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Mishra V, Adlakha N. Cross Talking Calcium, IP 3 and Buffer Dynamics Alters ATP and NADH Level in Obese and Normal Hepatocyte Cell. Cell Biochem Biophys 2024; 82:1537-1553. [PMID: 38789660 DOI: 10.1007/s12013-024-01306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
The cross talk between calcium (Ca2+), IP3 and buffer dynamics regulate various mechanisms in hepatocyte cells. The study of independent systems of calcium, IP3, and buffer signaling provides limited information about cell dynamics. In the current study, coupled reaction-diffusion equations are used to design a cross-talk model for IP3, buffer, and calcium dynamics in a hepatocyte cell. The one-way feedback of calcium, buffer, and IP3 in ATP production, ATP degradation, and NADH production rate is incorporated into the model. Numerical simulation has been done using the Finite Element Method (FEM) along the spatial direction and the Crank-Nicolson (C-N) method along the temporal direction. The numerical results are analysed to determine the effects of alterations in processes of cross-talking dynamics of IP3, buffer, and calcium on ATP and NADH production and degradation rate of ATP in a hepatocyte cell under normal and obesity conditions. The comparative analysis of these findings unveils notable distinctions induced by obesity in calcium dynamics, ATP and NADH synthesis, and ATP degradation kinetics.
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Affiliation(s)
- Vedika Mishra
- Department of Mathematics, SVNIT, Surat, 395007, Gujarat, India.
| | - Neeru Adlakha
- Department of Mathematics, SVNIT, Surat, 395007, Gujarat, India
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2
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Kothiya A, Adlakha N. Regulatory disturbances in the dynamical signaling systems of C a 2 + and NO in fibroblasts cause fibrotic disorders. J Biol Phys 2024; 50:229-251. [PMID: 38753214 PMCID: PMC11106231 DOI: 10.1007/s10867-024-09657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Studying the calcium dynamics within a fibroblast cell individually has provided only a restricted understanding of its functions. However, research efforts focusing on systems biology approaches for such investigations have been largely neglected by researchers until now. Fibroblast cells rely on signaling from calcium ( C a 2 + ) and nitric oxide (NO) to maintain their physiological functions and structural stability. Various studies have demonstrated the correlation between NO and the control of C a 2 + dynamics in cells. However, there is currently no existing model to assess the disruptions caused by various factors in regulatory dynamics, potentially resulting in diverse fibrotic disorders. A mathematical model has been developed to investigate the effects of changes in parameters such as buffer, receptor, sarcoplasmic endoplasmic reticulum C a 2 + -ATPase (SERCA) pump, and source influx on the regulation and dysregulation of spatiotemporal calcium and NO dynamics in fibroblast cells. This model is based on a system of reaction-diffusion equations, and numerical simulations are conducted using the finite element method. Disturbances in key processes related to calcium and nitric oxide, including source influx, buffer mechanism, SERCA pump, and inositol trisphosphate ( I P 3 ) receptor, may contribute to deregulation in the calcium and NO dynamics within fibroblasts. The findings also provide new insights into the extent and severity of disorders resulting from alterations in various parameters, potentially leading to deregulation and the development of fibrotic disease.
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Affiliation(s)
- Ankit Kothiya
- DoM, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India.
| | - Neeru Adlakha
- DoM, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
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Li Y. Differential behaviors of calcium-induced calcium release in one dimensional dendrite by Nernst-Planck equation, cable model and pure diffusion model. Cogn Neurodyn 2024; 18:1285-1305. [PMID: 38826668 PMCID: PMC11143177 DOI: 10.1007/s11571-023-09952-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/16/2023] [Accepted: 03/08/2023] [Indexed: 06/04/2024] Open
Abstract
The source and dynamics of calcium is the key factor that regulates dendritic integration. Apart from the voltage-gated and ligand-gated calcium influx, an important source of calcium is from inner store of endoplasmic reticulum with a regenerative process of calcium-induced calcium release (CICR). To trigger this process, inositol 1,4,5-trisphosphate (IP3) and calcium are needed to satisfy certain requirements. The aim of our paper is to investigate how the CICR depends on the dynamics of membrane potential. We utilize one dimensional dendritic model to calculate membrane potential by Nernst-Planck Equation (NPE) and cable model and Pure Diffusion (PD) model, computational simulations are carried out to inject the calcium influx by synaptic stimulation and to predict subsequent CICR and calcium wave propagation. Our results demonstrate that CICR initiation and calcium wave propagation have much difference between electro-diffusion process of NPE and cable model. We find that cable model has lower threshold of IP3 stimulation to trigger CICR but is more difficult for calcium propagation than NPE, PD model requires even higher threshold of IP3 to initiate CICR process and calcium duration is shorter than NPE; the regenerative calcium wave propagates with faster speed in NPE than that in cable model and in PD model. Our work addresses the important role of electro-diffusion dynamics of charged ions in regulating CICR process in dendritic structure; and provides theoretical predictions for neurological process which requires sustaining calcium for downstream signaling processes.
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Affiliation(s)
- Yinyun Li
- School of Systems Science, Beijing Normal University, Beijing, 100875 China
- Department of Mathematics and Statistics, Washington State University Vancouver, Vancouver, USA
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Pawar A, Pardasani KR. Modelling Cross Talk in the Spatiotemporal System Dynamics of Calcium, IP 3 and Nitric Oxide in Neuron Cells. Cell Biochem Biophys 2024; 82:787-803. [PMID: 38376737 DOI: 10.1007/s12013-024-01229-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
The bioenergetic system of calcium ([Ca2+]), inositol 1, 4, 5-trisphophate (IP3) and nitric oxide (NO) regulate the diverse mechanisms in neurons. The dysregulation in any or all of the calcium, IP3 and nitric oxide dynamics may cause neurotoxicity and cell death. Few studies are noted in the literature on the interactions of two systems like [Ca2+] with IP3 and [Ca2+] with nitric oxide in neuron cells, which gives limited insights into regulatory and dysregulatory processes in neuron cells. But, no study is available on the cross talk in dynamics of three systems [Ca2+], IP3 and NO in neurons. Thus, the cross talk in the system dynamics of [Ca2+], IP3 and NO regulation processes in neurons have been studied using mathematical model. The two-way feedback process between [Ca2+] and IP3 and two-way feedback process between [Ca2+] and NO through cyclic guanosine monophosphate (cGMP) with plasmalemmal [Ca2+]-ATPase (PMCA) have been incorporated in the proposed model. This coupling handles the indirect two-way feedback process between IP3 and nitric oxide in neuronal cells automatically. The numerical outcomes were acquired by employing the finite element method (FEM) with the Crank-Nicholson scheme (CNS). The present model incorporating the sodium-calcium exchanger (NCX) and voltage-gated calcium channel (VGCC) provides novel insights into the various regulatory and dysregulatory processes due to buffer, IP3-receptor, ryanodine receptor, cGMP kinetics through PMCA channel, etc. and their impacts on the interactive spatiotemporal system dynamics of [Ca2+], IP3 and NO in neurons. It is concluded that the behavior of different crucial mechanisms is quite different for interactions of two systems of [Ca2+] and NO and the interactions of three systems of [Ca2+], IP3 and nitric oxide in neuronal cell due to mutual regulatory adjustments. The association of several neurological disorders with the alterations in calcium, IP3 and NO has been explored in neurons.
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Affiliation(s)
- Anand Pawar
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, 462003, Madhya Pradesh, India.
| | - Kamal Raj Pardasani
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, 462003, Madhya Pradesh, India.
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Joshi H, Jha BK. 2D dynamic analysis of the disturbances in the calcium neuronal model and its implications in neurodegenerative disease. Cogn Neurodyn 2023; 17:1637-1648. [PMID: 37974576 PMCID: PMC10640547 DOI: 10.1007/s11571-022-09903-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/10/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Ca2+ signaling is an essential function of neurons to control synaptic activity, memory formation, fertilization, proliferation, etc. Protein and voltage-dependent calcium channels (VDCCs) maintain an adequate level of calcium concentration ([Ca2+]). An alteration in [Ca2+] leads to the death of the neurons that start the primary symptoms of the disease. The present study deals with cell memory-based mathematical modeling of Ca2+ that is characterized by the presence of protein and VDCC. We developed a two-dimensional Ca2+ neuronal model to study the spatiotemporal behavior of the Ca2+ profile. All principal parameters like buffer concentration, diffusion coefficient, VDCC fluxes, etc. are incorporated in this model. Apposite initial and boundary conditions are applied to the physiology of the problem. We obtained an approximate Ca2+ profile by the fractional integral transform method. The application of obtained results is performed to provide its implications to estimate the [Ca2+] in neurodegenerative disease. It is observed that the protein and VDCC provide a significant impact in the presence of cell memory. The memory of cells shrinks the Ca2+ flow from elevation and provides better results to estimated Ca2+ flow in the disease state.
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Affiliation(s)
- Hardik Joshi
- Department of Mathematics, LJ Institute of Engineering and Technology, LJ University, Ahmedabad, 382210 India
| | - Brajesh Kumar Jha
- Department of Mathematics, School of Technology, Pandit Deendayal Energy University, Gandhinagar, 382007 India
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Kothiya A, Adlakha N. Impact of Interdependent Ca 2+ and IP 3 Dynamics On ATP Regulation in A Fibroblast Model. Cell Biochem Biophys 2023; 81:795-811. [PMID: 37749442 DOI: 10.1007/s12013-023-01177-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
The vital participation of Ca2+ in human organ functions such as muscular contractions, heartbeat, brain functionality, skeletal activity, etc, motivated the scientists to thoroughly research the mechanisms of calcium (Ca2+) signalling in distinct human cells. Ca2+, inositol triphosphate (IP3), and adenosine triphosphate (ATP) play important roles in cell signaling and physiological processes. ATP and its derivatives are hypothesized to be important in the pathogenic process that leads to fibrotic illnesses like fibrosis. Fluctuations in Ca2+ and IP3 in a fibroblast cell influence ATP production. To date, no evidence of coupled Ca2+ and IP3 mechanics regulating ATP generation in a fibroblast cell during fibrotic disease has been found. The current work suggests an integrated mechanism for Ca2+ and IP3 dynamics in a fibroblast cell that regulates ATP generation. Simulation has been carried out using the finite element approach. The mechanics of interdependent systems findings vary dramatically from the results of basic independent system mechanics and give fresh information about the two systems' activities. The numerical results provide new insights into the impacts of disturbances in source influx, the serca pump, and buffers on interdependent Ca2+ and IP3 dynamics and ATP synthesis in a fibroblast cell. According to the findings of this study, fibrotic disorders cannot be attributed solely to disruptions in the processes of calcium signaling mechanics but also to disruptions in IP3 regulation mechanisms affecting the regulation of calcium in the fibroblast cell and ATP release.
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Affiliation(s)
- Ankit Kothiya
- DoM, S. V. National Institute of Technology, Surat, 395007, Gujarat, India.
| | - Neeru Adlakha
- DoM, S. V. National Institute of Technology, Surat, 395007, Gujarat, India
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Pawar A, Pardasani KR. Study of disorders in regulatory spatiotemporal neurodynamics of calcium and nitric oxide. Cogn Neurodyn 2023; 17:1661-1682. [PMID: 37974582 PMCID: PMC10640555 DOI: 10.1007/s11571-022-09902-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
Experimental studies have reported the dependence of nitric oxide (NO) on the regulation of neuronal calcium ([Ca2+]) dynamics in neurons. But, there is no model available to estimate the disorders caused by various parameters in their regulatory dynamics leading to various neuronal disorders. A mathematical model to analyze the impacts due to alterations in various parameters like buffer, ryanodine receptor, serca pump, source influx, etc. leading to regulation and dysregulation of the spatiotemporal calcium and NO dynamics in neuron cells is constructed using a system of reaction-diffusion equations. The numerical simulation is performed with the finite element approach. The disturbances in the different constitutive processes of [Ca2+] and nitric oxide including source influx, buffer mechanism, ryanodine receptor, serca pump, IP3 receptor, etc. can be responsible for the dysregulation in the [Ca2+] and NO dynamics in neurons. Also, the results reveal novel information about the magnitude and intensity of disorders in response to a range of alterations in various parameters of this neuronal dynamics, which can cause dysregulation leading to neuronal diseases like Parkinson's, cerebral ischemia, trauma, etc.
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Affiliation(s)
- Anand Pawar
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh 462003 India
| | - Kamal Raj Pardasani
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh 462003 India
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Mishra V, Adlakha N. Spatio temporal interdependent calcium and buffer dynamics regulating DAG in a hepatocyte cell due to obesity. J Bioenerg Biomembr 2023; 55:249-266. [PMID: 37460636 DOI: 10.1007/s10863-023-09973-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/23/2023] [Indexed: 09/12/2023]
Abstract
Calcium ions (Ca2+) serve as a crucial signaling mechanism in almost all cells. The buffers are proteins that bind free Ca2+ to reduce the cell's Ca2+ concentration. The most studies reported in the past on calcium signaling in various cells have considered the buffer concentration as constant in the cell. However, buffers also diffuse and their concentration varies dynamically in the cells. Almost no work has been reported on interdependent calcium and buffer dynamics in the cells. In the present study, a model is proposed for inter-dependent spatio-temporal dynamics of calcium and buffer by coupling reaction-diffusion equations of Ca2+ and buffer in a hepatocyte cell. Boundary and initial conditions are framed based on the physiological state of the cell. The effect of various parameters viz. inositol 1,4,5-triphosphate receptor (IP3R), diffusion coefficient, SERCA pump and ryanodine receptor (RyR) on spatio-temporal dynamics of calcium and buffer regulating diacylglycerol (DAG) in a normal and obese hepatocyte cell has been studied using finite element simulation. From the results, it is concluded that the dynamics of calcium and buffer impact each other significantly along the spatio-temporal dimensions, thereby affecting the regulation of all the processes including DAG in a hepatocyte cell. The proposed model is more realistic than the existing ones, as the interdependent system dynamics of calcium and buffer have different regulatory impacts as compared to the individual and independent dynamics of these signaling processes in a hepatocyte cell.
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Affiliation(s)
- Vedika Mishra
- Department of Mathematics, SVNIT, Gujarat, 395007, Surat, India.
| | - Neeru Adlakha
- Department of Mathematics, SVNIT, Gujarat, 395007, Surat, India
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Vatsal VH, Jha BK, Singh TP. To study the effect of ER flux with buffer on the neuronal calcium. EUROPEAN PHYSICAL JOURNAL PLUS 2023; 138:494. [PMID: 37304245 PMCID: PMC10240135 DOI: 10.1140/epjp/s13360-023-04077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/07/2023] [Indexed: 06/13/2023]
Abstract
Calcium signaling is decisive for cellular functions. This calcium random walk stipulates neuronal functions. Calcium concentration could provoke gene transcription, apoptosis, neuronal plasticity, etc. A malformation in calcium could change the neuron's intracellular behavior. Calcium concentration balancing is a complex cellular mechanism. This occurrence can be handled with the Caputo fractional reaction-diffusion equation. In this mathematical modeling, we have included the STIM-Orai mechanism and Endoplasmic Reticulum (ER) flux, Inositol Triphosphate Receptor (IPR), SERCA, plasma membrane flux, voltage-gated calcium entry, and different buffer interactions. A hybrid integral transform and Green's function approach were taken to solve the initial boundary problem. A closed-form solution of a Mittag-Leffler family function plotted using MATLAB software. Different parameters impact changes in the spatiotemporal behavior of the calcium concentration. Specific roles of organelles involved in Alzheimer's disease-affected neurons are computed. Ethylene glycol tetraacetic acid (EGTA), 1,2-bis(o-aminophenoxy)ethane N,N,N,N-tetraacetic acid (BAPTA), and S100B protein effects are also observed. In all simulations, we can say S100B and the STIM-Orai effect cannot be neglected. This model lights up the different approaches for calcium signaling pathway simulation. As a consequence, we determine that a generalized reaction-diffusion approach is a better fit realistic model.
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Affiliation(s)
- Vora Hardagna Vatsal
- Department of Mathematics, Pandit Deendayal Energy University, Gandhinagar, 382007 Gujarat India
| | - Brajesh Kumar Jha
- Department of Mathematics, Pandit Deendayal Energy University, Gandhinagar, 382007 Gujarat India
| | - Tajinder Pal Singh
- Department of Mathematics, Pandit Deendayal Energy University, Gandhinagar, 382007 Gujarat India
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Pawar A, Pardasani KR. Mechanistic insights of neuronal calcium and IP 3 signaling system regulating ATP release during ischemia in progression of Alzheimer's disease. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023:10.1007/s00249-023-01660-1. [PMID: 37222773 DOI: 10.1007/s00249-023-01660-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/21/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
The mechanisms of calcium ([Ca2+]) signaling in various human cells have been widely analyzed by scientists due to its crucial role in human organs like the heartbeat, muscle contractions, bone activity, brain functionality, etc. No study is reported for interdependent [Ca2+] and IP3 mechanics regulating the release of ATP in neuron cells during Ischemia in Alzheimer's disease advancement. In the present investigation, a finite element method (FEM) is framed to explore the interdependence of spatiotemporal [Ca2+] and IP3 signaling mechanics and its role in ATP release during Ischemia as well as in the advancement of Alzheimer's disorder in neuron cells. The results provide us insights of the mutual spatiotemporal impacts of [Ca2+] and IP3 mechanics as well as their contributions to ATP release during Ischemia in neuron cells. The results obtained for the mechanics of interdependent systems differ significantly from the results of simple independent system mechanics and provide new information about the processes of the two systems. From this study, it is concluded that neuronal disorders cannot only be simply attributed to the disturbance caused directly in the processes of calcium signaling mechanics, but also to the disturbances caused in IP3 regulation mechanisms impacting the calcium regulation in the neuron cell and ATP release.
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Affiliation(s)
- Anand Pawar
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, 462003, India.
| | - Kamal Raj Pardasani
- Department of Mathematics, Bioinformatics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, 462003, India
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Abstract
Inositol 1,4,5-trisphosphate (IP3) plays a key role in calcium signaling. After stimulation, it diffuses from the plasma membrane where it is produced to the endoplasmic reticulum where its receptors are localized. Based on in vitro measurements, IP3 was long thought to be a global messenger characterized by a diffusion coefficient of ~ 280 μm2s-1. However, in vivo observations revealed that this value does not match with the timing of localized Ca2+ increases induced by the confined release of a non-metabolizable IP3 analog. A theoretical analysis of these data concluded that in intact cells diffusion of IP3 is strongly hindered, leading to a 30-fold reduction of the diffusion coefficient. Here, we performed a new computational analysis of the same observations using a stochastic model of Ca2+ puffs. Our simulations concluded that the value of the effective IP3 diffusion coefficient is close to 100 μm2s-1. Such moderate reduction with respect to in vitro estimations quantitatively agrees with a buffering effect by non-fully bound inactive IP3 receptors. The model also reveals that IP3 spreading is not much affected by the endoplasmic reticulum, which represents an obstacle to the free displacement of molecules, but can be significantly increased in cells displaying elongated, 1-dimensional like geometries.
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