ArticleBiophysical journal2014
Applying molecular crowding models to simulations of virus capsid assembly in vitro.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Review
- Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions.eLife · 2023Article
- Virus Mechanics under Molecular Crowding.The journal of physical chemistry. B · 2021Article
- Crystal structure of tomato spotted wilt virus GProceedings of the National Academy of Sciences of the United States of America · 2020Article
- A method for efficient Bayesian optimization of self-assembly systems from scattering data.BMC systems biology · 2018Article
- Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction.Synthetic biology (Oxford, England) · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Multiscale Modeling of Diffusion in a Crowded Environment.Bulletin of mathematical biology · 2017Article
- Kinetic constraints on self-assembly into closed supramolecular structures.Scientific reports · 2017Article
- Quantitative computational models of molecular self-assembly in systems biology.Physical biology · 2017Review
- Allosteric Control of Icosahedral Capsid Assembly.The journal of physical chemistry. B · 2016Article
- Recent advances in coarse-grained modeling of virus assembly.Current opinion in virology · 2016Review
- Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly.Nature communications · 2016Article
- Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation.PloS one · 2016Article
- Mechanisms of virus assembly.Annual review of physical chemistry · 2015Review
- Using Markov state models to study self-assembly.The Journal of chemical physics · 2014Article
- Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data.IEEE/ACM transactions on computational biology and bioinformaticsArticle
- Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications.Journal of tissue engineeringArticle
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Virus capsid assembly has been widely studied as a biophysical system, both for its biological and medical significance and as an important model for complex self-assembly processes. No current technology can monitor assembly in detail and what information we have on assembly kinetics comes exclusively from in vitro studies. There are many differences between the intracellular environment and that of an in vitro assembly assay, however, that might be expected to alter assembly pathways. Here, we explore one specific feature characteristic of the intracellular environment and known to have large effects on macromolecular assembly processes: molecular crowding. We combine prior particle simulation methods for estimating crowding effects with coarse-grained stochastic models of capsid assembly, using the crowding models to adjust kinetics of capsid simulations to examine possible effects of crowding on assembly pathways. Simulations suggest a striking difference depending on whether or not a system uses nucleation-limited assembly, with crowding tending to promote off-pathway growth in a nonnucleation-limited model but often enhancing assembly efficiency at high crowding levels even while impeding it at lower crowding levels in a nucleation-limited model. These models may help us understand how complicated assembly systems may have evolved to function with high efficiency and fidelity in the densely crowded environment of the cell.
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Registered trials
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.