ArticleProceedings of the National Academy of Sciences of the United States of America1998
How evolution makes proteins fold quickly.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1998. 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.
- In silico evolution of globular protein folds from random sequences.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design.Molecular biotechnology · 2025Review
- Structural Lessons From the Mutant Proinsulin Syndrome.Frontiers in endocrinology · 2021Review
- Funneled energy landscape unifies principles of protein binding and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins.Protein engineering, design & selection : PEDS · 2019Article
- Folding of the Ig-Like Domain of the Dengue Virus Envelope Protein Analyzed by High-Hydrostatic-Pressure NMR at a Residue-Level Resolution.Biomolecules · 2019Article
- Article
- Molecular ensembles make evolution unpredictable.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Global computational mutagenesis provides a critical stability framework in protein structures.PloS one · 2017Article
- Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity.Biophysical journal · 2016Article
- Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?Journal of the Royal Society, Interface · 2015Article
- Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.Molecular biology and evolution · 2015Article
- Prediction of protein structural features from sequence data based on Shannon entropy and Kolmogorov complexity.PloS one · 2015Article
- Fractal globules: a new approach to artificial molecular machines.Biophysical journal · 2014Article
- The influence of selection for protein stability on dN/dS estimations.Genome biology and evolution · 2014Article
- Article
- Detecting selection on protein stability through statistical mechanical models of folding and evolution.Biomolecules · 2014Review
- Article
- Diabetes mellitus due to the toxic misfolding of proinsulin variants.FEBS letters · 2013Review
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3 authors.
Funding
Abstract
Sequences of fast-folding model proteins (48 residues long on a cubic lattice) were generated by an evolution-like selection toward fast folding. We find that fast-folding proteins exhibit a specific folding mechanism in which all transition state conformations share a smaller subset of common contacts (folding nucleus). Acceleration of folding was accompanied by dramatic strengthening of interactions in the folding nucleus whereas average energy of nonnucleus interactions remained largely unchanged. Furthermore, the residues involved in the nucleus are the most conserved ones within families of evolved sequences. Our results imply that for each protein structure there is a small number of conserved positions that are key determinants of fast folding into that structure. This conjecture was tested on two protein superfamilies: the first having the classical monophosphate binding fold (CMBF; 98 families) and the second having type-III repeat fold (47 families). For each superfamily, we discovered a few positions that exhibit very strong and statistically significant "conservatism of conservatism"-amino acids in those positions are conserved within every family whereas the actual types of amino acids varied from family to family. Those amino acids are in spatial contact with each other. The experimental data of Serrano and coworkers [Lopez-Hernandez, E. & Serrano, L. (1996) Fold. Des. (London) 1, 43-55]. for one of the proteins of the CMBF superfamily (CheY) show that residues identified this way indeed belong to the folding nucleus. Further analysis revealed deep connections between nucleation in CMBF proteins and their function.
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