ArticleThe journal of physical chemistry. B2017
Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Label-Free SERS Fingerprinting of Neuroprotein Conformational Dynamics in Human Saliva.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Lipoprotein diffusion in dense yolk plasma is governed by softness, hydrodynamics, and caging: Insights from MHz-XPCS.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment.The journal of physical chemistry. B · 2025Article
- Cytoplasmic fluidity and the cold life: proteome stability is decoupled from viability in psychrophiles.Nature communications · 2025Article
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.Journal of chemical theory and computation · 2025Article
- Enzymes in a human cytoplasm model organize into submetabolon complexes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Diffusion and Viscosity in Mixed Protein Solutions.The journal of physical chemistry. B · 2024Article
- COCOMO2: A coarse-grained model for interacting folded and disordered proteins.bioRxiv : the preprint server for biology · 2024Article
- Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.The journal of physical chemistry. B · 2024Article
- Actin-driven nanotopography promotes stable integrin adhesion formation in developing tissue.Nature communications · 2024Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.Nature communications · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- What determines sub-diffusive behavior in crowded protein solutions?Biophysical journal · 2024Article
- Autoinhibition in the Signal Transducer CIN85 Modulates B Cell Activation.Journal of the American Chemical Society · 2024Article
- Probing macromolecular crowding at the lipid membrane interface with genetically-encoded sensors.Protein science : a publication of the Protein Society · 2023Article
- Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects.The Journal of chemical physics · 2023Review
- Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.The journal of physical chemistry. B · 2023Article
- Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.