadopodia and the importance of its transient peak in the degradation of the ECM.


Assuntos
Matriz Extracelular , Metaloproteinase 14 da Matriz/metabolismo , Modelos Biológicos , Processos Neoplásicos , Linhagem Celular Tumoral , Biologia Computacional , Simulação por Computador , Matriz Extracelular/química , Matriz Extracelular/metabolismo , Humanos , Metaloproteinase 14 da Matriz/química
11.
PLoS One ; 7(10): e46911, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23056526

RESUMO

Transcription factor NF-κB resides in the cytoplasm and translocates to the nucleus by application of extracellular stimuli. It is known that the nuclear NF-κB oscillates and different oscillation patterns lead to different gene expression. Nearly forty reports on modeling and simulation of nuclear NF-κB have been published to date. The computational models reported so far are temporal or two-dimensional, and the discussions on spatial parameters have not been involved or limited. Since spatial parameters in cancer cells such as nuclear to cytoplasmic volume (N/C) ratio are different from normal cells, it is important to understand the relationship between oscillation patterns and spatial parameters. Here we report simulations of a 3D computational model for the oscillation of nuclear NF-κB using A-Cell software. First, we found that the default biochemical kinetic constants used in the temporal model cannot replicate the experimentally observed oscillation in the 3D model. Thus, the default parameters should be changed in the 3D model. Second, spatial parameters such as N/C ratio, nuclear transport, diffusion coefficients, and the location of IκB synthesis were found to alter the oscillation pattern. Third, among them, larger N/C ratios resulted in persistent oscillation of nuclear NF-κB, and larger nuclear transport resulted in faster oscillation frequency. Our simulation results suggest that the changes in spatial parameters seen in cancer cells is one possible mechanism for alteration in the oscillation pattern of nuclear NF-κB and lead to the altered gene expression in these cells.


Assuntos
Núcleo Celular/metabolismo , Forma Celular , Simulação por Computador , NF-kappa B/metabolismo , Transporte Ativo do Núcleo Celular , Citoplasma/metabolismo , Difusão , Regulação da Expressão Gênica , Humanos , Quinase I-kappa B/metabolismo , Modelos Biológicos , Fatores de Tempo
12.
Theor Biol Med Model ; 9: 33, 2012 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-22863329

RESUMO

BACKGROUND: Proteolytic degradation of the extracellular matrix (ECM) is a key event in tumour metastasis and invasion. Matrix metalloproteinases (MMPs) are a family of endopeptidases that degrade most of the components of the ECM. Several broad-spectrum MMP inhibitors (MMPIs) have been developed, but have had little success due to side effects. Thus, it is important to develop mathematical methods to provide new drug treatment strategies. Matrix metalloproteinase 2 (MMP2) activation occurs via a mechanism involving complex formation that consists of membrane type 1 MMP (MT1-MMP), tissue inhibitor of matrix metalloproteinase 2 (TIMP2) and MMP2. Here, we focus on developing a method for analysing the complex formation process. RESULTS: We used control analysis to investigate inhibitor responses in complex formation processes. The essence of the analysis is to define the response coefficient which measures the inhibitory efficiency, a small fractional change of concentration of a targeting molecule in response to a small fractional change of concentration of an inhibitor. First, by using the response coefficient, we investigated models for general classes of complex formation processes: chain reaction systems composed of ordered steps, and chain reaction systems and site-binding reaction systems composed of unordered multi-branched steps. By analysing the ordered step models, we showed that parameter-independent inequalities between the response coefficients held. For the unordered multi-branched step models, we showed that independence of the response coefficients with respect to equilibrium constants held. As an application of our analysis, we discuss a mathematical model for the MMP2 activation process. By putting the experimentally derived parameter values into the model, we were able to conclude that the TIMP2 and MMP2 interaction is the most efficient interaction to consider in selecting inhibitors. CONCLUSIONS: Our result identifies a new drug target in the process of the MMP2 activation. Thus, our analysis will provide new insight into the design of more efficient drug strategies for cancer treatment.


Assuntos
Endopeptidases/metabolismo , Matriz Extracelular/metabolismo , Humanos , Cinética , Metaloproteinase 14 da Matriz/metabolismo , Metaloproteinase 2 da Matriz/metabolismo , Modelos Teóricos , Invasividade Neoplásica , Inibidores de Proteases/farmacologia , Teoria de Sistemas , Inibidor Tecidual de Metaloproteinase-2/metabolismo
13.
PLoS Comput Biol ; 8(4): e1002479, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22511862

RESUMO

MT1-MMP is a potent invasion-promoting membrane protease employed by aggressive cancer cells. MT1-MMP localizes preferentially at membrane protrusions called invadopodia where it plays a central role in degradation of the surrounding extracellular matrix (ECM). Previous reports suggested a role for a continuous supply of MT1-MMP in ECM degradation. However, the turnover rate of MT1-MMP and the extent to which the turnover contributes to the ECM degradation at invadopodia have not been clarified. To approach this problem, we first performed FRAP (Fluorescence Recovery after Photobleaching) experiments with fluorescence-tagged MT1-MMP focusing on a single invadopodium and found very rapid recovery in FRAP signals, approximated by double-exponential plots with time constants of 26 s and 259 s. The recovery depended primarily on vesicle transport, but negligibly on lateral diffusion. Next we constructed a computational model employing the observed kinetics of the FRAP experiments. The simulations successfully reproduced our FRAP experiments. Next we inhibited the vesicle transport both experimentally, and in simulation. Addition of drugs inhibiting vesicle transport blocked ECM degradation experimentally, and the simulation showed no appreciable ECM degradation under conditions inhibiting vesicle transport. In addition, the degree of the reduction in ECM degradation depended on the degree of the reduction in the MT1-MMP turnover. Thus, our experiments and simulations have established the role of the rapid turnover of MT1-MMP in ECM degradation at invadopodia. Furthermore, our simulations suggested synergetic contributions of proteolytic activity and the MT1-MMP turnover to ECM degradation because there was a nonlinear and marked reduction in ECM degradation if both factors were reduced simultaneously. Thus our computational model provides a new in silico tool to design and evaluate intervention strategies in cancer cell invasion.


Assuntos
Carcinoma de Células Escamosas/metabolismo , Membrana Celular/metabolismo , Matriz Extracelular/metabolismo , Metaloproteinase 14 da Matriz/metabolismo , Modelos Biológicos , Transdução de Sinais , Animais , Linhagem Celular Tumoral , Simulação por Computador
14.
J Theor Biol ; 298: 138-46, 2012 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-22212912

RESUMO

In invasive cancer cells, specialized sub-cellular membrane structures which carry out a pivotal process in cancer invasion, termed invadopodia, are observed. Invadopodia appear irregularly within the cytoplasm and their general shape is small punctuated finger-like protrusions with dimension up to several µm long. They may exist and persist on a timescale between several tens of minutes to one hour. The formation of invadopodia requires the integration of several processes that include actin reorganization, extracellular matrix (ECM) degradation, signaling processes through receptors such as the epidermal growth factor receptor (EGFR) and matrix metalloproteinase (MMP) synthesis and delivery to the location of the invading front. In this paper, we consider a mathematical model investigating the coupling of these fundamental processes, and we investigate how invadopodia appear in this model. We investigate the spatio-temporal dynamics of the model in two spatial dimensions by using numerical computational simulations. We show that in a special parameter region of the model, random fluctuations of ECM degradation and a positive feedback loop regarding the up-regulation of MMPs allow us to reproduce finger-like protrusions which have similar size and lifetime as invadopodia. This study provides a new insight into how invadopodia appear in cancer cells and why space and time scales exist for invadopodia.


Assuntos
Extensões da Superfície Celular/ultraestrutura , Modelos Biológicos , Neoplasias/ultraestrutura , Actinas/metabolismo , Extensões da Superfície Celular/metabolismo , Simulação por Computador , Receptores ErbB/metabolismo , Matriz Extracelular/metabolismo , Retroalimentação Fisiológica , Humanos , Metaloproteinases da Matriz/biossíntese , Invasividade Neoplásica , Neoplasias/metabolismo , Neoplasias/patologia , Transdução de Sinais/fisiologia
15.
Biosystems ; 105(3): 173-80, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21605621

RESUMO

Localized activation of proteins in a cell is crucial for the segregation of cellular functions leading, for example, to the development of polarized cells and chemotaxis. If there is a physical diffusion barrier, localized activation of proteins will emerge. In case of no physical barrier, however, it is not clear to what extent the protein activation is localized within a three dimensional intracellular space. In the previous report we showed a simulation result of localized activation of Ca(2+)/calmodulin-dependent kinase II (CaMKII) within a dendritic spine of a neuron, and this localization was enhanced by the diffusion of calmodulin. However, a dendritic spine will act as a physical diffusion barrier. Here, we report that the localization of activated proteins is seen in more simplified morphology with no diffusion barrier. Furthermore, this localization was seen with a simple reaction scheme. In case that a Ca(2+) source was located at the center of the spherical cell with diameter of 20µm, which is the extreme case without any physical diffusion barrier, the simulation results showed localized activation of a protein around the Ca(2+) source. This localized activation was also enhanced by the diffusion of calmodulin. These localizations were not blurred with time within the tested time range. The reason for the increase in the localization by the diffusion of calmodulin was the replenishment of free calmodulin from surrounding regions. These simulation results indicate that the localized activation of proteins emerges in biological cells without any physical diffusion barrier, and the replenishment of proteins by diffusion can act as an enhancer of localized activation of downstream proteins.


Assuntos
Proteína Quinase Tipo 2 Dependente de Cálcio-Calmodulina/metabolismo , Calmodulina/metabolismo , Simulação por Computador , Dendritos/enzimologia , Modelos Neurológicos , Animais , Cálcio/metabolismo , Polaridade Celular , Quimiotaxia , Dendritos/química , Dendritos/ultraestrutura , Ativação Enzimática , Espaço Intracelular/metabolismo , Ligação Proteica
16.
Phys Biol ; 7(4): 046010, 2010 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-21119218

RESUMO

Molecular events in biological cells occur in local subregions, where the molecules tend to be small in number. The cytoskeleton, which is important for both the structural changes of cells and their functions, is also a countable entity because of its long fibrous shape. To simulate the local environment using a computer, stochastic simulations should be run. We herein report a new method of stochastic simulation based on random walk and reaction by the collision of all molecules. The microscopic reaction rate P(r) is calculated from the macroscopic rate constant k. The formula involves only local parameters embedded for each molecule. The results of the stochastic simulations of simple second-order, polymerization, Michaelis-Menten-type and other reactions agreed quite well with those of deterministic simulations when the number of molecules was sufficiently large. An analysis of the theory indicated a relationship between variance and the number of molecules in the system, and results of multiple stochastic simulation runs confirmed this relationship. We simulated Ca²(+) dynamics in a cell by inward flow from a point on the cell surface and the polymerization of G-actin forming F-actin. Our results showed that this theory and method can be used to simulate spatially inhomogeneous events.


Assuntos
Actinas/química , Biopolímeros/química , Modelos Teóricos , Processos Estocásticos , Algoritmos , Cinética
17.
J Biol Chem ; 282(9): 6677-84, 2007 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-17194706

RESUMO

Signal transduction in rod cells begins with photon absorption by rhodopsin and leads to the generation of an electrical response. The response profile is determined by the molecular properties of the phototransduction components. To examine how the molecular properties of rhodopsin correlate with the rod-response profile, we have generated a knock-in mouse with rhodopsin replaced by its E122Q mutant, which exhibits properties different from those of wild-type (WT) rhodopsin. Knock-in mouse rods with E122Q rhodopsin exhibited a photosensitivity about 70% of WT. Correspondingly, their single-photon response had an amplitude about 80% of WT, and a rate of decline from peak about 1.3 times of WT. The overall 30% lower photosensitivity of mutant rods can be explained by a lower pigment photosensitivity (0.9) and the smaller single-photon response (0.8). The slower decline of the response, however, did not correlate with the 10-fold shorter lifetime of the meta-II state of E122Q rhodopsin. This shorter lifetime became evident in the recovery phase of rod cells only when arrestin was absent. Simulation analysis of the photoresponse profile indicated that the slower decline and the smaller amplitude of the single-photon response can both be explained by the shift in the meta-I/meta-II equilibrium of E122Q rhodopsin toward meta-I. The difference in meta-III lifetime between WT and E122Q mutant became obvious in the recovery phase of the dark current after moderate photobleaching of rod cells. Thus, the present study clearly reveals how the molecular properties of rhodopsin affect the amplitude, shape, and kinetics of the rod response.


Assuntos
Células Fotorreceptoras Retinianas Bastonetes/fisiologia , Visão Ocular , Animais , Arrestina , Meia-Vida , Cinética , Camundongos , Mutação de Sentido Incorreto , Fótons , Rodopsina/genética
18.
Neuroinformatics ; 3(1): 49-64, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-15897616

RESUMO

A-Cell-3D was developed to model and simulate a neuron with three-dimensional (3D) morphology utilizing graphic user interface (GUI)-based operations. A-Cell-3D generates and compartmentalizes 3D morphologies of a whole cell or a part of a cell based on a small number of parameters. A-Cell-3D has functions for embedding biochemical reactions and electrical equivalent circuits in the generated 3D morphology, automatically generating a simulation program for spatiotemporal numerical integration, and for visualizing the simulation results. A-Cell-3D is a free software and will be a powerful tool for both experimental and theoretical researchers in modeling and simulating neurons. The Ca2+ dynamics in a dendritic spine and its parent dendrite were modeled and simulated to demonstrate the capabilities of A-Cell-3D. The constructed reaction-diffusion model comprised Ca2+ entry at the spine head, Ca2+ buffering by endogenous buffers, Ca2+ extrusion, and Ca2+ diffusion with or without exogenous Ca2+ indicator dyes. A simulation program was generated by A-Cell-3D, and differential equations were numerically integrated by the fourth-order Runge-Kutta method.


Assuntos
Simulação por Computador , Imageamento Tridimensional/métodos , Modelos Neurológicos , Neurônios/citologia , Software , Interface Usuário-Computador , Cálcio/metabolismo , Neurônios/metabolismo
19.
Biochem Biophys Res Commun ; 304(1): 153-9, 2003 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-12705900

RESUMO

Activity of thalamic neurons has been shown to be modulated via type-1 metabotropic glutamate receptor (mGluR1) activation, which initiates an intracellular Ca signaling cascade involving phospholipase Cbeta4 (PLCbeta4) and leading to the activation of conventional protein kinase C (cPKC). In the present study, we investigated the role of PLCbeta4 in thalamic neuron. PLCbeta4-deficient mutant mice were found to exhibit three phenotypic characteristics: (1) a 2-Hz increase in the peak frequency of electroencephalogram (EEG) of rapid eye movement (REM) sleep, (2) an increase in the frequency of miniature excitatory postsynaptic currents (mEPSCs) recorded in thalamus, and (3) waveform distortion of EEG. We postulate here that changes in protein phosphorylation due to reduced cPKC activity by PLCbeta4 deletion in thalamic neurons may give rise to these phenotypic characteristics. Taken together, these results indicate that reduced PLCbeta4 activity in thalamic neurons may underlie high-cortical oscillation frequency.


Assuntos
Isoenzimas/fisiologia , Neurônios/enzimologia , Fases do Sono , Tálamo/fisiologia , Fosfolipases Tipo C/fisiologia , Animais , Encéfalo/anatomia & histologia , Encéfalo/enzimologia , Cálcio/metabolismo , Células Cultivadas , Giro Denteado/metabolismo , Eletroencefalografia , Potenciais Pós-Sinápticos Excitadores , Isoenzimas/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Neurônios/fisiologia , Técnicas de Patch-Clamp , Fosfolipase C beta , Sono REM , Tálamo/citologia , Fosfolipases Tipo C/genética
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