ArticleBiophysical journal2008
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 98 papers.
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98 citing papers in PubMed, 206 citations in OpenAlex.
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- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds.Nano letters · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
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- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.PLoS computational biology · 2023Article
- Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations.Protein science : a publication of the Protein Society · 2023Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses.Nature communications · 2022Article
- Understanding the functional role of membrane confinements in TNF-mediated signaling by multiscale simulations.Communications biology · 2022Article
- Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.Biophysical journal · 2022Article
- Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations.Integrative biology : quantitative biosciences from nano to macro · 2021Article
- A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells.PLoS computational biology · 2021Article
- Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a general-purpose model for biomolecular simulations at the molecular level that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing and reacting particles with physical dimensions. To validate the model, we first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the macroscopic coefficients for diffusion and reaction rate. We then compared simulation results with Smoluchowski theory for diffusion-limited irreversible reactions and the best available approximation for diffusion-influenced reversible reactions. To simulate the volumetric effects of a crowded intracellular environment, we created a virtual cytoplasm composed of a heterogeneous population of particles diffusing at rates appropriate to their size. The particle-size distribution was estimated from the relative abundance, mass, and stoichiometries of protein complexes using an experimentally derived proteome catalog from Escherichia coli K12. Simulated diffusion constants exhibited anomalous behavior as a function of time and crowding. Although significant, the volumetric impact of crowding on diffusion cannot fully account for retarded protein mobility in vivo, suggesting that other biophysical factors are at play. The simulated effect of crowding on barnase-barstar dimerization, an experimentally characterized example of a bimolecular association reaction, reveals a biphasic time course, indicating that crowding exerts different effects over different timescales. These observations illustrate that quantitative realism in biosimulation will depend to some extent on mesoscale phenomena that are not currently well understood.
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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.