Hugo Van Ingen

Hugo Van Ingen
Utrecht University · NMR Group

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Research items (50)
Article
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Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E...
Article
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NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, the...
Article
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USP7 is a highly abundant deubiquitinating enzyme (DUB), involved in cellular processes including DNA damage response and apoptosis. USP7 has an unusual catalytic mechanism, where the low intrinsic activity of the catalytic domain (CD) increases when the C-terminal Ubl domains (Ubl45) fold onto the CD, allowing binding of the activating C-terminal...
Article
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USP7 is a highly abundant deubiquitinating enzyme (DUB), involved in cellular processes including DNA damage response and apoptosis. USP7 has an unusual catalytic mechanism, where the low intrinsic activity of the catalytic domain (CD) increases when the C-terminal Ubl domains (Ubl45) fold onto the CD, allowing binding of the activating C-terminal...
Article
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The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the...
Chapter
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Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understandi...
Article
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Cells organize their actions partly through tightly controlled protein-protein interactions - collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the protein-protein interactions in intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. Fro...
Article
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Genome replication, transcription and repair require the assembly/disassembly of the nucleosome. Histone chaperones are regulators of this process by preventing formation of non-nucleosomal histone-DNA complexes. Aprataxin and polynucleotide kinase like factor (APLF) is a non-homologous end-joining (NHEJ) DNA repair factor that possesses histone ch...
Article
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Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conf...
Article
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Chromatin function depends on a dense network of interactions between nucleosomes and wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Here, we show that the structure, dynamics and interactions of nucle...
Article
Chromatin function depends on a dense network of interactions between nucleosomes and wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Here, we show that the structure, dynamics and interactions of nucle...
Article
Magnetic inequivalence of nuclear spins is well known to cause additional splittings that complicate spectral analysis. Here, we present an extraordinary case of magnetic inequivalence, manifested in the 13-spin system of a (13)C,(15)N-labeled trimethylated amine. All methyl group protons are chemically equivalent due to the molecular symmetry, but...
Article
Proteins come together in macromolecular assemblies, recognizing and binding to each other through their structures, and operating on their substrates through their motions. Detailed characterization of these processes is particularly suited to NMR, a high-resolution technique sensitive to structure, dynamics, and interactions. Advances in isotope-...
Article
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Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nic...
Article
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Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic information can, however, be difficult to acquire for interesting systems such as high molecular weight and multi-subunit complexes. For these, low-resolution and/or sparse data from a variety of source...
Article
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Background Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for...
Article
Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells...
Article
Strong (1)H-(1)H coupling can significantly reduce the accuracy of (1)J(CH) measured from frequency differences in coupled HSQC spectra. Although accurate (1)J(CH) values can be extracted from spectral simulation, it would be more convenient if the same accurate (1)J(CH) values can be obtained experimentally. Furthermore, simulations reach their li...
Article
J couplings are essential for measuring RDCs (residual dipolar couplings), now routinely used to deduce molecular structure and dynamics of glycans and proteins. Accurate measurement of (1)J(CH) is critical for RDCs to reflect the true structure and dynamics in the molecule of interest. We report noticeable discrepancies between (1)J(CH) values mea...
Article
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Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility group nucleosomal (HMGN) protein family that regulates various chromatin functions, including transcription. Here, we report the architecture...
Article
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Leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1), one of the most widely spread immune receptors, attenuates immune cell activation when bound to specific sites in collagen. The collagen-binding domain of LAIR-1 is homologous to that of glycoprotein VI (GPVI), a collagen receptor crucial for platelet activation. Because LAIR-1 and GPVI...
Article
Marginally and transiently populated conformational states of biomolecules can play important functional roles in biochemical processes. It is of significant interest, therefore, to develop tools for characterizing the structural and dynamical properties of these excited states. One recent development has been the emergence of spin-state-selective...
Article
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Pax-8 is a transcription factor belonging to the PAX genes superfamily and its crucial role has been proven both in embryo and in the adult organism. Pax-8 activity is regulated via a redox-based mechanism centered on the glutathionylation of specific cysteines in the N-terminal region (Cys45 and Cys57). These residues belong to a highly evolutiona...
Article
Trimethylation of lysine residue K4 of histone H3 (H3K4me3) strongly correlates with active promoters for RNA polymerase II-transcribed genes. Several reader proteins, including the basal transcription factor TFIID, for this nucleosomal mark have been identified. Its TAF3 subunit specifically binds the H3K4me3 mark via its conserved plant homeodoma...
Article
The co-repressor Sin3 is the essential scaffold protein of the Sin3/HDAC co-repressor complex, which is recruited to the DNA by a diverse group of transcriptional repressors, targeting genes involved in the regulation of the cell cycle, proliferation and differentiation. Sin3 contains four repeats commonly denoted as paired amphipathic helix (PAH1-...
Article
Protein conformations that are only marginally populated often play important roles as intermediate states in many processes such as ligand binding, enzyme catalysis, allostery, and protein folding. An NMR method is presented that can give valuable information about the structure of these "excited states" by measuring the relative position of excha...
Article
Proefschrift Radboud Universiteit Nijmegen. Met bibliogr., lit. opg. - Met samenvatting in het Nederlands.
Article
Sin3 forms the scaffold for a multiprotein corepressor complex that silences transcription via the action of histone deacetylases. Sin3 is recruited to the DNA by several DNA binding repressors, such as the helix-loop-helix proteins of the Mad family. Here, we elaborate on the Mad-Sin3 interaction based on a binding study, solution structure, and d...
Article
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Various chimeras of the ErbB1-specific ligands epidermal growth factor (EGF) and transforming growth factor-alpha (TGFalpha) display an enlarged repertoire as activators of ErbB2.ErbB3 heterodimers. Mutational analysis indicated that particularly residues in the N terminus and B-loop region of these ligands are involved in the broadened receptor sp...
Article
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We present a 3D double sensitivity enhanced X-filtered homonuclear TOCSY-TOCSY experiment for the assignment of unlabeled molecules complexed to labeled protein- or nucleic acid-domains. The resulting spectrum is clean, can be measured in a reasonable amount of time and allows for increased resolution of overlapping resonances when compared to 2D m...
Article
Many heteronuclear NMR experiments employ decoupling to collapse the heteronuclear multiplet, using decoupling schemes with a periodic phase modulation like WALTZ, MLEV, or GARP. Because of the periodic nature of these schemes, cycling sidebands are generated, whose intensity can be strongly reduced by decoupling asynchronously. We show that the mo...