ArticleProceedings of the National Academy of Sciences of the United States of America2009
Computing protein stabilities from their chain lengths.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Unifying perspectives on the activity and genotypic targeting of pharmacological chaperones.The Journal of biological chemistry · 2025Review
- Predicting absolute protein folding stability using generative models.Protein science : a publication of the Protein Society · 2025Article
- Origins of Life: The Protein Folding Problem all over again?Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes.Protein science : a publication of the Protein Society · 2023Article
- Highly Abundant Proteins Are Highly Thermostable.Genome biology and evolution · 2023Article
- Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome.Proteins · 2023Article
- ProTstab2 for Prediction of Protein Thermal Stabilities.International journal of molecular sciences · 2022Article
- Von Willebrand factor A1 domain stability and affinity for GPIbα are differentially regulated by itseLife · 2022Article
- A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life.Molecular biology and evolution · 2022Article
- The Protein Folding Problem: The Role of Theory.Journal of molecular biology · 2021Review
- Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage.Biomedicines · 2021Article
- Quantifying the Mutational Robustness of Protein-Coding Genes.Journal of molecular evolution · 2021Article
- Avoidance of protein unfolding constrains protein stability in long-term evolution.Biophysical journal · 2021Article
- The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions.The journal of physical chemistry. B · 2020Article
- Proteostasis is adaptive: Balancing chaperone holdases against foldases.PLoS computational biology · 2020Article
- A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes.The Journal of chemical physics · 2020Article
- Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.PLoS computational biology · 2019Article
- ProTstab - predictor for cellular protein stability.BMC genomics · 2019Article
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2 authors.
Funding
Abstract
New amino acid sequences of proteins are being learned at a rapid rate, thanks to modern genomics. The native structures and functions of those proteins can often be inferred using bioinformatics methods. We show here that it is also possible to infer the stabilities and thermal folding properties of proteins, given only simple genomics information: the chain length and the numbers of charged side chains. In particular, our model predicts DeltaH(T), DeltaS(T), DeltaC(p), and DeltaF(T)--the folding enthalpy, entropy, heat capacity, and free energy--as functions of temperature T; the denaturant m values in guanidine and urea; the pH-temperature-salt phase diagrams, and the energy of confinement F(s) of the protein inside a cavity of radius s. All combinations of these phase equilibria can also then be computed from that information. As one illustration, we compute the pH and salt conditions that would denature a protein inside a small confined cavity. Because the model is analytical, it is computationally efficient enough that it could be used to automatically annotate whole proteomes with protein stability information.
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