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  1. Book: Protein dimerization and oligomerization in biology

    Matthews, Jacqueline M.

    (Advances in experimental medicine and biology ; 747)

    2012  

    Abstract: This volume has a strong focus on homo-oligomerization, which is surprisingly common. However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so ...

    Author's details ed. by Jacqueline M. Matthews
    Series title Advances in experimental medicine and biology ; 747
    Collection
    Abstract "This volume has a strong focus on homo-oligomerization, which is surprisingly common. However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so this volume also covers many aspects of hetero-oligomerization"--Provided by publisher
    Keywords Protein Multimerization ; Protein Folding
    Language English
    Size XIV, 170 S. : Ill., graph. Darst.
    Publisher Springer u.a.
    Publishing place New York
    Publishing country United States
    Document type Book
    Note Includes bibliographical references and index ; Machine generated contents note: Dimers, Oligomers, Everywhere.- The Detection and Quantitation of Protein Oligomerization -- Computational and Structural Characterisation of Protein Associations.- Death by Caspase Dimerization -- The Relationship between Oligomeric State and Protein Function -- Oligonucleotide Binding Proteins: The Occurrence of Dimer and Multimer Formation -- Homo and Heterodimerization in Transcriptional Regulation -- Oligomerization at the Membrane: Potassium Channel Structure and Function -- Implications of 3D Domain Swapping for Protein Folding, Misfolding and Function -- From artificial antibodies to nanosprings: The biophysical properties of repeat proteins
    HBZ-ID HT017330326
    ISBN 978-1-4614-3228-9 ; 1-4614-3228-6
    Database Catalogue ZB MED Medicine, Health

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  2. Article: Protein-protein interactions. Preface.

    Matthews, Jacqueline M

    Advances in experimental medicine and biology

    2012  Volume 747, Page(s) v–vi

    MeSH term(s) Protein Multimerization ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/metabolism ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism
    Chemical Substances Protein Subunits ; Proteins
    Language English
    Publishing date 2012
    Publishing country United States
    Document type Introductory Journal Article
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The characterization of protein interactions – what, how and how much?

    Walport, Louise J. / Low, Jason K. K. / Matthews, Jacqueline M. / Mackay, Joel P.

    Chemical Society reviews. 2021 Nov. 15, v. 50, no. 22

    2021  

    Abstract: Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each ... ...

    Abstract Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each approach has its own advantages and limitations, and it can be difficult for the newcomer to determine which methodology would best suit their system. This review provides an overview of many of the techniques most widely used to identify protein partners, assess stoichiometry and binding affinity, and determine low-resolution models for complexes. Key methods covered include: yeast two-hybrid analysis, affinity purification mass spectrometry and proximity labelling to identify partners; size-exclusion chromatography, scattering methods, native mass spectrometry and analytical ultracentrifugation to estimate stoichiometry; isothermal titration calorimetry, biosensors and fluorometric methods (including microscale thermophoresis, anisotropy/polarisation, resonance energy transfer, AlphaScreen, and differential scanning fluorimetry) to measure binding affinity; and crosslinking and hydrogen-deuterium exchange mass spectrometry to probe the structure of complexes.
    Keywords anisotropy ; biochemical compounds ; biosensors ; calorimetry ; crosslinking ; energy transfer ; fluorometry ; gel chromatography ; mass spectrometry ; stoichiometry ; titration ; two hybrid system techniques ; ultracentrifugation
    Language English
    Dates of publication 2021-1115
    Size p. 12292-12307.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/d1cs00548k
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Binding and folding in transcriptional complexes.

    Smith, Ngaio C / Kuravsky, Mikhail / Shammas, Sarah L / Matthews, Jacqueline M

    Current opinion in structural biology

    2020  Volume 66, Page(s) 156–162

    Abstract: Transcription factors are among the classes of proteins with the highest levels of disorder. Investigation of these regulatory proteins is uncovering not just the mechanisms that underlie gene regulation, but relationships that apply to all intrinsically ...

    Abstract Transcription factors are among the classes of proteins with the highest levels of disorder. Investigation of these regulatory proteins is uncovering not just the mechanisms that underlie gene regulation, but relationships that apply to all intrinsically disordered proteins. Recent studies confirm that binding does not necessarily induce folding but that when it does, it tends to follow induced fit mechanisms. Other work emphasises the importance of electrostatics to interactions involving intrinsically disordered proteins, and roles of intrinsic disorder in phase transitions. All these features help direct transcription factors to target sites in the genome to upregulate or downregulate transcription.
    MeSH term(s) Intrinsically Disordered Proteins/metabolism ; Protein Binding ; Protein Folding ; Transcription Factors
    Chemical Substances Intrinsically Disordered Proteins ; Transcription Factors
    Language English
    Publishing date 2020-11-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2020.10.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors.

    Smith, Ngaio C / Matthews, Jacqueline M

    Current opinion in structural biology

    2016  Volume 38, Page(s) 68–74

    Abstract: Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ... ...

    Abstract Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ability to discriminate target and variant non-target DNA sequences. Here, we summarise established mechanisms of protein-DNA recognition, as specified by both macromolecules. We also review recent advances in the fields of genome binding, molecular dynamics and biomolecular interaction studies that bring us close to a full understanding of how eukaryotic transcription factors find and target DNA in vivo to form functional centres of gene regulation through networks of protein-protein and protein-DNA interactions.
    Language English
    Publishing date 2016-06
    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.2016.05.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The characterization of protein interactions - what, how and how much?

    Walport, Louise J / Low, Jason K K / Matthews, Jacqueline M / Mackay, Joel P

    Chemical Society reviews

    2021  Volume 50, Issue 22, Page(s) 12292–12307

    Abstract: Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each ... ...

    Abstract Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each approach has its own advantages and limitations, and it can be difficult for the newcomer to determine which methodology would best suit their system. This review provides an overview of many of the techniques most widely used to identify protein partners, assess stoichiometry and binding affinity, and determine low-resolution models for complexes. Key methods covered include: yeast two-hybrid analysis, affinity purification mass spectrometry and proximity labelling to identify partners; size-exclusion chromatography, scattering methods, native mass spectrometry and analytical ultracentrifugation to estimate stoichiometry; isothermal titration calorimetry, biosensors and fluorometric methods (including microscale thermophoresis, anisotropy/polarisation, resonance energy transfer, AlphaScreen, and differential scanning fluorimetry) to measure binding affinity; and crosslinking and hydrogen-deuterium exchange mass spectrometry to probe the structure of complexes.
    MeSH term(s) Chromatography, Affinity ; Mass Spectrometry ; Proteins
    Chemical Substances Proteins
    Language English
    Publishing date 2021-11-15
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/d1cs00548k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book: Protein dimerization and oligomerization in biology

    Matthews, Jacqueline M

    (Advances in experimental medicine and biology ; v. 747)

    2012  

    Abstract: This volume has a strong focus on homo-oligomerization, which is surprisingly common. However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so ...

    Author's details edited by Jacqueline M. Matthews
    Series title Advances in experimental medicine and biology ; v. 747
    Abstract "This volume has a strong focus on homo-oligomerization, which is surprisingly common. However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so this volume also covers many aspects of hetero-oligomerization"--Provided by publisher.
    MeSH term(s) Protein Multimerization ; Protein Folding
    Language English
    Size xiv, 170 p. :, ill., port.
    Publisher Springer Science+Business Media ; Landes Bioscience
    Publishing place New York ; Austin, Tex
    Document type Book
    ISBN 9781461432289 ; 1461432286
    Database Catalogue of the US National Library of Medicine (NLM)

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  8. Article ; Online: Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification.

    Smith, Ngaio C / Wilkinson-White, Lorna E / Kwan, Ann H Y / Trewhella, Jill / Matthews, Jacqueline M

    Journal of structural biology: X

    2020  Volume 5, Page(s) 100043

    Abstract: The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their ... ...

    Abstract The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.
    Language English
    Publishing date 2020-12-15
    Publishing country United States
    Document type Journal Article
    ISSN 2590-1524
    ISSN (online) 2590-1524
    DOI 10.1016/j.yjsbx.2020.100043
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The molecular details of a novel phosphorylation-dependent interaction between MRN and the SOSS complex.

    El-Kamand, Serene / Adams, Mark N / Matthews, Jacqueline M / Du Plessis, Mar-Dean / Crossett, Ben / Connolly, Angela / Breen, Natasha / Dudley, Alexander / Richard, Derek J / Gamsjaeger, Roland / Cubeddu, Liza

    Protein science : a publication of the Protein Society

    2023  Volume 32, Issue 10, Page(s) e4782

    Abstract: The repair of double-strand DNA breaks (DSBs) by homologous recombination is crucial in the maintenance of genome integrity. While the key role of the Mre11-Rad50-Nbs1 (MRN) complex in repair is well known, hSSB1 (SOSSB and OBFC2B), one of the main ... ...

    Abstract The repair of double-strand DNA breaks (DSBs) by homologous recombination is crucial in the maintenance of genome integrity. While the key role of the Mre11-Rad50-Nbs1 (MRN) complex in repair is well known, hSSB1 (SOSSB and OBFC2B), one of the main components of the sensor of single-stranded DNA (SOSS) protein complex, has also been shown to rapidly localize to DSB breaks and promote repair. We have previously demonstrated that hSSB1 binds directly to Nbs1, a component of the MRN complex, in a DNA damage-independent manner. However, recruitment of the MRN complex has also been demonstrated by an interaction between Integrator Complex Subunit 3 (INTS3; also known as SOSSA), another member of the SOSS complex, and Nbs1. In this study, we utilize a combined approach of in silico, biochemical, and functional experiments to uncover the molecular details of INTS3 binding to Nbs1. We demonstrate that the forkhead-associated domain of Nbs1 interacts with INTS3 via phosphorylation-dependent binding to INTS3 at Threonine 592, with contributions from Serine 590. Based on these data, we propose a model of MRN recruitment to a DSB via INTS3.
    MeSH term(s) Phosphorylation ; MRE11 Homologue Protein/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; DNA Breaks, Double-Stranded ; DNA Repair
    Chemical Substances MRE11 Homologue Protein (EC 3.1.-) ; Cell Cycle Proteins ; Nuclear Proteins
    Language English
    Publishing date 2023-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4782
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3407: Show issues Location:
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  10. Article ; Online: mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome.

    Low, Jason K K / Patel, Karishma / Jones, Natasha / Solomon, Paul / Norman, Alexander / Maxwell, Joshua W C / Pachl, Petr / Matthews, Jacqueline M / Payne, Richard J / Passioura, Toby / Suga, Hiroaki / Walport, Louise J / Mackay, Joel P

    The Journal of biological chemistry

    2023  Volume 299, Issue 12, Page(s) 105482

    Abstract: Bromodomains (BDs) regulate gene expression by recognizing protein motifs containing acetyllysine. Although originally characterized as histone-binding proteins, it has since become clear that these domains interact with other acetylated proteins, ... ...

    Abstract Bromodomains (BDs) regulate gene expression by recognizing protein motifs containing acetyllysine. Although originally characterized as histone-binding proteins, it has since become clear that these domains interact with other acetylated proteins, perhaps most prominently transcription factors. The likely transient nature and low stoichiometry of such modifications, however, has made it challenging to fully define the interactome of any given BD. To begin to address this knowledge gap in an unbiased manner, we carried out mRNA display screens against a BD-the N-terminal BD of BRD3-using peptide libraries that contained either one or two acetyllysine residues. We discovered peptides with very strong consensus sequences and with affinities that are significantly higher than typical BD-peptide interactions. X-ray crystal structures also revealed modes of binding that have not been seen with natural ligands. Intriguingly, however, our sequences are not found in the human proteome, perhaps suggesting that strong binders to BDs might have been selected against during evolution.
    MeSH term(s) Humans ; Proteome/metabolism ; Transcription Factors/metabolism ; Protein Domains ; Amino Acid Motifs ; Peptides/metabolism ; Protein Binding ; Acetylation
    Chemical Substances Proteome ; Transcription Factors ; Peptides
    Language English
    Publishing date 2023-11-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.105482
    Database MEDical Literature Analysis and Retrieval System OnLINE

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