Dept of Chemistry

2025

A novel peptidoglycan deacetylase modulates daughter cell separation in E. coli.

Hernandez-Rocamora, V., Martorana, A. M., Belloso, A., Ballesteros, D., Zaccaria, M., Perez, A. J., Iorga, B. I., Abia, D., Gray, J., Breukink, E., Xiao, J., Pazos, M., Polissi, A. & Vollmer, W., 19 Feb 2025, bioRxiv, 84 p.

Research output: Working paper › Preprint › Academic

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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

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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

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Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles

Giulini, M., Xu, X. & Bonvin, A. M. J. J., 28 Feb 2025, bioRxiv, 6 p.

Research output: Working paper › Preprint › Academic

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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

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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

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2024

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

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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

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

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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

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Cell-Surface RNA Associates with Heparan Sulfate and RNA-Binding Proteins to Modulate Receptor-Ligand Interactions

Li, Z., Joshi, B. S., Wijdeven, R. H., Santos-Barriopedro, I., Shademan, M., Bos, E., Tanenbaum, M., Boons, G.-J., Sharp, T., Vermeulen, M., Raz, V. & Joo, C., 24 Jul 2024, bioRxiv, p. 1-38, 38 p.

Research output: Working paper › Preprint › Academic

Open Access

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Epistasis in the receptor binding domain of contemporary H3N2 viruses that reverted to bind sialylated diLacNAc repeats

Liang, R., Peccati, F., Ponse, N. L. D., Uslu, E., Boons, G.-J., Unione, L. & de Vries, R. P., 26 Nov 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

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High-throughput antibody screening with high-quality factor nanophotonics and bioprinting

Abdollahramezani, S., Omo-Lamai, D., Bosman, G., Hemmatyar, O., Dagli, S., Dolia, V., Chang, K., Güsken, N. A., Delgado, H. C., Boons, G.-J., Brongersma, M. L., Safir, F., Khuri-Yakub, B. T., Moradifar, P. & Dionne, J., 27 Nov 2024, arXiv, 18 p. (arXiv ).

Research output: Working paper › Preprint › Academic

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Modelling Protein-Glycan Interactions with HADDOCK

Ranaudo, A., Giulini, M., Ayuso, A. P. & Bonvin, A. M. J. J., 31 Jul 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

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Nanoparticle display of neuraminidase elicits enhanced antibody responses and protection against influenza A virus challenge in mice

Pascha, M. N., Ballegeer, M., Roelofs, M. C., Meuris, L., Albulescu, I. C., Kuppeveld, F. J. M. V., Hurdiss, D. L., Bosch, B.-J., Zeev-Ben-Mordehai, T., Saelens, X. & Haan, C. A. M. D., 26 Jan 2024, Research Square.

Research output: Working paper › Preprint › Academic

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Predicting binding events in very flexible, allosteric, multi-domain proteins

Basciu, A., Athar, M., Kurt, H., Neville, C., Malloci, G., Muredda, F. C., Bosin, A., Ruggerone, P., Bonvin, A. M. J. J. & Vargiu, A. V., 3 Jun 2024, bioRxiv, 17 p.

Research output: Working paper › Preprint › Academic

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pytom-match-pick: a tophat-transform constraint for automated classification in template matching

Chaillet, M. L., Roet, S., Veltkamp, R. C. & Förster, F., 19 Sept 2024, bioRxiv, p. 1-25, 25 p.

Research output: Working paper › Preprint › Academic

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Receptor Binding Specificity of a Bovine A(H5N1) Influenza Virus

Chopra, P., Page, C. K., Shepard, J. D., Ray, S. D., Kandeil, A., Jeevan, T., Bowman, A. S., Ellebedy, A. H., Webby, R. J., de Vries, R. P., Tompkins, S. M. & Boons, G.-J., 31 Jul 2024, bioRxiv.

Research output: Working paper › Preprint › Academic

Open Access

Structural basis for recognition of the FLAG-tag by anti-FLAG M2

Beugelink, J. W., Sweep, E., Janssen, B. J. C., Snijder, J. & Pronker, M. F., 28 Mar 2024, bioRxiv, 21 p.

Research output: Working paper › Preprint › Academic

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Synthesis and biological evaluation of lipid A derived from commensal Bacteroides

Verpalen, E., Ehlers, A., van Wingaarden, A., Brouwer, A. & Boons, G.-J., 16 Aug 2024, ChemRxiv.

Research output: Working paper › Preprint › Academic

Open Access

The HCoV-HKU1 N-terminal domain binds a wide range of 9-O-acetylated sialic acids presented on different glycan cores

Tomris, I., Kimpel, A., Liang, R., Woude, R. V. D., Boons, G.-J., Li, Z. & Vries, R. P. D., 24 May 2024, bioRxiv, p. 1-21, (bioRxiv : the preprint server for biology).

Research output: Working paper › Preprint › Academic

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2023

A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein

Thijssen, V., Hurdiss, D. L., Debski-Antoniak, O. J., Spence, M. A., Franck, C., Norman, A., Aggarwal, A., Mokiem, N. J., Dongen, D. A. A. V., Vermeir, S. W., Liu, M., Li, W., Chatziandreou, M., Donselaar, T., Du, W., Drulyte, I., Bosch, B.-J., Snijder, J., Turville, S. & Payne, R. J. & 3 others, Jackson, C. J., Kuppeveld, F. J. M. V. & Jongkees, S. A. K., 28 Feb 2023, bioRxiv, p. 1-27.

Research output: Working paper › Preprint › Academic

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A new antibiotic from an uncultured bacterium binds to an immutable target

Shukla, R., Peoples, A. J., Ludwig, K. C., Maity, S., Derks, M. G. N., de Benedetti, S., Krueger, A. M., Vermeulen, B. J. A., Lavore, F., Honorato, R. V., Grein, F., Bonvin, A., Kubitscheck, U., Breukink, E., Achorn, C., Nitti, A., Schwalen, C. J., Spoering, A. L., Ling, L. L. & Hughes, D. & 5 others, Lelli, M., Roos, W. H., Lewis, K., Schneider, T. & Weingarth, M., 15 May 2023, bioRxiv, p. 1-30, 30 p.

Research output: Working paper › Preprint › Academic

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ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

Giulini, M., Honorato, R. V., Rivera, J. L. & Bonvin, A. M. J. J., 11 Jul 2023, bioRxiv.

Research output: Working paper › Preprint › Academic

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Asymmetrical Bi-antennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses

Ma, S., Liu, L., Eggink, D., Herfst, S., Fouchier, R. A. M., de Vries, R. P. & Boons, G.-J., 9 Nov 2023, bioRxiv, p. 1-24, 24 p.

Research output: Working paper › Preprint › Academic

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Compact localized boundary states in a quasi-1D electronic diamond-necklace chain

Kempkes, S. N., Capiod, P., Ismaili, S., Mulkens, J., Swart, I. & Smith, C. M., 28 Feb 2023, 1 ed., arXiv, p. 1-19.

Research output: Working paper › Preprint › Academic

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DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

Xu, X. & Bonvin, A. M. J. J., 24 Jun 2023, bioRxiv, p. 1-23, 23 p.

Research output: Working paper › Preprint › Academic

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Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs

van Bergen, W., Fiala, J., Heck, A. & Baggelaar, M., 19 Oct 2023, bioRxiv, p. 1-28 , 28 p.

Research output: Working paper › Preprint › Academic

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Full-Length Single-Molecule Protein Fingerprinting

Filius, M., Wee, R. V., Lannoy, C. D., Westerlaken, I., Li, Z., Kim, S. H., Pinto, C. D. A., Wu, Y., Boons, G.-J., Pabst, M., Ridder, D. D. & Joo, C., 28 Sept 2023, bioRxiv, 20 p. (bioRxiv).

Research output: Working paper › Preprint › Academic

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Genipin Crosslinks the Extracellular Matrix to Rescue Developmental and Degenerative Defects, and Accelerates Regeneration of Peripheral Neurons

Saito-Diaz, K., Dietrich, P., Wu, H.-F., Sun, X., Jayesh Patel, A., Gale Wzientek, C., Robert Prudden, A., Boons, G.-J., Chen, S., Studer, L., Xu, B., Dragatsis, I. & Zeltner, N., 24 Mar 2023, bioRxiv, 79 p. (bioRxiv).

Research output: Working paper › Preprint › Academic

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Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Lensink, M., Brysbaert, G., Raouraoua, N., Bates, P., Giulini, M., Honorato, R. V., Noort, C. V., Teixeira, J., Bonvin, A. M. J. J., Kong, R., Shi, H., Lu, X., Chang, S., Liu, J., Guo, Z., Chen, X., Morehead, A., Roy, R., Wu, T. & Giri, N. & 93 others, Quadir, F., Chen, C., Cheng, J., Carpio, C. D., Ichiishi, E., Luis, R.-L. A., Fernández-Recio, J., Harmalkar, A., Chu, L.-S., Canner, S., Smanta, R., Gray, J., Li, H., Lin, P., He, J., Tao, H., Huang, S., Roel, J., Jimenez-Garcia, B., Christoffer, C., Anika, J. J., Kagaya, Y., Kannan, H., Nakamura, T., Terashi, G., Verburgt, J., Zhang, Y., Zhang, Z., Fujuta, H., Sekijima, M., Kihara, D., Khan, O., Kotelnikov, S., Ghani, U., Padhorny, D., Beglov, D., Vajda, S., Kozakov, D., Surendra, N. S., Ricciardelli, T., Barradas-Bautista, D., Cao, Z., Chawla, M., Cavallo, L., Oliva, R., Yin, R., Cheung, M., Guest, J., Lee, J., Pierce, B., Shor, B., Cohen, T., Halfon, M., Schneidman-Duhovny, D., Zhu, S., Yin, R., Sun, Y., Shen, Y., Maszota-Zieleniak, M., Krzysztof, B. K., Lubecka, E., Marcisz, M., Danielsson, A., Dziadek, L., Gaardlos, M., Giełdoń, A., Liwo, J., Samsonov, S., Slusarz, R., Zieba, K., Sieradzan, A., Czaplewski, C., Kobayashi, S., Miyakawa, Y., Kiyota, Y., Takeda-Shitaka, M., Olechnovič, K., Valančauskas, L., Dapkūnas, J., Venclovas, C., Wallner, B., Yang, L., Hou, C., He, X., Guo, S., Jiang, S., Ma, X., Duan, R., Qiu, L., Xu, X., Zou, X., Velankar, S. & Shoshana, W. J., 9 Jul 2023, Authorea, 5 p.

Research output: Working paper › Preprint › Academic

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Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Antanasijevic, A., Borst, A. J., Lai, S.-H., Wang, J. Y. J., Mallik, B. B., 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., 19 Oct 2023, bioRxiv, p. 1-32, 32 p.

Research output: Working paper › Preprint › Academic

Reverse engineering the anti-MUC1 hybridoma antibody 139H2 by mass spectrometry-based de novo sequencing

Peng, W., Giesbers, K. C. A. P., Šiborová, M., Beugelink, J. W., Pronker, M. F., Schulte, D., Hilkens, J., Janssen, B. J. C., Strijbis, K. & Snijder, J., 5 Jul 2023, bioRxiv, 24 p.

Research output: Working paper › Preprint › Academic

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Structure and replication cycle of a virus infecting climate-modulating algaEmiliania huxleyi

Homola, M., Büttner, C. R., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., Chaillet, M., Förster, F., Wilson, W. H., Schroeder, D. C. & Plevka, P., 30 Jun 2023, bioRxiv, p. 1-54, 54 p.

Research output: Working paper › Preprint › Academic

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Sucrose-mediated translational stalling involves a conserved ribosomal pocket

Horst, S. V. D., Englmeier, R., Hanson, J., Smeekens, S. & Förster, F., 27 Aug 2023, bioRxiv, p. 1-19.

Research output: Working paper › Preprint › Academic

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Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Giulini, M., Schneider, C., Cutting, D., Desai, N., Deane, C. M. & Bonvin, A. M. J. J., 17 Nov 2023, bioRxiv.

Research output: Working paper › Preprint › Academic

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Visualization of translation reorganization upon persistent collision stress in mammalian cells

Fedry, J., Silva, J., Vanevic, M., Fronik, S., Mechulam, Y., Schmitt, E., des Georges, A., Faller, W. & Förster, F., 24 Mar 2023, bioRxiv, (bioRxiv).

Research output: Working paper › Preprint › Academic

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2022

Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection

Spruit, C. M., Sweet, I. R., Bestebroer, T., Lexmond, P., Qiu, B., Damen, M. J. A., Fouchier, R. A. M., Snijder, J., Herfst, S., Boons, G.-J. & Vries, R. P. D., 16 Nov 2022, bioRxiv, p. 1-48.

Research output: Working paper › Preprint › Academic

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Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis

Keulen, S. C. V. & Bonvin, A. M. J. J., 4 Nov 2022, bioRxiv, p. 1-22.

Research output: Working paper › Preprint › Academic

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Increased microtubule lattice spacing correlates with selective binding of kinesin-1 in cells

Jager, L. D., Jansen, K. I., Kapitein, L. C., Förster, F. & Howes, S. C., 25 May 2022, bioRxiv, p. 1-24.

Research output: Working paper › Preprint › Academic

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MRPS36 provides a missing link in the eukaryotic 2-oxoglutarate dehydrogenase complex for recruitment of E3 to the E2 core

Hevler, J. F., Albanese, P., Cabrera-Orefice, A., Potter, A., Jankevics, A., Misic, J., Scheltema, R. A., Brandt, U., Arnold, S. & Heck, A. J. R., 8 Oct 2022, bioRxiv, p. 1-11, 11 p.

Research output: Working paper › Preprint › Academic

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Potential impacts of prolonged absence of influenza virus circulation on subsequent epidemics

de Jong, S. P. J., Felix Garza, Z. C., Gibson, J. C., Han, A. X., van Leeuwen, S., de Vries, R. P., Boons, G.-J., van Hoesel, M., de Haan, K., van Groeningen, L. E., Hulme, K. D., van Willigen, H. D. G., Wynberg, E., de Bree, G. J., Matser, A., Bakker, M., van der Hoek, L., Prins, M., Kootstra, N. A. & Eggink, D. & 3 others, Nichols, B. E., de Jong, M. D. & Russell, C. A., 16 Nov 2022, medRxiv, 21 p.

Research output: Working paper › Preprint › Academic

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SEC62 and TMX4 control asymmetric autophagy of the nuclear envelope upon LINC complex disassembly

Kucińska, M. K., Fedry, J., Galli, C., Morone, D., Raimondi, A., Soldà, T., Förster, F. & Molinari, M., 5 Oct 2022, bioRxiv, p. 1-28.

Research output: Working paper › Preprint › Academic

Spectral Interferences Impede the High-Resolution Mass Analysis of Recombinant Adeno-Associated Viruses

Yin, V., Devine, P. W. A., Saunders, J. C., Hines, A., Shepherd, S., Dembek, M., Dobson, C. L., Snijder, J., Bond, N. J. & Heck, A. J. R., 27 Aug 2022, bioRxiv, 20 p.

Research output: Working paper › Preprint › Academic

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Synthetic HNK-1 containing glycans provide insight into binding properties of serum antibodies from MAG-neuropathy patients

Bunyatov, M., Wolfert, M. A., Huizinga, R., Schreurs, M. W. J., Jacobs, B. C. & Boons, G.-J., 25 Jul 2022, bioRxiv, 25 p.

Research output: Working paper › Preprint › Academic

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The SARS-CoV-2 spike N-terminal domain engages 9-O -acetylated α2-8-linked sialic acids

Tomris, I., Unione, L., Nguyen, L., Zaree, P., Bouwman, K. M., Liu, L., Li, Z., Fok, J. A., Ríos Carrasco, M., van der Woude, R., Kimpel, A. L. M., Linthorst, M. W., Verpalen, E. C. J. M., Caniels, T. G., Sanders, R. W., Heesters, B. A., Pieters, R. J., Jiménez-Barbero, J., Klassen, J. S. & Boons, G.-J. & 1 others, de Vries, R. P., 15 Oct 2022, bioRxiv, p. 1-25.

Research output: Working paper › Preprint › Academic

Unraveling the intricate microtubule inner protein networks that reinforce mammalian sperm flagella

Leung, M. R., Roelofs, M. C., Chiozzi, R. Z., Hevler, J. F., Heck, A. J. R. & Zeev-Ben-Mordehai, T., 30 Sept 2022, bioRxiv, 32 p.

Research output: Working paper › Preprint › Academic

2021

3D visualization of SARS-CoV-2 infection and receptor distribution in Syrian hamster lung lobes display distinct spatial arrangements

Tomris, I., Bouwman, K. M., Adolf, Y., Noack, D., Van Der Woude, R., Herfst, S., Boons, G.-J., Haagmans, B. L., Pasterkamp, R. J., Rockx, B. & De Vries, R. P., 24 Mar 2021, bioRxiv, 27 p.

Research output: Working paper › Preprint › Academic

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Dept of Chemistry

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