ArticleProceedings of the National Academy of Sciences of the United States of America2014
Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- Article
- From static structures to dynamic energy landscapes: the latest revolution in molecular biology.Current opinion in structural biology · 2026Review
- Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization.Journal of medicinal chemistry · 2026Article
- Results of a large scale study of the binding of 50 type II inhibitors to 348 kinases: The role of protein reorganization.bioRxiv : the preprint server for biology · 2026Article
- Probing the dark energy in the functional protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Predicting Protein Folding Dynamics Using Sequence Information.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Energy Landscapes of Model Knotted Polymers.Journal of chemical theory and computation · 2025Article
- Inferring protein-folding mechanisms from natural sequence diversity.Biophysical journal · 2025Article
- Frustration in physiology and molecular medicine.Molecular aspects of medicine · 2025Review
- Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2.Research square · 2025Article
- Identification of coevolving positions by ancestral reconstruction.Communications biology · 2025Article
- Emergent time scales of epistasis in protein evolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.Nature communications · 2024Article
- Sequence-Based Protein Design: A Review of Using Statistical Models to Characterize Coevolutionary Traits for Developing Hybrid Proteins as Genetic Sensors.International journal of molecular sciences · 2024Review
- Machine learning in biological physics: From biomolecular prediction to design.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Simultaneous enhancement of multiple functional properties using evolution-informed protein design.Nature communications · 2024Article
- DIProT: A deep learning based interactive toolkit for efficient and effective Protein design.Synthetic and systems biotechnology · 2024Article
- Solvent constraints for biopolymer folding and evolution in extraterrestrial environments.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.Research square · 2024Article
25 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
The energy landscape used by nature over evolutionary timescales to select protein sequences is essentially the same as the one that folds these sequences into functioning proteins, sometimes in microseconds. We show that genomic data, physical coarse-grained free energy functions, and family-specific information theoretic models can be combined to give consistent estimates of energy landscape characteristics of natural proteins. One such characteristic is the effective temperature T(sel) at which these foldable sequences have been selected in sequence space by evolution. T(sel) quantifies the importance of folded-state energetics and structural specificity for molecular evolution. Across all protein families studied, our estimates for T(sel) are well below the experimental folding temperatures, indicating that the energy landscapes of natural foldable proteins are strongly funneled toward the native state.
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