ArticleBiophysical journal2012
A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Martini 3 coarse-grained model of enzymes: Framework with validation by all-atom simulations and x-ray diffraction measurements.The Journal of chemical physics · 2025Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Effect of Protein-Protein Interactions on Translational Diffusion of Spheroidal Proteins.International journal of molecular sciences · 2022Review
- Article
- Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.The journal of physical chemistry. B · 2019Article
- Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions.Physical chemistry chemical physics : PCCP · 2018Article
- Towards developing principles of protein folding and dynamics in the cell.Physical biology · 2018Review
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Computer Simulations of the Bacterial Cytoplasm.Biophysical reviews · 2013Article
- Protein-protein interactions in a crowded environment.Biophysical reviews · 2013Review
- Where soft matter meets living matter--protein structure, stability, and folding in the cell.Current opinion in structural biology · 2013Review
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2 authors.
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Abstract
We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λ(c) = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature T(f) of a test protein (apoazurin) in a PD model is ~5° greater than that in a F70 model. In addition, the deviation of T(f) in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.
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