ArticleBiophysical journal2009
Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A multiscale model of the regulation of aquaporin 2 recycling.NPJ systems biology and applications · 2022Article
- Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.Bulletin of mathematical biology · 2019Review
- Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells.Nature materials · 2018Article
- Dissecting the actin cortex density and membrane-cortex distance in living cells by super-resolution microscopy.Journal of physics D: Applied physics · 2017Article
- Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.BMC systems biology · 2016Article
- A spatial model for integrin clustering as a result of feedback between integrin activation and integrin binding.Biophysical journal · 2012Article
- Hybrid spatial Gillespie and particle tracking simulation.Bioinformatics (Oxford, England) · 2012Article
- From microscopy data to in silico environments for in vivo-oriented simulations.EURASIP journal on bioinformatics & systems biology · 2012Article
- Spatial simulations in systems biology: from molecules to cells.International journal of molecular sciences · 2012Review
- Spatial modeling of vesicle transport and the cytoskeleton: the challenge of hitting the right road.PloS one · 2012Article
- Nonparametric simulation of signal transduction networks with semi-synchronized update.PloS one · 2012Article
- Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants.BMC systems biology · 2011Article
- Diffusion in crowded biological environments: applications of Brownian dynamics.BMC biophysics · 2011Article
- A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation.Systems and synthetic biology · 2010Article
- Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.Biophysical reviews · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transduction of signals depends on the translocation of signaling molecules to specific targets. Undirected diffusion processes play a key role in the bridging of spaces between different cellular compartments. The diffusion of the molecules is, in turn, governed by the intracellular architecture. Molecular crowding and the cytoskeleton decrease macroscopic diffusion. This article shows the use of a stochastic simulation method to study the effects of the cytoskeleton structure on the mobility of macromolecules. Brownian dynamics and single particle tracking were used to simulate the diffusion process of individual molecules through a model cytoskeleton. The resulting average effective diffusion is in line with data obtained in the in vitro and in vivo experiments. It shows that the cytoskeleton structure strongly influences the diffusion of macromolecules. The simulation method used also allows the inclusion of reactions in order to model complete signaling pathways in their spatio-temporal dynamics, taking into account the effects of the cellular architecture.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.