ArticleBiophysical journal2009
Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability.
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 55 papers.
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Who cites it
55 citing papers in PubMed.
- Protein oxidation in crowded environments.The Biochemical journal · 2026Review
- Pitfalls of Using ANS Dye Under Molecular Crowding Conditions.International journal of molecular sciences · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Molecular Crowding: The History and Development of a Scientific Paradigm.Chemical reviews · 2024Review
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
- Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex.The journal of physical chemistry letters · 2022Article
- Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase.Biophysical journal · 2019Article
- Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder.Biomolecules · 2019Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- 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
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- 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
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- 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
- Effects of crowding on the stability of a surface-tethered biopolymer: an experimental study of folding in a highly crowded regime.Journal of the American Chemical Society · 2014Article
- Macromolecular crowding as a regulator of gene transcription.Biophysical journal · 2014Article
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.The journal of physical chemistry. B · 2014Article
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2 authors.
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Abstract
Theoretical models predict that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different. In this study, we represented the native and denatured states atomistically, with conformations sampled from explicit-solvent molecular dynamics simulations at room temperature and high temperature, respectively. We then designed an efficient algorithm to calculate the allowed fraction, f, when the protein molecule is placed inside a box of crowders. That a fraction of placements of the protein molecule is disallowed because of volume exclusion by the crowders leads to an increase in chemical potential, given by Deltamu = -k(B)T lnf. The difference in Deltamu between the native and denatured states predicts the effect of crowding on the folding free energy. Even when the crowders occupied 35% of the solution volume, the stabilization reached only 1.5 kcal/mol for cytochrome b562. The modest stabilization predicted is consistent with experimental studies. Interestingly, a mixture of different sized crowders was found to exert a greater effect than the sum of the individual species of crowders. The stabilization of crowding on the binding stability of barnase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromolecular crowding inside cells.
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