ArticleFrontiers in synaptic neuroscience2015
Computational reconstitution of spine calcium transients from individual proteins.
Article in Frontiers in synaptic neuroscience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 115 citations in OpenAlex.
- Calmodulin controls spatial and temporal specificity of calcium-induced calcium release.PLoS computational biology · 2026Article
- Presynaptic Vesicles Supply Membrane for Axonal Bouton Enlargement during Long Term Potentiation.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Calcium dynamics in small spaces: Lessons learned from modeling in dendritic spines.Biophysical journal · 2025Review
- The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.Cell reports methods · 2025Article
- Dynamic regulation of vesicle pools in a detailed spatial model of the complete synaptic vesicle cycle.Science advances · 2025Article
- The architecture of invaginating rod synapses slows glutamate diffusion and shapes synaptic responses.The Journal of general physiology · 2025Article
- Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time.Biophysical journal · 2025Article
- A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping.Frontiers in synaptic neuroscience · 2025Article
- A spatial model of autophosphorylation of CabioRxiv : the preprint server for biology · 2024Article
- Electrophysical cardiac remodeling at the molecular level: Insights into ryanodine receptor activation and calcium-induced calcium release from a stochastic explicit-particle model.Biophysical journal · 2024Article
- Synapse-specific structural plasticity that protects and refines local circuits during LTP and LTD.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling.Briefings in bioinformatics · 2024Article
- Nano-organization of synaptic calcium signaling.Biochemical Society transactions · 2024Review
- Celebrating the Birthday of AMPA Receptor Nanodomains: Illuminating the Nanoscale Organization of Excitatory Synapses with 10 Nanocandles.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Review
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease.PNAS nexus · 2024Article
- Making time and space for calcium control of neuron activity.Current opinion in neurobiology · 2023Review
- Mitochondrial morphology governs ATP production rate.The Journal of general physiology · 2023Article
- A stochastic model of hippocampal synaptic plasticity with geometrical readout of enzyme dynamics.eLife · 2023Article
- Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling.NPJ systems biology and applications · 2023Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 1 country.
Funding
Abstract
We have built a stochastic model in the program MCell that simulates Ca(2+) transients in spines from the principal molecular components believed to control Ca(2+) entry and exit. Proteins, with their kinetic models, are located within two segments of dendrites containing 88 intact spines, centered in a fully reconstructed 6 × 6 × 5 μm(3) cube of hippocampal neuropil. Protein components include AMPA- and NMDA-type glutamate receptors, L- and R-type voltage-dependent Ca(2+) channels, Na(+)/Ca(2+) exchangers, plasma membrane Ca(2+) ATPases, smooth endoplasmic reticulum Ca(2+) ATPases, immobile Ca(2+) buffers, and calbindin. Kinetic models for each protein were taken from published studies of the isolated proteins in vitro. For simulation of electrical stimuli, the time course of voltage changes in the dendritic spine was generated with the desired stimulus in the program NEURON. Voltage-dependent parameters were then continuously re-adjusted during simulations in MCell to reproduce the effects of the stimulus. Nine parameters of the model were optimized within realistic experimental limits by a process that compared results of simulations to published data. We find that simulations in the optimized model reproduce the timing and amplitude of Ca(2+) transients measured experimentally in intact neurons. Thus, we demonstrate that the characteristics of individual isolated proteins determined in vitro can accurately reproduce the dynamics of experimentally measured Ca(2+) transients in spines. The model will provide a test bed for exploring the roles of additional proteins that regulate Ca(2+) influx into spines and for studying the behavior of protein targets in the spine that are regulated by Ca(2+) influx.
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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.