dr. H. (Hugo) van Ingen
h.vaningen@uu.nl
Gegenereerd op 2018-05-25 03:44:49


Profile

Research in my group focusses on the processes operating on the smallest units of chromatin, called nucleosomes. Using a combination of state-of-the-art NMR, biochemical and computational methods, we aim to decipher the molecular basis of chromatin function at atomic detail.

Involved in the following study programme(s)
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Curriculum vitae

Scientific:

  • since 2017: assistant professor NMR Spectroscopy, University Utrecht
  • 2014-2017: tenure-track assistant professor Macromolecular Biochemistry, University Leiden
  • 2011-2014: post-doc NMR Spectroscopy, University Utrecht
  • 2008-2010: post-doc NMR groep Lewis Kay, University of Toronto, Canada
  • 2006-2008: post-doc with Rolf Boelens, NMR Spectroscopy, University Utrecht
  • 2001-2005: PhD candidate with Geerten Vuister & Cees Hilbers, Biophysical Chemistry, Radboud University Nijmegen

Teaching:

  • 2003-2005: curriculum development Chemistry, Molecular Life Sciences and Natural Sciences, Radboud University Nijmegen
  • 2001-2002: high-shool teacher Chemistry and Physics

Education:

  • 2004-2006: qualification University teaching (BKO), Radboud University Nijmegen
  • 2000: qualification high-school teacher Chemistry, Radboud University Nijmegen
  • 1994-1999: BSc & MSc Chemistry, Radboud University Nijmegen
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You can find a complete list via my ORCID athor-id: http://orcid.org/0000-0002-0808-3811

All publications
  2017 - Scholarly publications
Kitevski-Leblanc, Julianne, Fradet-Turcotte, Amélie, Kukic, Predrag, Wilson, Marcus D., Portella, Guillem, Yuwen, Tairan, Panier, Stephanie, Duan, Shili, Canny, Marella D., Van Ingen, Hugo, Arrowsmith, Cheryl H., Rubinstein, John L., Vendruscolo, Michele, Durocher, Daniel & Kay, Lewis E (13.04.2017). The rnf168 paralog rnf169 defines a new class of ubiquitylated histone reader involved in the response to dna damage. eLife, 6.
le Paige, Ulric B., Smits, Bauke, t Hart, Peter, Lefeber, Fons, Martin, Nathaniel I. & van Ingen, Hugo (01.05.2017). Weak coupling between magnetically inequivalent spins - The deceptively simple, complicated spectrum of a 13C-labeled trimethylated amine. Journal of Magnetic Resonance, 278, (pp. 96-103) (8 p.).
  2014 - Scholarly publications
Van Ingen, Hugo & Bonvin, Alexandre M J J (01.01.2014). Information-driven modeling of large macromolecular assemblies using NMR data. Journal of Magnetic Resonance, 241 (1), (pp. 103-114) (12 p.).
Khan, Fariha, Daniëls, Mark A., Folkers, Gert E., Boelens, Rolf, Saqlan Naqvi, S. M. & Van Ingen, Hugo (01.01.2014). Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein - Implications for its RNA chaperone function. Nucleic Acids Research, 42 (13), (pp. 8705-8718) (14 p.).
  2013 - Scholarly publications
Yu, B., van Ingen, H. & Freedberg, D.I. (2013). Constant time INEPT CT-HSQC (CTi-CT-HSQC) – A new NMR method to measure accurate one-bond J and RDCs with strong 1H–1H couplings in natural abundance. Journal of Magnetic Resonance, 228, (pp. 159-166) (8 p.).
Spruijt, C.G., Gnerlich, F., Smits, A.H., Pfaffeneder, T., Jansen, P.W.T.C., Bauer, C., Munzel, M., Wagner, M., Müller, M., Khan, F., Eberl, H.C., Mensinga, A., Brinkman, A.B., Lephikov, K., Muller, U., Walter, J., Boelens, R., van Ingen, H., Leonhardt, H. & Carell, T. (2013). Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell, 152, (pp. 1146-1159) (14 p.).
van Nuland, R., van Schaik, F.M.A., Simonis, M.J., Cuppen, E.P.J.G., Boelens, R., Timmers, H.T.M. & van Ingen, H. (2013). Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain. Epigenetics and Chromatin, 6, (pp. 1-12) (12 p.).
  2012 - Scholarly publications
Yu, B., van Ingen, H., Vivekanandan, S., Rademacher, C., Norris, S.E. & Freedberg, D.I. (2012). More accurate 1JCH coupling measurement in the presence of 3JHH strong coupling in in natural abundance. Journal of Magnetic Resonance, 215, (pp. 10-22) (13 p.).
  2011 - Scholarly publications
Kato, Hidenori, Van Ingen, Hugo, Zhou, Bing-Rui, Feng, Hanqiao, Bustin, Michael, Kay, Lewis E & Bai, Yawen (26.07.2011). Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proceedings of the National Academy of Sciences of the United States of America, 108 (30), (pp. 12283-12288) (6 p.).
  2010 - Scholarly publications
Brondijk, T.H.C., de Ruiter, T., Ballering, J., Wienk, H., Lebbink, R.J., van Ingen, H., Boelens, R., Farndale, R.W., Meyaard, L. & Huizinga, E.G. (2010). Crystal structure and collagen-binding site of immune inhibitory receptor LAIR-1: unexpected implications for collagen binding by platelet receptor GPVI. Blood, 115 (7), (pp. 1364-1373) (10 p.).
  2009 - Scholarly publications
van Ingen, Hugo, Korzhnev, Dmitry M & Kay, Lewis E (2009). An analysis of the effects of 1HN-(1)HN dipolar couplings on the measurement of amide bond vector orientations in invisible protein states by relaxation dispersion NMR. Journal of Physical Chemistry B, 113 (29), (pp. 9968-9977) (10 p.).
van Ingen, H., van Schaik, F.M.A., Wienk, H., Rehmann, H., Kruijtzer, J.A.W., Liskamp, R.M.J., Timmers, H.T.M. & Boelens, R. (2009). Recognition of trimethylated K4 of histone H3 by the TFIID subunit TAF3. Journal of Biomolecular Structure and Dynamics, 26, (pp. 909) (1 p.).
  2008 - Scholarly publications
van Ingen, H., van Schaik, F.M.A., Wienk, H., Ballering, J., Rehmann, H., Dechesne, A.C., Kruijzer, J.A.W., Liskamp, R.M.J., Timmers, H.T.M. & Boelens, R. (2008). Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure with Folding & design, 16 (8), (pp. 1245-1256) (12 p.).
Codutti, L., van Ingen, H., Vascotto, C., Fogolari, F., Corazza, A., Tell, G., Quadrifoglio, F., Viglino, P., Boelens, R. & Esposito, G. (28.11.2008). The solution structure of DNA-free Pax-8 paired box domain accounts for redox regulation of transcriptional activity in the Pax protein family. Journal of Biological Chemistry, 283 (48), (pp. 33321-33328) (8 p.).
  2006 - Scholarly publications
Van Ingen, Hugo, Vuister, Geerten W., Wijmenga, Sybren & Tessari, Marco (29.03.2006). CEESY: Characterizing the conformation of unobservable protein states. Journal of the American Chemical Society, 128 (12), (pp. 3856-3857) (2 p.).
van Ingen, Hugo, Baltussen, Maria A.H., Aelen, Jan & Vuister, Geerten W. (28.04.2006). Role of Structural and Dynamical Plasticity in Sin3: The Free PAH2 Domain is a Folded Module in mSin3B. Journal of Molecular Biology, 358 (2), (pp. 485-497) (13 p.).
  2004 - Scholarly publications
Van Ingen, Hugo, Lasonder, Edwin, Jansen, Jacobus F. A., Kaan, Anita M., Spronk, Christian A.E.M., Stunnenberg, Henk G & Vuister, Geerten W. (13.01.2004). Extension of the Binding Motif of the Sin3 Interacting Domain of the Mad Family Proteins. Biochemistry, 43 (1), (pp. 46-54) (9 p.).
  2003 - Scholarly publications
Wingens, Miriam, Walma, Tine, Van Ingen, Hugo, Stortelers, Catelijne, Van Leeuwen, Jeroen E. M., Van Zoelen, Everardus J. J. & Vuister, Geerten W. (03.10.2003). Structural analysis of an epidermal growth factor/transforming growth factor-α chimera with unique ErbB binding specificity. Journal of Biological Chemistry, 278 (40), (pp. 39114-39123) (10 p.).
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Gegenereerd op 2018-05-25 03:44:49

Research in the group of Hugo van Ingen focusses primarily on the molecular basis of chromatin function. We are mostly interested in the interactions of histone proteins and nucleosomes with other chromatin factors such as chaperones, remodelers, or proteins that control epigenetics. We aspire to create a new perspective on protein-nucleosome complexes, afforded by the unique sensitivity of NMR spectroscopy to structure, dynamics and interactions. We apply and develop new approaches to tackle these challenging systems. Next to the nucleosome-focused research, we also engage in collaborative projects ranging from protein interaction studies to NMR theory.

Team

PhD students: Ivan Corbeski (joined with prof. dr. Rolf Boelens), Velten Horn, Ulric le Paige, Clara van Emmerik, Heyi Zhang, Vincenzo Lobbia

Molecular basis of chromatin function

The packaging of DNA into chromatin represents one of the most fundamental layers of cell biology. Chromatin provides the required structural compaction of the DNA to fit in the nucleus, and plays crucial roles in controlling cell fate and protecting genomic integrity. These functions ultimately depend on the interactions of a wide range of proteins with the nucleosome, chromatin’s fundamental building block. But how these proteins recognize, bind and perturb nucleosomes? We aim to answer this question, and to thereby provide a guide for the rational search for new therapeutics.

The nucleosome is a 200,000 Da supramolecular assembly of roughly one part DNA and one part protein. The massive size of the nucleosome calls for state-of-the-art NMR techniques that are tailored for such high-molecular weight systems. These can be applied both in solution, as in a sediment. In solution, the methyl-TROSY approach allows the ultra-sensitive observation of methyl-groups in the proteins to produce beautiful high-quality spectra. In the sediment, we showed, in close collaboration with the Utrecht solid-state NMR group, that 1H-detected solid-state NMR can give high quality spectra of the nucleosome core. In both cases, the NMR signals act as molecular probes to monitor the structure, dynamics and interactions of the nucleosome.

Protein dynamics

Proteins and nucleic acids have inherently dynamic structures. Nature exploits these dynamics to make the impossible possible like tunneling through the activation barrier of a chemcial reaction or ligand binding to the inside of a protein. Conformational dynamics also play a key role in molecular recognition and protein folding. NMR has a a unique set of tools to detect and analyze such motions at atomic resolution over a wide range of time scales. We apply and develop these methods for a better understanding of protein function in general and chromatin in particular.

NMR theory and methodology.

As the saying goes, in theory there is no difference between theory and practice. In practice, this is only true for NMR. Well, at least practically true. NMR is essentially an applied form of quantum mechanics, allowing one to accurately design and simulate experiments.

As it turns out, our group has spent considerable time on analyzing the effects of strong coupling in NMR experiments and spectra. Strong coupling occurs when the J-coupling is small compared to the frequency separation and is probably best known for the roofing effect in AB-type spectra. While strong coupling has been studied intensively since the late 50’s, there are still fundamental and new aspects to be discovered in this fascinating corner of spectroscopy.

Completed projects

Project:
ManiFold 01.09.2012 to 31.08.2016
General project description

ManiFold is an Innovative Doctoral Programme organised by members of the Bijvoet Center for Biomolecular Research and its Graduate Research School, at Utrecht University in the Netherlands. The European Union selected the most innovative doctoral programmes in Europe for funding in the prestigious Marie-Curie Initial Training Networks scheme. ManiFold was the only Innovative Doctoral Programme in the Life Sciences funded in 2012.

 
Role Researcher Funding
EU grant
Project members UU
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Additional functions and activities

secretary of the Dutch Society for the Advancement of Biochemistry and Molecular Biology (NVBMB)

see: www.nvbmb.kncv.nl

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Full name
dr. H. van Ingen Contact details
Nicolaas Bloembergengebouw

Padualaan 12
Room 1.04
3584 CH  UTRECHT
The Netherlands


Phone number (direct) +31 30 253 9934
Phone number (department) +31 30 253 2652
Availability
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Morning
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Visiting address: 
Nicolaas Bloembergengebouw, room 1.04
Padualaan 8, 3584 CH Utrecht
Accessible via Kruyt Building -> first floor -> bridge to Sjoerd Groenman Building
See
https://www.uu.nl/en/research/nmr/contact/route

Postal address:
Universiteit Utrecht, NMR
Padualaan 8, 3584 CH Utrecht


Phone
 (direct)
: +31 30 253 9934

Phone (secr): +31 30 253 2652

Gegenereerd op 2018-05-25 03:44:50
Last updated 04.04.2018