ArticleMolecules (Basel, Switzerland)2018
Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions.
Article in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Amyloid-β, Tau Protein, α-Synuclein, TDP-43, and FUS in Mixed Pathology: And Intrinsic Disorder to Rule Them All.International journal of molecular sciences · 2026Review
- Human pumilio proteins use fuzzy multivalent hydrophobic interactions to recruit the CCR4-NOT deadenylase complex to repress mRNAs.The Journal of biological chemistry · 2026Article
- Human Pumilio proteins use fuzzy multivalent hydrophobic interactions to recruit the CCR4-NOT deadenylase complex to repress mRNAs.bioRxiv : the preprint server for biology · 2025Article
- Toward universal models for collective interactions in biomolecular condensates.Biophysics reviews · 2025Article
- Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches.International journal of molecular sciences · 2024Review
- Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure.Protein science : a publication of the Protein Society · 2024Review
- FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.Nucleic acids research · 2023Article
- Protein interactions: anything new?Essays in biochemistry · 2022Article
- Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept.Cellular and molecular life sciences : CMLS · 2022Review
- FuzDB: a new phase in understanding fuzzy interactions.Nucleic acids research · 2022Article
- Protein conformational dynamics and phenotypic switching.Biophysical reviews · 2021Review
- Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer.Scientific reports · 2020Article
- The Fuzziness in Molecular, Supramolecular, and Systems Chemistry.Molecules (Basel, Switzerland) · 2020Article
- Moonlighting Proteins in the Fuzzy Logic of Cellular Metabolism.Molecules (Basel, Switzerland) · 2020Review
- Computational Structural Biology: Successes, Future Directions, and Challenges.Molecules (Basel, Switzerland) · 2019Review
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Abstract
The deterministic sequence → structure → function relationship is not applicable to describe how proteins dynamically adapt to different cellular conditions. A stochastic model is required to capture functional promiscuity, redundant sequence motifs, dynamic interactions, or conformational heterogeneity, which facilitate the decision-making in regulatory processes, ranging from enzymes to membraneless cellular compartments. The fuzzy set theory offers a quantitative framework to address these problems. The fuzzy formalism allows the simultaneous involvement of proteins in multiple activities, the degree of which is given by the corresponding memberships. Adaptation is described via a fuzzy inference system, which relates heterogeneous conformational ensembles to different biological activities. Sequence redundancies (e.g., tandem motifs) can also be treated by fuzzy sets to characterize structural transitions affecting the heterogeneous interaction patterns (e.g., pathological fibrillization of stress granules). The proposed framework can provide quantitative protein models, under stochastic cellular conditions.
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