ArticleScientific reports2015
Intrinsically disordered energy landscapes.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- SIRT1 Exon 2-Encoded IDR Gates CREB-Dependent Transcriptional Timing During Fasting.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Disentangling Intrachain Folding from Interchain Assembly through Multidimensional Visualization.The journal of physical chemistry. B · 2026Article
- Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.Journal of biological physics · 2026Review
- Intrinsic Disorder as a Biomimetic Design Paradigm.Biomimetics (Basel, Switzerland) · 2026Article
- Evaluating the Impact of Phosphorylation on the Dynamics of the Tau Protein Proline-Rich Region.Journal of chemical theory and computation · 2026Article
- Oligomerization enables the selective targeting of an intrinsically disordered region by a small molecule.Science advances · 2026Article
- Restoration of the Y220C p53 Full-Length Mutant by PK11000: a Molecular Dynamics Study of an Intrinsically Disordered Protein.ACS omega · 2026Article
- A Review of Global Optimization Methods for Molecular Structures: Algorithms, Applications and Perspectives.Journal of computational chemistry · 2025Review
- Combining simulations and experiments - a perspective on maximum entropy methods.Physical chemistry chemical physics : PCCP · 2025Review
- Umbrella Refinement of Ensembles-An Alternative View of Ensemble Optimization.Molecules (Basel, Switzerland) · 2025Article
- Decoding Solubility Signatures from Amyloid Monomer Energy Landscapes.Journal of chemical theory and computation · 2025Article
- Heterogeneous Slowdown of Dynamics in the Condensate of an Intrinsically Disordered Protein.The journal of physical chemistry letters · 2024Article
- Navigating the complexity of p53-DNA binding: implications for cancer therapy.Biophysical reviews · 2024Review
- The Rapid Evolution of De Novo Proteins in Structure and Complex.Genome biology and evolution · 2024Article
- Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain.Biopolymers · 2024Review
- Machine-learning-based methods to generate conformational ensembles of disordered proteins.Biophysical journal · 2024Article
- Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.Journal of chemical information and modeling · 2023Article
- Transition Networks Unveil Disorder-to-Order Transformations in AInternational journal of molecular sciences · 2023Article
- Article
- Oligomeric State and Holding Activity of Hsp60.International journal of molecular sciences · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such 'intrinsically disordered' landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an α-helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.