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  1. Article: A dive into the unknome.

    Rappsilber, Juri

    Trends in genetics : TIG

    2023  Volume 40, Issue 1, Page(s) 15–16

    Abstract: We may never understand the function of all genes, findings by Freeman, Munro and colleagues suggest, unless we rethink our approaches. They make a thorough attempt at quantifying the unknownness of protein-coding genes and experimentally prove that many ...

    Abstract We may never understand the function of all genes, findings by Freeman, Munro and colleagues suggest, unless we rethink our approaches. They make a thorough attempt at quantifying the unknownness of protein-coding genes and experimentally prove that many neglected genes hold the seed of important discoveries.
    MeSH term(s) Genes
    Language English
    Publishing date 2023-11-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2023.10.011
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2272: Show issues Location:
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  2. Article ; Online: Protein structure dynamics by crosslinking mass spectrometry.

    Chen, Zhuo Angel / Rappsilber, Juri

    Current opinion in structural biology

    2023  Volume 80, Page(s) 102599

    Abstract: Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can ...

    Abstract Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.
    MeSH term(s) Cross-Linking Reagents/chemistry ; Proteins/chemistry ; Mass Spectrometry ; Protein Conformation
    Chemical Substances Cross-Linking Reagents ; Proteins
    Language English
    Publishing date 2023-04-25
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2023.102599
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    Zs.A 3206: Show issues Location:
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  3. Article ; Online: Cleavable Cross-Linkers Redefined by a Novel MS³‑Trigger Algorithm

    Kolbowski, Lars / Fischer, Lutz / Rappsilber, Juri

    Analytical Chemistry. 2023 Oct. 10, v. 95, no. 42 p.15461-15464

    2023  

    Abstract: Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a MS³ ...

    Abstract Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a MS³-based approach for identifying cross-linked peptides. However, MS² (MS/MS)-based approaches currently outperform approaches utilizing MS³. We show here that the sensitivity and specificity of triggering MS³ have been hampered algorithmically. Our four-step MS³-trigger algorithm greatly outperformed currently employed methods and comes close to reaching the theoretical limit.
    Keywords algorithms ; analytical chemistry ; crosslinking ; mass spectrometry ; peptides ; structural biology
    Language English
    Dates of publication 2023-1010
    Size p. 15461-15464.
    Publishing place American Chemical Society
    Document type Article ; Online
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c01673
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  4. Article ; Online: Cleavable Cross-Linkers Redefined by a Novel MS

    Kolbowski, Lars / Fischer, Lutz / Rappsilber, Juri

    Analytical chemistry

    2023  Volume 95, Issue 42, Page(s) 15461–15464

    Abstract: Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a ... ...

    Abstract Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a MS
    MeSH term(s) Tandem Mass Spectrometry/methods ; Cross-Linking Reagents/chemistry ; Peptides/chemistry ; Algorithms ; Molecular Biology
    Chemical Substances Cross-Linking Reagents ; Peptides
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c01673
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
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  5. Article ; Online: Leveraging crosslinking mass spectrometry in structural and cell biology.

    Graziadei, Andrea / Rappsilber, Juri

    Structure (London, England : 1993)

    2021  Volume 30, Issue 1, Page(s) 37–54

    Abstract: Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein ... ...

    Abstract Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein structures proposed by other methods and have helped derive models of protein complexes by integrative structural biology approaches. The use of crosslinking-MS in integrative approaches is underpinned by progress in estimating error rates in crosslinking-MS data and in combining these data with other information. The flexible and high-throughput nature of crosslinking-MS has allowed it to complement the ongoing resolution revolution in electron microscopy by providing system-wide residue-residue distance restraints, especially for flexible regions or systems. Here, we review how crosslinking-MS information has been leveraged in structural model validation and integrative modeling. Crosslinking-MS has also been a key technology for cell biology studies and structural systems biology where, in conjunction with cryoelectron tomography, it can provide structural and mechanistic insights directly in situ.
    MeSH term(s) Cross-Linking Reagents/chemistry ; Mass Spectrometry/methods ; Microscopy, Electron ; Models, Molecular ; Protein Binding ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Cross-Linking Reagents ; Proteins
    Language English
    Publishing date 2021-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2021.11.007
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    Zs.A 4141: Show issues Location:
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  6. Article ; Online: Differentiation granules, a dynamic regulator of T. brucei development.

    Cayla, Mathieu / Spanos, Christos / McWilliam, Kirsty / Waskett, Eliza / Rappsilber, Juri / Matthews, Keith R

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2972

    Abstract: Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles ...

    Abstract Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles composed of poly-A RNA and proteins. The African trypanosome Trypanosoma brucei is exquisitely sensitive to well-defined environmental stimuli that trigger cellular adaptations through differentiation events that characterise its complex life cycle. The parasite has been shown to form stress granules in vitro, and it has been proposed that such a stress response could have been repurposed to enable differentiation and facilitate parasite transmission. Therefore, we explored the composition and positional dynamics of membraneless granules formed in response to starvation stress and during differentiation in the mammalian host between the replicative slender and transmission-adapted stumpy forms. We find that T. brucei differentiation does not reflect the default response to environmental stress. Instead, the developmental response of the parasites involves a specific and programmed hierarchy of membraneless granule assembly, with distinct components and regulation by protein kinases such as TbDYRK, that are required for the parasite to successfully progress through its life cycle development and prepare for transmission.
    MeSH term(s) Animals ; Trypanosoma ; Trypanosoma brucei brucei/genetics ; Trypanosoma brucei brucei/metabolism ; Mammals
    Language English
    Publishing date 2024-04-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47309-1
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  7. Article ; Online: Ki-67 is necessary during DNA replication for fork protection and genome stability.

    Stamatiou, Konstantinos / Huguet, Florentin / Serapinas, Lukas V / Spanos, Christos / Rappsilber, Juri / Vagnarelli, Paola

    Genome biology

    2024  Volume 25, Issue 1, Page(s) 105

    Abstract: Background: The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regulate both the composition of the ... ...

    Abstract Background: The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin organisation and gene transcription. However, how the different roles for Ki-67 across the cell cycle are regulated and coordinated remain poorly understood. The progress towards understanding Ki-67 function have been limited by the tools available to deplete the protein, coupled to its abundance and fluctuation during the cell cycle.
    Results: Here, we use a doxycycline-inducible E3 ligase together with an auxin-inducible degron tag to achieve a rapid, acute and homogeneous degradation of Ki-67 in HCT116 cells. This system, coupled with APEX2 proteomics and phospho-proteomics approaches, allows us to show that Ki-67 plays a role during DNA replication. In its absence, DNA replication is severely delayed, the replication machinery is unloaded, causing DNA damage that is not sensed by the canonical pathways and dependent on HUWE1 ligase. This leads to defects in replication and sister chromatids cohesion, but it also triggers an interferon response mediated by the cGAS/STING pathway in all the cell lines tested.
    Conclusions: We unveil a new function of Ki-67 in DNA replication and genome maintenance that is independent of its previously known role in mitosis and gene regulation.
    MeSH term(s) Humans ; DNA Damage ; DNA Replication ; Genomic Instability ; HCT116 Cells ; Ki-67 Antigen/metabolism ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Ki-67 Antigen ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; MKI67 protein, human
    Language English
    Publishing date 2024-04-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-024-03243-5
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  8. Article ; Online: Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning.

    Stahl, Kolja / Graziadei, Andrea / Dau, Therese / Brock, Oliver / Rappsilber, Juri

    Nature biotechnology

    2023  Volume 41, Issue 12, Page(s) 1810–1819

    Abstract: While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the ...

    Abstract While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its network architecture. By employing sparse experimental contacts as anchor points, AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets. We confirm this experimentally by using the noncanonical amino acid photo-leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. The program can predict distinct conformations of proteins on the basis of the distance restraints provided, demonstrating the value of experimental data in driving protein structure prediction. The noise-tolerant framework for integrating data in protein structure prediction presented here opens a path to accurate characterization of protein structures from in-cell data.
    MeSH term(s) Protein Conformation ; Deep Learning ; Proteins/metabolism ; Algorithms ; Mass Spectrometry
    Chemical Substances Proteins
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-023-01704-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2167: Show issues Location:
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  9. Book ; Online ; Thesis: Mass spectrometry of crosslinked peptides

    Kolbowski, Lars Bernhard [Verfasser] / Rappsilber, Juri [Akademischer Betreuer] / Rappsilber, Juri [Gutachter] / Leitner, Alexander [Gutachter]

    2023  

    Author's details Lars Bernhard Kolbowski ; Gutachter: Juri Rappsilber, Alexander Leitner ; Betreuer: Juri Rappsilber
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Technische Universität Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
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  10. Book ; Online ; Thesis: The role of p53 on metabolic flexibility of the liver

    Oster, Moritz André [Verfasser] / Rappsilber, Juri [Akademischer Betreuer] / Rappsilber, Juri [Gutachter] / Schupp, Michael [Gutachter]

    2023  

    Author's details Moritz André Oster ; Gutachter: Juri Rappsilber, Michael Schupp ; Betreuer: Juri Rappsilber
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Technische Universität Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
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