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Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions
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 heterogen...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278454/ https://www.ncbi.nlm.nih.gov/pubmed/30453632 http://dx.doi.org/10.3390/molecules23113008 |
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author | Fuxreiter, Monika |
author_facet | Fuxreiter, Monika |
author_sort | Fuxreiter, Monika |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6278454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62784542018-12-13 Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions Fuxreiter, Monika Molecules Perspective 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. MDPI 2018-11-17 /pmc/articles/PMC6278454/ /pubmed/30453632 http://dx.doi.org/10.3390/molecules23113008 Text en © 2018 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Perspective Fuxreiter, Monika Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title | Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title_full | Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title_fullStr | Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title_full_unstemmed | Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title_short | Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions |
title_sort | towards a stochastic paradigm: from fuzzy ensembles to cellular functions |
topic | Perspective |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278454/ https://www.ncbi.nlm.nih.gov/pubmed/30453632 http://dx.doi.org/10.3390/molecules23113008 |
work_keys_str_mv | AT fuxreitermonika towardsastochasticparadigmfromfuzzyensemblestocellularfunctions |