ArticleScientific reports2019
Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 65 citations in OpenAlex.
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- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- Stability and Conformational Dynamics of Interferons: Structural Insights into the Urea- and Guanidinium Chloride-Induced Unfolding.ACS omega · 2026Article
- Label-free optical observation of disordered-to-ordered transitions in single intrinsically disordered proteins.Npj biosensing · 2026Article
- Direct comparison of the structural dynamics between spontaneous and ligand-induced folding of staphylococcal nuclease.Protein science : a publication of the Protein Society · 2025Article
- Conformational ensembles for protein structure prediction.Scientific reports · 2025Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Acetylation-Dependent Compaction of the Histone H4 Tail Ensemble.The journal of physical chemistry. B · 2024Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules.JACS Au · 2024Article
- Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics.Scientific reports · 2023Article
- Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies.Proteins · 2023Article
- Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages.Science advances · 2023Article
- Review
- A little less aggregation a little more replication: Viral manipulation of stress granules.Wiley interdisciplinary reviews. RNA · 2023Review
- Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase.Protein science : a publication of the Protein Society · 2022Article
- The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.Frontiers in molecular biosciences · 2022Article
- Recombinant Protein Production and Purification of Insoluble Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.Chemical science · 2021Article
- Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast.Journal of molecular biology · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Folding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca. -50 kcal/mol, meaning that the free energy decreases by ~5 kcal/mol upon the formation of 10% native contacts. On the other hand, the landscape of pKID is funneled but considerably shallower (slope of -24 kcal/mol), which explains why pKID is disordered in free environments. Upon binding to KIX, the landscape of pKID now becomes significantly steep (slope of -54 kcal/mol), which enables otherwise disordered pKID to fold. We also show that it is the pKID-KIX intermolecular interactions originating from hydrophobic residues that mainly confer the steep folding funnel. The present work not only provides the quantitative characterization of the protein folding free energy landscape, but also establishes the usefulness of the folding funnel concept to IDPs.
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