ArticleBiophysical journal2009
Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates.Biomacromolecules · 2023Article
- Co-Immobilization of Lactase and Glucose Isomerase on the Novel g-CNanomaterials (Basel, Switzerland) · 2022Article
- Preparation of ZIF@ADH/NAD-MSN/LDH Core Shell Nanocomposites for the Enhancement of Coenzyme Catalyzed Double Enzyme Cascade.Nanomaterials (Basel, Switzerland) · 2021Article
- Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders.Biomolecules · 2020Article
- Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder.Biomolecules · 2019Article
- Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.The journal of physical chemistry. B · 2019Article
- Towards developing principles of protein folding and dynamics in the cell.Physical biology · 2018Review
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Structure and Conformational Properties of d-Glucose/d-Galactose-Binding Protein in Crowded Milieu.Molecules (Basel, Switzerland) · 2017Article
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
- Predicting Molecular Crowding Effects in Ion-RNA Interactions.The journal of physical chemistry. B · 2016Article
- Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.Biophysical journal · 2016Article
- Transport regulation of two-dimensional receptor-ligand association.Biophysical journal · 2015Article
- What macromolecular crowding can do to a protein.International journal of molecular sciences · 2014Review
- Article
- The limitations of an exclusively colloidal view of protein solution hydrodynamics and rheology.Biophysical journal · 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
- Effects of macromolecular crowding agents on protein folding in vitro and in silico.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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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein dynamics in cells may be different from those in dilute solutions in vitro, because the environment in cells is highly concentrated with other macromolecules. This volume exclusion because of macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, we investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents, using in silico and in vitro approaches. By means of coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fractions of crowding agents (phi(c)) as well as of crowding agent geometry (sphere or spherocylinder) at high phi(c). Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we identified the in silico crowding conditions that best enhance protein stability, and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. Our test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. Macromolecular crowding effects may be a tool for the manipulation of protein-folding and function in living cells.
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