ArticleProceedings of the National Academy of Sciences of the United States of America2010
Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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122 citing papers in PubMed, 324 citations in OpenAlex.
- From static structures to dynamic energy landscapes: the latest revolution in molecular biology.Current opinion in structural biology · 2026Review
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
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- Getting gene expression "just right".Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Human protein synthesis requires aminoacyl-tRNA pivoting during proofreading.Nature communications · 2025Article
- Dynamic Cytoplasm: A Physical Regulator of Enzymatic Function.Biochemistry · 2025Review
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- Multiple kinesins speed up cargo transport in crowded environments by sharing load.Communications biology · 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
- Effects of Molecular Crowding on the Structural, Dynamic, and Functional Properties of Biological Macromolecules: A General Overview.Sub-cellular biochemistry · 2025Review
- Recent Advances in DNA Origami-Enabled Optical Biosensors for Multi-Scenario Application.Nanomaterials (Basel, Switzerland) · 2024Review
- Polyethylene Glycol Impacts Conformation and Dynamics ofBiochemistry · 2024Article
- What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems?International journal of molecular sciences · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Molecular Crowding: The History and Development of a Scientific Paradigm.Chemical reviews · 2024Review
- The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α-synuclein.Protein science : a publication of the Protein Society · 2024Article
- Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation.The journal of physical chemistry letters · 2024Article
- Cellular and epigenetic perspective of protein stability and its implications in the biological system.Epigenomics · 2024Review
- In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non-native interactions.Protein science : a publication of the Protein Society · 2023Article
- Regulation of phosphoglycerate kinase 1 and its critical role in cancer.Cell communication and signaling : CCS · 2023Review
62 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function, and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal), and Sph (spherical compact). With an adjustment for viscosity, crowded wild-type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a previously undescribed solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: Rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates. We also examine T-jump unfolding of PGK as a function of crowding experimentally. We uncover a nonmonotonic folding relaxation time vs. Ficoll concentration. Theory and modeling explain why an optimum concentration exists for fastest folding. Below the optimum, folding slows down because the unfolded state is stabilized relative to the transition state. Above the optimum, folding slows down because of increased viscosity.
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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.