ArticleThe journal of physical chemistry. B2019
Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS.Scientific reports · 2024Article
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
- Review
- Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures.Biochemistry · 2022Article
- Crowding-induced protein destabilization in the absence of soft attractions.Biophysical journal · 2022Article
- Protein assembly and crowding simulations.Current opinion in structural biology · 2022Review
- Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex.Biophysical journal · 2021Article
- Impact of crowded environments on binding between protein and single-stranded DNA.Scientific reports · 2021Article
- The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions.The journal of physical chemistry. B · 2020Article
- Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase.Biophysical journal · 2019Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
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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.