ArticleThe journal of physical chemistry letters2010
Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease.
Article in The journal of physical chemistry letters, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions.European biophysics journal : EBJ · 2019Article
- Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.The journal of physical chemistry. B · 2019Article
- Both Ligands and Macromolecular Crowders Preferentially Bind to Closed Conformations of Maltose Binding Protein.Biochemistry · 2019Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- 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
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 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
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- 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
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation.Physical biology · 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
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding.
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