ArticleBiophysical reviews2013
Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details.
Article in Biophysical reviews, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Crowder-directed interactions and conformational dynamics in multistimuli-responsive intrinsically disordered protein.Science advances · 2022Article
- Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.The journal of physical chemistry. B · 2022Article
- Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism.Biophysical journal · 2019Article
- Explicit Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Protein Mixtures. 2. Effects of Varying Hard and Soft Interactions upon Prototypical Chemical Equilibria.The journal of physical chemistry. B · 2017Article
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- 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
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- Modeling protein association mechanisms and kinetics.Current opinion in structural biology · 2013Review
- 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
- Influence of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling.FEBS letters · 2013Review
- Molecular crowding inhibits U-insertion/deletion RNA editing in vitro: consequences for the in vivo reaction.PloS one · 2013Article
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2 authors.
Funding
Abstract
Recent experimental studies of protein folding and binding under crowded solutions suggest that crowding agents exert subtle influences on the thermodynamic and kinetic properties of the proteins. While some of the crowding effects can be understood qualitatively from simple models of the proteins, quantitative rationalization of these effects requires an atomistic representation of the protein molecules in modeling their interactions with crowders. A computational approach, known as postprocessing, has opened the door for atomistic modeling of crowding effects. This review summarizes the applications of the postprocessing approach for studying crowding effects on the thermodynamics and kinetics of protein folding, conformational transition, and binding. The integration of atomistic modeling with experiments in crowded solutions promises new insight into biochemical processes in cellular environments.
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