Dr I.M. (Ioana) Ilie
Faculty of Science
Van 't Hoff Institute for Molecular Sciences
Visiting address
- Science Park 904
- Room number: C2.233
Postal address
-
Postbus 94157
1090 GD Amsterdam
Contact details
-
Publications
2024
Durukan, C., Arbore, F., Klintrot, R., Bigiotti, C., Ilie, I. M., Vreede, J., Grossmann, T. N., & Hennig, S. (2024). Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF−Y. ChemBioChem, 25(9), Article e202400020. https://doi.org/10.1002/cbic.202400020 [details]- Giubertoni, G., Chagri, S., Argudo, P. G., Prädel, L., Maltseva, D., Greco, A., Caporaletti, F., Pavan, A., Ilie, I. M., Ren, Y., Ng, D. Y. W., Bonn, M., Weil, T., & Woutersen, S. (2024). Structural adaptability and surface activity of peptides derived from tardigrade proteins. Protein Science, 33(9), Article e5135. https://doi.org/10.1002/pro.5135 [details]
- Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., van der Net, A., Castro-Linares, G., Caporaletti, F., Micha, D., Hunger, J., Deblais, A., Bonn, D., Sommerdijk, N., Šarić, A., Ilie, I. M., Koenderink, G. H., & Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America, 121(11), Article e2313162121. https://doi.org/10.1073/pnas.2313162121 [details]
- Paesani, M., & Ilie, I. M. (2024). Metaparticles: Computationally engineered nanomaterials with tunable and responsive properties. Journal of Chemical Physics, 161(24), Article 244905. https://doi.org/10.1063/5.0232274 [details]
- Zhou, J., Assenza, S., Tatli, M., Tian, J., Ilie, I. M., Starostin, E. L., Caflisch, A., Knowles, T. P. J., Dietler, G., Ruggeri, F. S., Stahlberg, H., Sekatskii, S. K., & Mezzenga, R. (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science, 11(32), Article 2402740. https://doi.org/10.1002/advs.202402740 [details]
- de Raffele, D., & Ilie, I. M. (2024). Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chemical Communications, 60(6), 632-645. https://doi.org/10.1039/d3cc04630c [details]
2023
- Ilie, I. M., Ehrhardt, C., Caflisch, A., & Weitz-Schmidt, G. (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12), 3878-3891. https://doi.org/10.1021/acs.jcim.3c00480 [details]
2022
- Dehabadi, M. H., Caflisch, A., Ilie, I. M., & Firouzi, R. (2022). Interactions of Curcumin’s Degradation Products with the Aβ42 Dimer: A Computational Study. Journal of Physical Chemistry B, 126(39), Article 76267. https://doi.org/10.1021/acs.jpcb.2c05846 [details]
- Ilie, I. M. (2022). Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. Biochimica et Biophysica Acta. Proteins and Proteomics, 1870.
- Ilie, I. M. (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Journal of Biological Chemistry, 1, 101403.
- Ilie, I. M., & Caflisch, A. (2022). Antibody binding increases the flexibility of the prion protein. Biochimica et Biophysica Acta. Proteins and Proteomics, 1870(11-12), Article 140827. https://doi.org/10.1016/j.bbapap.2022.140827 [details]
- Ilie, I. M., Bacci, M., Vitalis, A., & Caflisch, A. (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121(14), 2813-2825. https://doi.org/10.1016/j.bpj.2022.06.007 [details]
- Nass, K. J., Ilie, I. M., Saller, M. J., Driessen, A. J. M., Caflisch, A., Kammerer, R. A., & Li, X. (2022). The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochimica et Biophysica Acta Biomembranes, 1864(3), Article 183825. https://doi.org/10.1016/j.bbamem.2021.183825 [details]
2021
- Mallona, I., Ilie, I. M., Karemaker, I. D., Butz, S., Manzo, M., Caflisch, A., & Baubec, T. (2021). Flanking sequence preference modulated de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49, 145-157. https://doi.org/10.1093/nar/gkaa1168
2019
- Ilie, I. M., & Caflisch, A. (2019). Simulation Studies of Amyloidogenic Peptides and their Aggregates. Chemical Reviews, 119(12), 6956-6993. https://doi.org/10.1021/acs.chemrev.8b00731
2018
- Ilie, I. M., & Caflisch, A. (2018). Disorder at the tips of a disease-relevant Aβ amyloid fibril. A Molecular Dynamics study. The journal of Physical Chemistry. B, 122, 11072-11083. https://doi.org/10.1021/acs.jpcb.8b05236
- Ilie, I. M., Nayar, D., den Otter, W. K., van der Vegt, N. F. A., & Briels, W. J. (2018). Intrinsic conformational preferences in α-synuclein fibrils: Insights from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 14, 3298-3310. https://ris.utwente.nl/ws/portalfiles/portal/92366269/acs.jctc.8b00183.pdf
2017
- Ilie, I. M. (2017). The attachment of α-synuclein to a fiber: a coarse-grain approach. Journal of Chemical Physics, 146, 115102. https://doi.org/10.1063/1.4978297
2016
- Ilie, I. M., den Otter, W. K., & Briels, W. (2016). A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation. Journal of Chemical Physics, 144(8), 085103. https://doi.org/10.1063/1.4942115
2015
- Ilie, I. M., Briels, W. J., & den Otter, W. K. (2015). An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles. Journal of Chemical Physics, 142, 114103. https://doi.org/10.1063/1.4914322
2014
- Ilie, I. M., den Otter, W. K., & Briels, W. J. (2014). Rotational Brownian Dynamics of Clathrin Cage Formation. Journal of Chemical Physics, 141, 065101. https://doi.org/10.1063/1.4891306
Prize / grant
- Ilie, I., Reek, J. & Fitzsimons, C. (2024). MMD hub grant: Digital development of drug nanocarriers for Alzheimer’s disease. https://hims.uva.nl/shared/faculteiten/en/faculteit-der-natuurwetenschappen-wiskunde-en-informatica/news/2024/07/nine-research-projects-chos…
- van der Heide, L., Ilie, I. & Coveney, P. (2024). MMD hub grant: Towards a novel therapeutic approach for Parkinson’s disease: Boosting dopamine production and neuronal survival by activating the Gucy2c receptor.
- Ilie, I. (2022). Career Development Award.
Membership / relevant position
- Ilie, I. (2024-). Member Scientific committee DuComs, Scientific committee DuComs.
- Ilie, I. (2024-). Adviser NextGenChem.nl, NextGenChem.nl.
- Ilie, I. (2023-). Member Program committee Chains2024, Program committee Chains2024.
- Ilie, I. (2023). president, Assistant Professor Network. https://hims.uva.nl/content/news/2023/10/ioana-ilie-elected-president-of-assistant-professor-network-netherlands.html?origin=4zNaIwCsT1iMc%2FL4U9Sh2Q
- Ilie, I. (2022-). Assistant Professor Network.
Media appearance
- Ilie, I. (05-08-2024). Podium: Ioana Ilie C2W. Podium: Ioana Ilie. https://www.sciencelink.net/features/podium-ioana-ilie/22117.article
- Ilie, I. (23-01-2024). ChemComm Milestones – Ioana M. Ilie Chemical Communications Blog. ChemComm Milestones – Ioana M. Ilie. https://blogs.rsc.org/cc/2024/01/23/chemcomm-milestones-ioana-m-ilie/?doing_wp_cron=1737020132.1540439128875732421875
Journal editor
- Ilie, I. (editor) (2022). eLife (Journal).
- Ilie, I. (editor) (2022). Frontiers: New approaches to Biophysical Investigation of Protein Disorder and Folding (Journal).
Talk / presentation
- Ilie, I. (speaker) (22-11-2022). Rationally designed peptides to inhibit prion toxicity, Synapsis Forum, Gerzensee.
- Ilie, I. (speaker) (14-11-2022). Antibody binding modulates the dynamics of the cellular prion protein, Lennard Jones Seminars.
- Ilie, I. (speaker) (14-11-2022). Multiscale simulations of biomolecular systems, Dutch Soft Matter Meeting, Wageningen.
- Ilie, I. (speaker) (1-10-2022). Antibody binding modulates the dynamics of the membrane-bound prion protein, Dutch Biophysics.
- Ilie, I. (speaker) (1-9-2022). Antibody binding modulates the dynamics of the cellular prion protein, IDP Seminars.
- Ilie, I. (speaker) (12-5-2022). Multiscale simulations of protein folding, aggregation and disease inhibition, Molecular Bases of Proteinopathies Symposium.
- Ilie, I. (speaker) (31-1-2022). Antibody binding modulates the dynamics of the cellular prion protein, II Physics Postgraduate Weel, Lavras.
Others
- Ilie, I. (organiser) (2025). KNAW-NWO Physics of Life seminars. Co-organizer KNAW-NWO Physics of Life seminars (organising a conference, workshop, ...).
- Ilie, I. (organiser) (31-5-2024). Dutch Peptide Symposium. co-organizer Dutch Peptide Symposium (organising a conference, workshop, ...).
- Ilie, I. (organiser) (29-6-2023 - 30-6-2023). NextGenChem@NL (organising a conference, workshop, ...).
- Ilie, I. (other) (1-1-2023). Outreach: Jury member Akademikus/AkademiX (other).
- Ilie, I. (participant) (2023). Dutch Soft Matter Meeting. Co-organizer Dutch Soft Matter Meeting (organising a conference, workshop, ...).
- Ilie, I. (participant) (21-9-2022). CHAINS, Veldhoven (participating in a conference, workshop, ...).
- Ilie, I. (participant) (1-9-2022). StatMech Erice (IT) (participating in a conference, workshop, ...).
- Ilie, I. (participant) (1-5-2022). NWO Life (participating in a conference, workshop, ...).
- Ilie, I. (participant) (1-4-2022). KNCV-CTC-PhD+ Seminars. KNCV-CTC-PhD+ Seminars supported by the Computational and Theoretical Chemistry (CTC) division of the Royal Netherlands Chemical Society (KNCV) (organising a conference, workshop, ...).
- Ilie, I. (organiser) (2022). KNCV-CTC-PhD+ Seminar series (organising a conference, workshop, ...).
2024
- Vreede, J., Ilie, I., Hennig, S., Grossmann, T. N. & Bigiotti, C. (8-3-2024). Stapled peptide in complex with transcription factor NF-Y. Universiteit van Amsterdam. https://doi.org/10.21942/uva.25368475.v1
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Ancillary activities
No ancillary activities
Durukan, C., Arbore, F., Klintrot, R., Bigiotti, C., Ilie, I. M., Vreede, J., Grossmann, T. N., & Hennig, S. (2024). Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF−Y. ChemBioChem, 25(9), Article e202400020.