ArticleProceedings of the National Academy of Sciences of the United States of America2019
Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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75 citing papers in PubMed.
- Dynamic yet well-defined organization of the FUS RGG3 dense phase.Communications chemistry · 2026Article
- Non-Fickian diffusion within assemblies of the intrinsically disordered protein β-casein.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- MYC modulates TOP2A diffusion to promote substrate detection and activity.Nature communications · 2026Article
- Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The viscosity of protein and nucleic acid solutions and their folded structures explored using the free-volume concept and Eyring's rate process theory.RSC advances · 2025Article
- Coherent X-rays reveal anomalous molecular diffusion and cage effects in crowded protein solutions.Nature communications · 2025Article
- Viscosity of concentrated antibodies from a dynamic model of electrostatics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cytoplasmic fluidity and the cold life: proteome stability is decoupled from viability in psychrophiles.Nature communications · 2025Article
- Preserving enzyme conformation and catalytic efficiency in crowded and active environments.Nanoscale advances · 2025Article
- Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus.Journal of nanobiotechnology · 2025Article
- Dynamic Cytoplasm: A Physical Regulator of Enzymatic Function.Biochemistry · 2025Review
- Prediction of phase-separation propensities of disordered proteins from sequence.Proceedings of the National Academy of Sciences of the United States of America · 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
- Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation.JACS Au · 2024Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- Portable Microfluidic Viscometer for Formulation Development and in Situ Quality Control of Protein and Antibody Solutions.Analytical chemistry · 2024Article
- O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning.Biomacromolecules · 2024Article
- Modeling reveals the strength of weak interactions in stacked-ring assembly.Biophysical journal · 2024Article
- Fatty acid binding to the human transport proteins FABP3, FABP4, and FABP5 from a Ligand's perspective.The Journal of biological chemistry · 2024Article
15 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
We develop a detailed description of protein translational and rotational diffusion in concentrated solution on the basis of all-atom molecular dynamics simulations in explicit solvent. Our systems contain up to 540 fully flexible proteins with 3.6 million atoms. In concentrated protein solutions (100 mg/mL and higher), the proteins ubiquitin and lysozyme, as well as the protein domains third IgG-binding domain of protein G and villin headpiece, diffuse not as isolated particles, but as members of transient clusters between which they constantly exchange. A dynamic cluster model nearly quantitatively explains the increase in viscosity and the decrease in protein diffusivity with protein volume fraction, which both exceed the predictions from widely used colloid models. The Stokes-Einstein relations for translational and rotational diffusion remain valid, but the effective hydrodynamic radius grows linearly with protein volume fraction. This increase follows the observed increase in cluster size and explains the more dramatic slowdown of protein rotation compared with translation. Baxter's sticky-sphere model of colloidal suspensions captures the concentration dependence of cluster size, viscosity, and rotational and translational diffusion. The consistency between simulations and experiments for a diverse set of soluble globular proteins indicates that the cluster model applies broadly to concentrated protein solutions, with equilibrium dissociation constants for nonspecific protein-protein binding in the K
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