ArticleBiophysical journal2008
Prediction of protein solubility from calculation of transfer free energy.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 60 citations in OpenAlex.
- Complementarity of Deep Learning and Physics-Based Approaches in the Design of New Antibodies.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ProSol-multi: Protein solubility prediction via amino acids multi-level correlation and discriminative distribution.Heliyon · 2024Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Two physics-based models for pH-dependent calculations of protein solubility.Protein science : a publication of the Protein Society · 2022Article
- Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map.Journal of cheminformatics · 2021Article
- Structure-guided evolution of Green2 toward photostability and quantum yield enhancement by F145Y substitution.Protein science : a publication of the Protein Society · 2020Article
- Solubility analysis of homologous series of amino acids and solvation energetics in aqueous potassium sulfate solution.Heliyon · 2019Article
- Computational prediction of drug solubility in water-based systems: Qualitative and quantitative approaches used in the current drug discovery and development setting.International journal of pharmaceutics · 2018Review
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Predicting Molecular Crowding Effects in Ion-RNA Interactions.The journal of physical chemistry. B · 2016Article
- Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.The journal of physical chemistry. B · 2016Article
- Conformational preferences of DNA in reduced dielectric environments.The journal of physical chemistry. B · 2014Article
- Article
- 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
- Discrimination of soluble and aggregation-prone proteins based on sequence information.Molecular bioSystems · 2013Article
- A method for computing association rate constants of atomistically represented proteins under macromolecular crowding.Physical biology · 2012Article
- Protein crowding affects hydration structure and dynamics.Journal of the American Chemical Society · 2012Article
- Identification of proteins sensitive to thermal stress in human neuroblastoma and glioma cell lines.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility.
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Registered trials
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