ArticleProceedings of the National Academy of Sciences of the United States of America2012
Hydrophobic forces and the length limit of foldable protein domains.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The barcoded binding assay: Multiplexed profiling of chaperone binding selectivity for hydrophobic substrates.Cell stress & chaperones · 2026Article
- SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.Bioinformatics (Oxford, England) · 2025Article
- Advances in the chemical synthesis of human proteoforms.Science China. Life sciences · 2025Review
- Enzyme miniaturization: Revolutionizing future biocatalysts.Biotechnology advances · 2025Review
- Chemical Synthesis of Human Proteoforms and Application in Biomedicine.ACS central science · 2024Review
- Genome-Wide Libraries for Protozoan Pathogen Drug Target Screening Using Yeast Surface Display.ACS infectious diseases · 2023Article
- MIND-S is a deep-learning prediction model for elucidating protein post-translational modifications in human diseases.Cell reports methods · 2023Article
- Article
- Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors.Cell systems · 2021Article
- Article
- Is the hydrophobic core a universal structural element in proteins?Journal of molecular modeling · 2017Article
- Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins.PloS one · 2016Article
- Interaction Potentials of Anisotropic Nanocrystals from the Trajectory Sampling of Particle Motion using in Situ Liquid Phase Transmission Electron Microscopy.ACS central science · 2015Article
- GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding.Cell · 2014Article
- Are proposed early genetic codes capable of encoding viable proteins?Journal of molecular evolution · 2014Article
- The ribosome as a hub for protein quality control.Molecular cell · 2013Review
- The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis.Cell · 2013Article
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2 authors.
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Abstract
To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated primarily by inherent physical forces, whereas natural selection determines the native state.
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