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  1. Article ; Online: Context-dependent, fuzzy protein interactions: Towards sequence-based insights.

    Fuxreiter, Monika

    Current opinion in structural biology

    2024  Volume 87, Page(s) 102834

    Abstract: Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound ... ...

    Abstract Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.
    Language English
    Publishing date 2024-05-16
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2024.102834
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book: Fuzziness

    Fuxreiter, Monika / Tompa, Peter

    structural disorder in protein complexes

    (Advances in experimental medicine and biology ; 725)

    2012  

    Author's details ed. by Monika Fuxreiter; Peter Tompa
    Series title Advances in experimental medicine and biology ; 725
    Collection
    Keywords Protein Conformation ; Protein Denaturation
    Language English
    Size XX, 194 S. : Ill., graph. Darst.
    Publisher Springer
    Publishing place New York
    Publishing country United States
    Document type Book
    Note Includes bibliographical references and index ; Fuzzy complexes : a more stochastic view of protein function / Monika Fuxreiter and Peter Tompa -- Dynamic fuzziness during linker histone action / Steven J. McBryant and Jeffrey C. Hansen -- Intrinsic protein flexibility in regulation of cell proliferation : advantages for signaling and opportunities for novel therapeutics / Ariele Viacava Follis, Charles A. Galea, and Richard W. Kriwacki -- Interplay between protein order, disorder and oligomericity in receptor signaling / Alexander B. Sigalov -- Consequences of fuzziness in the NFB/IB interaction / Elizabeth A. Komives -- Roles for intrinsic disorder and ̂fuzziness in generating context specific function in ultrabithorax : a hox transcription factor / Sarah E. Bondos and Hao Ching Hsiao -- Molecular recognition by the EWS transcriptional activation domain / Kevin A.W. Lee -- The measles virus NTAILXD complex : an illustrative example of fuzziness / Sonia Longhi -- Fuzziness in the core of the human pathogenic viruses HCV and HIV / Roland Ivanyi Nagy and Jean Luc Darlix -- Structural disorder and protein elasticity / Sarah Rauscher and Røgis Pomès
    HBZ-ID HT017115856
    ISBN 978-1-4614-0658-7 ; 1-4614-0658-7
    Database Catalogue ZB MED Medicine, Health

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  3. Article ; Online: Electrostatics tunes protein interactions to context.

    Fuxreiter, Monika

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 31, Page(s) e2209201119

    MeSH term(s) Models, Molecular ; Proteins/chemistry ; Static Electricity
    Chemical Substances Proteins
    Language English
    Publishing date 2022-07-15
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2209201119
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  4. Article ; Online: Spot in a drop: mutations in aberrant condensates.

    Fuxreiter, Monika

    Nature reviews. Molecular cell biology

    2021  Volume 22, Issue 3, Page(s) 162–163

    MeSH term(s) Amyotrophic Lateral Sclerosis ; Frontotemporal Dementia ; Humans ; Mutation/genetics ; RNA ; RNA-Binding Protein FUS
    Chemical Substances FUS protein, human ; RNA-Binding Protein FUS ; RNA (63231-63-0)
    Language English
    Publishing date 2021-01-28
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2031313-5
    ISSN 1471-0080 ; 1471-0072
    ISSN (online) 1471-0080
    ISSN 1471-0072
    DOI 10.1038/s41580-021-00338-w
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  5. Article ; Online: Protein interactions in liquid-liquid phase separation.

    Fuxreiter, Monika

    Journal of molecular biology

    2021  Volume 434, Issue 1, Page(s) 167388

    MeSH term(s) Biophysical Phenomena ; Heat-Shock Proteins, Small/chemistry ; Heat-Shock Proteins, Small/metabolism ; Leukemia/genetics ; Phase Transition ; Proteins/chemistry ; Proteins/metabolism ; RNA/chemistry ; RNA/metabolism ; RNA Polymerase II/chemistry ; RNA Polymerase II/metabolism ; Transcriptional Elongation Factors/chemistry ; Transcriptional Elongation Factors/genetics ; Transcriptional Elongation Factors/metabolism
    Chemical Substances ELL protein, human ; Heat-Shock Proteins, Small ; Proteins ; Transcriptional Elongation Factors ; RNA (63231-63-0) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-12-03
    Publishing country England
    Document type Introductory Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167388
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  6. Article ; Online: Fuzzy protein theory for disordered proteins.

    Fuxreiter, Monika

    Biochemical Society transactions

    2020  Volume 48, Issue 6, Page(s) 2557–2564

    Abstract: Why proteins are fuzzy? Constant adaptation to the cellular environment requires a wide range of changes in protein structure and interactions. Conformational ensembles of disordered proteins in particular exhibit large shifts to activate or inhibit ... ...

    Abstract Why proteins are fuzzy? Constant adaptation to the cellular environment requires a wide range of changes in protein structure and interactions. Conformational ensembles of disordered proteins in particular exhibit large shifts to activate or inhibit alternative pathways. Fuzziness is critical for liquid-liquid phase separation and conversion of biomolecular condensates into fibrils. Interpretation of these phenomena presents a challenge for the classical structure-function paradigm. Here I discuss a multi-valued formalism, based on fuzzy logic, which can be applied to describe complex cellular behavior of proteins.
    MeSH term(s) Amyloid/chemistry ; Cytoskeleton/metabolism ; Escherichia coli/metabolism ; Fuzzy Logic ; Humans ; Intrinsically Disordered Proteins/chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping ; Proteins/chemistry ; Proteins/physiology ; Proto-Oncogene Proteins c-mdm2/chemistry ; Signal Transduction ; Tumor Suppressor Protein p53/chemistry
    Chemical Substances Amyloid ; Intrinsically Disordered Proteins ; Proteins ; TP53 protein, human ; Tumor Suppressor Protein p53 ; MDM2 protein, human (EC 2.3.2.27) ; Proto-Oncogene Proteins c-mdm2 (EC 2.3.2.27)
    Language English
    Publishing date 2020-11-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/BST20200239
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Classifying the Binding Modes of Disordered Proteins.

    Fuxreiter, Monika

    International journal of molecular sciences

    2020  Volume 21, Issue 22

    Abstract: Disordered proteins often act as interaction hubs in cellular pathways, via the specific recognition of a distinguished set of partners. While disordered regions can adopt a well-defined conformation upon binding, the coupled folding to binding model ... ...

    Abstract Disordered proteins often act as interaction hubs in cellular pathways, via the specific recognition of a distinguished set of partners. While disordered regions can adopt a well-defined conformation upon binding, the coupled folding to binding model does not explain how interaction versatility is achieved. Here, I present a classification scheme for the binding modes of disordered protein regions, based on their conformational heterogeneity in the bound state. Binding modes are defined as (i)
    MeSH term(s) Intrinsically Disordered Proteins/chemistry ; Models, Molecular ; Protein Folding
    Chemical Substances Intrinsically Disordered Proteins
    Language English
    Publishing date 2020-11-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21228615
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  8. Article ; Online: Towards sequence-based principles for protein phase separation predictions.

    Vendruscolo, Michele / Fuxreiter, Monika

    Current opinion in chemical biology

    2023  Volume 75, Page(s) 102317

    Abstract: The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the ... ...

    Abstract The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
    MeSH term(s) Amyloid ; Amino Acid Sequence ; Cell Physiological Phenomena
    Chemical Substances Amyloid
    Language English
    Publishing date 2023-05-17
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2023.102317
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  9. Article ; Online: Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions.

    Fuxreiter, Monika

    Molecules (Basel, Switzerland)

    2018  Volume 23, Issue 11

    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, ... ...

    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.
    MeSH term(s) Algorithms ; Artificial Intelligence ; Fuzzy Logic ; Proteins/chemistry ; Stochastic Processes ; Structure-Activity Relationship
    Chemical Substances Proteins
    Language English
    Publishing date 2018-11-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules23113008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Fuzziness in Protein Interactions-A Historical Perspective.

    Fuxreiter, Monika

    Journal of molecular biology

    2018  Volume 430, Issue 16, Page(s) 2278–2287

    Abstract: The proposal that coupled folding to binding is not an obligatory mechanism for intrinsically disordered (ID) proteins was put forward 10 years ago. The notion of fuzziness implies that conformational heterogeneity can be maintained upon interactions of ... ...

    Abstract The proposal that coupled folding to binding is not an obligatory mechanism for intrinsically disordered (ID) proteins was put forward 10 years ago. The notion of fuzziness implies that conformational heterogeneity can be maintained upon interactions of ID proteins, which has a functional impact either on regulated assembly or activity of the corresponding complexes. Here I review how the concept has evolved in the past decade, via increasing experimental data providing insights into the mechanisms, pathways and regulatory modes. The effects of structural diversity and transient contacts on protein assemblies have been collected and systematically analyzed (Fuzzy Complexes Database, http://protdyn-database.org). Fuzziness has also been exploited as a framework to decipher molecular organization of higher-order protein structures. Quantification of conformational heterogeneity opens exciting future perspectives for drug discovery from small molecule-ID protein interactions to supramolecular assemblies.
    MeSH term(s) Biophysical Phenomena ; Databases, Protein ; Fuzzy Logic ; Gene Expression Regulation ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Models, Molecular ; Protein Binding ; Protein Folding
    Chemical Substances Intrinsically Disordered Proteins
    Language English
    Publishing date 2018-02-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2018.02.015
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