Chemistry Research: Bijvoet Centre for Biomolecular Research

2025

Acquisition of Fc-afucosylation of PfEMP1-specific IgG is age-dependent and associated with clinical protection against malaria

Lopez-Perez, M., Seidu, Z., Larsen, M. D., Wang, W., Nouta, J., Wuhrer, M., Vidarsson, G., Ofori, M. F. & Hviid, L., 2 Jan 2025, In: Nature Communications. 16, 1, 237.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Addition and Oxidation Reactivity of a Pentacoordinate Nickelacyclobutane

Sansores-Paredes, M. L. G., Lutz, M. & Moret, M. E., 6 Mar 2025, In: Chemistry - A European Journal. 31, 14, e202404133.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth

Saunders, H. A. J., van den Berg, C. M., Hoogebeen, R. A., Schweizer, D., Stecker, K. E., Roepman, R., Howes, S. C. & Akhmanova, A., 24 Jan 2025, (E-pub ahead of print) In: Nature Structural and Molecular Biology.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Biomolecular Systems in the Context of Sustainable Applications Studied by NMR

Safeer, A. A., 20 Jan 2025, Utrecht: Utrecht University. 183 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Bisecting N-Acetylglucosamine of the N-Glycan of Immunoglobulin G Does Not Affect Binding to Fc Gamma Receptors

Bosman, G. P., Stoof, I. D., Bastiaansen, H. P., Quarles van Ufford, L., Dobruchowska, J. M., Langenbach, J. W. H., Boruah, B. M., Moremen, K. W., Bentlage, A. E. H., Lissenberg-Thunnissen, S. N., Vidarsson, G. & Boons, G. J., 21 Mar 2025, In: ACS Chemical Biology. 20, 3, p. 680-689 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Cardiomyocyte SORBS2 expression increases in heart failure and regulates integrin interactions and extracellular matrix composition

Timmer, L. T., den Hertog, E., Versteeg, D., Post, H., Verdonschot, J. A. J., Monshouwer-Kloots, J., Kyriakopoulou, E., Perini, I., Koopmans, T., van der Kraak, P., Zentilin, L., Heymans, S. R. B., Vink, A., Giacca, M., Heck, A. J. R. & van Rooij, E., 17 Feb 2025, (E-pub ahead of print) In: Cardiovascular Research. 16 p., cvaf021.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Chemical Synthesis of Oligosaccharides Derived fromStreptococcus pneumoniaeSerotype 35B and D to Investigate Binding of Complement and Serum Factors

Gagarinov, I. A., Liu, L. & Boons, G.-J., 28 Jan 2025, bioRxiv.

Research output: Working paper › Preprint › Academic

File

Chemoenzymatic Synthesis of Glycosphingolipids having an HNK-1 Epitope for Erythrocyte Cell Surface Remodeling

Bunyatov, M. I. & Boons, G.-J., 13 Mar 2025, bioRxiv, 21 p.

Research output: Working paper › Preprint › Academic

File

Chloride, Alkoxide, or Silicon: The Bridging Ligand Dictates the Spin State in Dicobalt Expanded Pincer Complexes

Bienenmann, R. L. M., Asundi, A. S., Lutz, M., Sarangi, R. & Broere, D. L. J., 13 Jan 2025, In: Organometallics. 44, 1, p. 94-104 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Correction to: π-HuB: the proteomic navigator of the human body (Nature, (2024), 636, 8042, (322-331), 10.1038/s41586-024-08280-5)

The π-HuB Consortium, He, F., Aebersold, R., Baker, M. S., Bian, X., Bo, X., Chan, D. W., Chang, C., Chen, L., Chen, X., Chen, Y. J., Cheng, H., Collins, B. C., Corrales, F., Cox, J., E, W., Van Eyk, J. E., Fan, J., Faridi, P. & Figeys, D. & 31 others, Gao, G. F., Gao, W., Gao, Z. H., Goda, K., Goh, W. W. B., Gu, D., Guo, C., Guo, T., He, Y., Heck, A. J. R., Hermjakob, H., Hunter, T., Iyer, N. G., Jiang, Y., Jimenez, C. R., Joshi, L., Kelleher, N. L., Li, M., Li, Y., Lin, Q., Liu, C. H., Liu, F., Liu, G. H., Liu, Y., Liu, Z., Low, T. Y., Lu, B., Mann, M., Meng, A., Moritz, R. L. & Nice, E., 2025, In: Nature. 637, 8046, p. E22

Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

Divergent Chemoenzymatic Synthesis of Sulfated Ganglio-Oligosaccharides for Probing Ligand Requirements of Glycan Binding Proteins

Bunyatov, M. I., Wolfert, M. A. & Boons, G.-J., 10 Mar 2025, In: Angewandte Chemie-International Edition. 64, 11, 10 p., e202415521.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Exploration of Antibacterial Mechanisms of Cold Atmospheric Plasma (CAP): Effects on cell membranes during responses to oxidative stress

Xie, M., 3 Feb 2025, Utrecht: Utrecht University. 240 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Open Access

File

Exploring Uncharted Territories in Immunoglobulomics: Comprehensive Profiling of Human Antibody Repertoires in Blood Using Mass Spectrometry

van Rijswijck, D. M. H., 29 Jan 2025, Utrecht: Utrecht University. 211 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Open Access

File

Genotype-dependent glycoproteoforms of histidine-rich glycoprotein illustrate the fine-tuning of the plasma proteome

Zou, Y., 5 Mar 2025, Utrecht: Utrecht University. 199 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Open Access

File

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer

Jager, S., Zeller, M., Pashkova, A., Schulte, D., Damoc, E., Reiding, K. R., Makarov, A. A. & Heck, A. J. R., 13 Mar 2025, In: Nature Communications. 16, 1, 2497.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Liposome-Encapsulated Escherichia coli Lysates to Reconstitute Intracellular Macromolecular Crowding Effects

Kalacheva, M. S., da Silva, N. R. & Boersma, A. J., 21 Mar 2025, In: ACS Synthetic Biology. 14, 3, p. 901-908 8 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. '., Miranda, M. C., Watkins, A. M., Ogohara, C., Caldwell, S., Wu, M., Heck, A. J. R., Veesler, D., Ward, A. B., Baker, D., Twarock, R. & King, N. P., 26 Feb 2025, (E-pub ahead of print) In: Nature Structural and Molecular Biology. 746.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Macromolecular localization in cryogenic electron tomograms

Chaillet, M. L., 5 Feb 2025, Utrecht: Utrecht University. 233 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Open Access

File

Multitiered Proteome Analysis Displays the Hyperpermeability of the Rheumatoid Synovial Compartment for Plasma Proteins

Stork, E. M., Nteak, S. K., van Rijswijck, D. M. H., Damen, J. M. A., Scherer, H. U., Toes, R. E. M., Bondt, A., Huizinga, T. W. J. & Heck, A. J. R., Feb 2025, In: Molecular and Cellular Proteomics. 24, 2, 14 p., 100900.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

NMR characterisation of the antibiotic resistance-mediating 32mer RNA from the 23S ribosomal RNA

Muhs, C., Kemper, L., Richter, C., Lavore, F., Weingarth, M., Wacker, A. & Schwalbe, H., 3 Apr 2025, (E-pub ahead of print) In: Biomolecular NMR Assignments.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements

Ebberink, E. H. T. M., Yin, V. C., Deslignière, E., Barendregt, A., Wörner, T. P., Fort, K. L., Makarov, A. A. & Heck, A. J. R., 2 Apr 2025, In: Journal of the American Chemical Society. 147, 13, p. 10925-10934 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Protein-bound and free glycation compounds in human milk: A comparative study with minimally processed infant formula and pasteurized bovine milk

Arena, S., De Pascale, S., Ciaravolo, V., Monroy, M. M., Gouw, J. W., Stahl, B., Bäuerl, C., Collado, M. C., De Filippo, C., Scaloni, A. & Troise, A. D., 15 Jan 2025, In: Food Chemistry. 463, Pt 2, 14 p., 141265.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Regulatory effects of Lacticaseibacillus rhamnosus ZFM216 and its bacteriocin on intestinal microbiota in vitro

Zhou, Q., Lou, Y., Shan, C., Ye, Z., Wu, D., Li, P., Breukink, E. & Gu, Q., Apr 2025, In: Food Bioscience. 66, 12 p., 106136.

Research output: Contribution to journal › Article › Academic › peer-review

Sialic acid-containing glycolipids extend the receptor repertoire of Enterovirus-D68

da Silva, A. K. P., van Trijp, J. P., Montenarie, A., Fok, J., Ayudhya, S. S. N., Pieters, R. J., Boons, G.-J., van Riel, D., de Vries, R. P. & Bauer, L., 18 Jan 2025, bioRxiv, 44 p.

Research output: Working paper › Preprint › Academic

File

Spatial organization of the sperm cell glycoproteome

Ji, R., Chiozzi, R. Z., van den Toorn, H., Leung, M., Zeev-Ben-Mordehai, T., Burke, N. D., Bromfield, E. G., Reiding, K. R. & Heck, A. J. R., Jan 2025, In: Molecular and Cellular Proteomics. 24, 1, 100893.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

StableMARK-decorated microtubules in cells have expanded lattices

de Jager, L., Jansen, K. I., Hoogebeen, R., Akhmanova, A., Kapitein, L. C., Förster, F. & Howes, S. C., 6 Jan 2025, In: The Journal of cell biology. 224, 1, 12 p., e202206143.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Structural diversity of axonemes across mammalian motile cilia

Leung, M. R., Sun, C., Zeng, J., Anderson, J. R., Niu, Q., Huang, W., Noteborn, W. E. M., Brown, A., Zeev-Ben-Mordehai, T. & Zhang, R., 30 Jan 2025, In: Nature. 637, 8048, p. 1170-1177 8 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Structure-property relationships to direct the dynamic properties of acylsemicarbazide-based materials

Maessen, S. J. D., Lekanne Deprez, S., Vermeeren, P., van den Bersselaar, B. W. L., Lutz, M., Heuts, J. P. A., Fonseca Guerra, C. & Palmans, A. R. A., 2025, In: Polymer Chemistry. 16, 3, p. 290-300 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Temperature adaptation of yeast phospholipid molecular species at the acyl chain positional level

Kelso, C., Maccarone, A. T., de Kroon, A. I. P. M., Mitchell, T. W. & Renne, M. F., Feb 2025, In: FEBS Letters. 599, 4, p. 530-544 15 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors

Carrasco, M. R., Lin, T.-H., Zhu, X., García, A. G., Uslu, E., Liang, R., Spruit, C. M., Richard, M., Boons, G.-J., Wilson, I. A. & de Vries, R. P., 11 Jan 2025, bioRxiv, 22 p.

Research output: Working paper › Preprint › Academic

File

Understanding Macromolecules and their Interactions: Computational Methods and Experimental Insights

de Vries, I., 3 Apr 2025, Utrecht: Utrecht University. 315 p.

Research output: Thesis › Doctoral thesis 2 (Research NOT UU / Graduation UU)

Open Access

File

2024

2,2-Difluoro Derivatives of Fucose Can Inhibit Cell Surface Fucosylation without Causing Slow Transfer to Acceptors

Liu, Y., Sweet, I. R. & Boons, G.-J., 28 Oct 2024, In: JACS Au. 4, 10, p. 3953–3963 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

2,2-Di-Fluoro-Derivatives of Fucose Can Inhibit Cell Surface Fucosylation Without Causing Slow Transfer to Acceptors

Liu, Y., Sweet, I. & Boons, G.-J., 30 Jul 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

Open Access

A biofilm-tropic Pseudomonas aeruginosa bacteriophage uses the exopolysaccharide Psl as receptor.

Walton, B., Abbondante, S., Marshall, M. E., Dobruchowska, J. M., Alvi, A., Gallagher, L. A., Vallikat, N., Zhang, Z., Wozniak, D. J., Yu, E. W., Boons, G.-J., Pearlman, E. & Rietsch, A., 12 Aug 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

Open Access

A Biomimetic Synthetic Strategy can Provide Keratan Sulfate I and II Oligosaccharides with Diverse Fucosylation and Sulfation Patterns

Wu, Y., Bosman, G., Chapla, D., Huang, C., Moremen, K., Vries, R. D. & Boons, G.-J., 10 Jan 2024, ChemRxiv.

Research output: Working paper › Preprint › Academic

File

A Biomimetic Synthetic Strategy Can Provide Keratan Sulfate I and II Oligosaccharides with Diverse Fucosylation and Sulfation Patterns

Wu, Y., Bosman, G. P., Chapla, D., Huang, C., Moremen, K. W., de Vries, R. P. & Boons, G.-J., 3 Apr 2024, In: Journal of the American Chemical Society. 146, 13, p. 9230-9240 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling

Bellinzona, G., Sassera, D. & Bonvin, A. M. J. J., 2024, In: Bioinformatics Advances. 4, 1, vbae153.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A Chemoenzymatic Strategy for Site-Specific Glyco-Tagging of Native Proteins for the Development of Biologicals

Gimeno, A., Ehlers, A. M., Delgado, S., Langenbach, J.-W. H., van den Bos, L. J., Kruijtzer, J. A. W., Guigas, B. G. A. & Boons, G.-J., 13 Aug 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

Open Access

Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape

Reinisch, I., Michenthaler, H., Sulaj, A., Moyschewitz, E., Krstic, J., Galhuber, M., Xu, R., Riahi, Z., Wang, T., Vujic, N., Amor, M., Zenezini Chiozzi, R., Wabitsch, M., Kolb, D., Georgiadi, A., Glawitsch, L., Heitzer, E., Schulz, T. J., Schupp, M. & Sun, W. & 11 others, Dong, H., Ghosh, A., Hoffmann, A., Kratky, D., Hinte, L. C., von Meyenn, F., Heck, A. J. R., Blüher, M., Herzig, S., Wolfrum, C. & Prokesch, A., 15 Feb 2024, In: Nature Communications. 15, 1, p. 1-21 21 p., 1391.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Afucosylated broadly neutralizing antibodies enhance clearance of HIV-1 infected cells through cell-mediated killing

de Taeye, S. W., Schriek, A. I., Umotoy, J. C., Grobben, M., Burger, J. A., Sanders, R. W., Vidarsson, G., Wuhrer, M., Falck, D., Kootstra, N. A. & van Gils, M. J., 9 Aug 2024, In: Communications Biology. 7, 1, 11 p., 964.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics

Schulte, D. & Snijder, J., 2 Aug 2024, In: Journal of Proteome Research. 23, 8, p. 3552-3559 8 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A Hybrid Orbitrap-Nanoelectromechanical Systems Approach for the Analysis of Individual, Intact Proteins in Real Time

Neumann, A. P., Sage, E., Boll, D., Reinhardt-Szyba, M., Fon, W., Masselon, C., Hentz, S., Sader, J. E., Makarov, A. & Roukes, M. L., 12 Aug 2024, In: Angewandte Chemie-International Edition. 63, 33, 8 p., e202317064.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A Light Sensitive Hyaluronic Acid-based Hydrogel for 3D Culturing, Differentiation, and Harvesting of Mesenchymal Stromal Cells

Palmieri, F., Gueye, M., Rio, L. V. D., Bunschuh, S., Chopra, P., Mihăilă, S., Vermonden, T., Levato, R. & Boons, G.-J., 13 Aug 2024, bioRxiv, 20 p.

Research output: Working paper › Preprint › Academic

File

AlphaFastPPi: a fast AlphaFold-Multimer-based pipeline for high-throughput screening

Bellinzona, G., Sassera, D. & Bonvin, A. M. J. J., 9 Jun 2024, bioRxiv, 7 p.

Research output: Working paper › Preprint › Academic

File

Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition

Gogou, C., Beugelink, J. W., Frias, C. P., Kresik, L., Jaroszynska, N., Drescher, U., Janssen, B. J. C., Hindges, R. & Meijer, D. H., 29 Apr 2024, In: Nature Communications. 15, 1, 15 p., 3648.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A molecular corset for spermatids: Insights into the regulation and function of the manchette during spermiogenesis

Judernatz, J. H., 29 Nov 2024, Utrecht: Utrecht University. 179 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum

Dsouza, L., Li, X., Erić, V., Huijser, A., Jansen, T. L. C., Holzwarth, A. R., Buda, F., Bryant, D. A., Bahri, S., Gupta, K. B. S. S., Sevink, G. J. A. & de Groot, H. J. M., Jun 2024, In: Physical Chemistry Chemical Physics. 26, 22, p. 15856-15867 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Antibiotic Action Beyond Simple Target Binding: Exploring Supramolecular Mechanisms of Membrane-Active Antibiotics

Derks, M. G. N., 23 Sept 2024, Utrecht: Utrecht University. 198 p.

Research output: Thesis › Doctoral thesis 1 (Research UU / Graduation UU)

Open Access

File

Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis

Stork, E. M., van Rijswijck, D. M. H., van Schie, K. A., Hoek, M., Kissel, T., Scherer, H. U., Huizinga, T. W. J., Heck, A. J. R., Toes, R. E. M. & Bondt, A., 10 Apr 2024, In: Nature Communications. 15, 1, 12 p., 3114.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

A Peptide Strategy for Inhibiting Different Protein Aggregation Pathways

Garfagnini, T., Ferrari, L., Koopman, M. B., Dekker, F. A., Halters, S., Van Kappel, E., Mayer, G., Bressler, S., Maurice, M. M., Rüdiger, S. G. D. & Friedler, A., 16 Sept 2024, In: Chemistry - A European Journal. 30, 52, e202400080.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

File

Chemistry Research: Bijvoet Centre for Biomolecular Research

Research output

Search results