ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2010
Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions.Communications chemistry · 2023Article
- Structure and Dynamics of dsDNA in Cell-like Environments.Entropy (Basel, Switzerland) · 2022Review
- Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex.The journal of physical chemistry letters · 2022Article
- Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.The journal of physical chemistry. B · 2019Article
- Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration.Frontiers in molecular biosciences · 2019Article
- Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein-Crowder Attraction.The journal of physical chemistry. B · 2018Article
- Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.Journal of molecular biology · 2018Article
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.The journal of physical chemistry. B · 2016Article
- Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed.Journal of chemical theory and computation · 2014Article
- Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study.Biophysical journal · 2014Article
- Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins.The journal of physical chemistry letters · 2013Article
- An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.Journal of chemical theory and computation · 2013Article
- Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation.Physical biology · 2013Article
- Crowders perturb the entropy of RNA energy landscapes to favor folding.Journal of the American Chemical Society · 2013Article
- Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details.Biophysical reviews · 2013Article
- Influence of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling.FEBS letters · 2013Review
- A method for computing association rate constants of atomistically represented proteins under macromolecular crowding.Physical biology · 2012Article
- Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents.Biophysical journal · 2012Article
- A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).Biophysical journal · 2012Article
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2 authors.
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Abstract
Macromolecular crowding inside cells affects the thermodynamic and kinetic properties of proteins. The scaled particle theory (SPT) has played an important role toward establishing a qualitative picture for the effects of crowding. However, SPT-based modeling lacks molecular details. Molecular dynamics simulations overcome this limitation, but at great computational cost. Here, we present a theoretical method for modeling crowding at the atomic level. The method makes it possible to achieve exhaustive conformational sampling in modeling crowding effects and to tackle challenges posed by large protein oligomers and by complex mixtures of crowders.
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