ArticlePhysical biology2013
Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation.
Article in Physical biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions.Communications chemistry · 2023Article
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed.Journal of chemical theory and computation · 2014Article
- Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study.Biophysical journal · 2014Article
- Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins.The journal of physical chemistry letters · 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
- Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details.Biophysical reviews · 2013Article
- Influence of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling.FEBS letters · 2013Review
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
We have developed a 'postprocessing' method for modeling biochemical processes such as protein folding under crowded conditions (Qin and Zhou 2009 Biophys. J. 97 12-19). In contrast to the direct simulation approach, in which the protein undergoing folding is simulated along with crowders, the postprocessing method requires only the folding simulation without crowders. The influence of the crowders is then obtained by taking conformations from the crowder-free simulation and calculating the free energies of transferring to the crowders. This postprocessing yields the folding free energy surface of the protein under crowding. Here the postprocessing results for the folding of three small proteins under 'repulsive' crowding are validated by those obtained previously by the direct simulation approach (Mittal and Best 2010 Biophys. J. 98 315-20). This validation confirms the accuracy of the postprocessing approach and highlights its distinct advantages in modeling biochemical processes under cell-like crowded conditions, such as enabling an atomistic representation of the test proteins.
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