Dr J. (Jocelyne) Vreede
Faculty of Science
Van 't Hoff Institute for Molecular Sciences
Visiting address
- Science Park 904
- Room number: C2.227
Postal address
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Postbus 94157
1090 GD Amsterdam
Contact details
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Student Projects
There are several topics available in my group for students to work on, at bachelor and master level. You can find a list of available projects on the website of the Computational Chemistry group. Also, you can contact me directly: J.Vreede@uva.nl
To do a project in my group, some background in chemistry is required.
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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]- Hu, Y., Schwab, S., Deiss, S., Escudeiro, P., van Heesch, T., Joiner, J. D., Vreede, J., Hartmann, M. D., Lupas, A. N., Alvarez, B. H., Alva, V., & Dame, R. T. (2024). Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Research, 52(14), 8193-8204. https://doi.org/10.1093/nar/gkae485 [details]
- Mohr, B., van Heesch, T., Pérez de Alba Ortíz, A., & Vreede, J. (2024). Enhanced sampling strategies for molecular simulation of DNA. Wiley interdisciplinary reviews. Computational molecular science , 14(2), Article e1712. https://doi.org/10.1002/wcms.1712 [details]
- van Heesch, T., van de Lagemaat, E. M., & Vreede, J. (2024). Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation. In Bacterial Chromatin (Vol. 2819, pp. 585-609). (Methods in molecular biology (Clifton, N.J.)). https://doi.org/10.1007/978-1-0716-3930-6_27
2023
- Voorspoels, A., Vreede, J., & Carlon, E. (2023). Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations. Journal of Chemical Theory and Computation, 19(3), 902-909. https://doi.org/10.1021/acs.jctc.2c00889 [details]
- van Heesch, T., Bolhuis, P. G., & Vreede, J. (2023). Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations. Nucleic Acids Research, 51(22), 12150-12160. https://doi.org/10.1093/nar/gkad1014 [details]
2022
- Pérez de Alba Ortíz, A., Vreede, J., & Ensing, B. (2022). Sequence dependence of transient Hoogsteen base pairing in DNA. PLoS Computational Biology, 18(5), Article e1010113. https://doi.org/10.1371/journal.pcbi.1010113 [details]
- Roet, S., Hooft, F., Bolhuis, P. G., Swenson, D. W. H., & Vreede, J. (2022). Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas. Journal of Physical Chemistry B, 126(48), 10034-10044. https://doi.org/10.1021/acs.jpcb.2c06235 [details]
2021
- Blinker, S., Vreede, J., Setlow, P., & Brul, S. (2021). Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis. International Journal of Molecular Sciences, 22(7), Article 3793. https://doi.org/10.3390/ijms22073793 [details]
- Skoruppa, E., Voorspoels, A., Vreede, J., & Carlon, E. (2021). Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models. Physical Review E, 103(4), Article 042408. https://doi.org/10.1103/PhysRevE.103.042408 [details]
2020
- Qin, L., Ben Bdira, F., Sterckx, Y. G. J., Volkov, A. N., Vreede, J., Giachin, G., van Schaik, P., Ubbink, M., & Dame, R. T. (2020). Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Research, 48(4), 2156-2172. https://doi.org/10.1093/nar/gkz1226 [details]
2019
- Dubbeldam, D., Vreede, J., Vlugt, T. J. H., & Calero, S. (2019). Highlights of (bio-)chemical tools and visualization software for computational science. Current Opinion in Chemical Engineering, 23, 1-13. https://doi.org/10.1016/j.coche.2019.02.001 [details]
- Pérez de Alba Ortíz, A., Vreede, J., & Ensing, B. (2019). The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. In M. Bonomi, & C. Camilloni (Eds.), Biomolecular Simulations: Methods and Protocols (pp. 255–290). (Methods in Molecular Biology; Vol. 2022). Humana Press. https://doi.org/10.1007/978-1-4939-9608-7_11 [details]
- Riccardi, E., van Mastbergen, E. C., Navarre, W. W., & Vreede, J. (2019). Predicting the mechanism and rate of H-NS binding to AT-rich DNA. PLoS Computational Biology, 15(3), Article e1006845. https://doi.org/10.1371/journal.pcbi.1006845 [details]
- Vreede, J., Pérez de Alba Ortíz, A., Bolhuis, P. G., & Swenson, D. W. H. (2019). Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Research, 47(21), 11069-11076. https://doi.org/10.1093/nar/gkz837 [details]
- Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J-P., Bolhuis, P. G., Vreede, J., ... McLeish, T. (2019). Allostery in Its Many Disguises: From Theory to Applications. Structure, 27(4), 566-578. https://doi.org/10.1016/j.str.2019.01.003 [details]
2018
- Muždalo, A., Saalfrank, P., Vreede, J., & Santer, M. (2018). Cis-to-Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics. Journal of Chemical Theory and Computation, 14(4), 2042-2051. Advance online publication. https://doi.org/10.1021/acs.jctc.7b01120 [details]
2017
- van der Valk, R. A., Vreede, J., Qin, L., Moolenaar, G. F., Hofmann, A., Goosen, N., & Dame, R. T. (2017). Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity. eLife, 6, Article e27369. https://doi.org/10.7554/eLife.27369 [details]
2016
- Meuzelaar, H., Vreede, J., & Woutersen, S. (2016). Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on a-Helical Stability and Folding Kinetics. Biophysical Journal, 110(11), 2328-2341. https://doi.org/10.1016/j.bpj.2016.04.015 [details]
2015
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. (2015). The Trigger Factor chaperone encapsulates and stabilizes partial folds of substrate proteins. PLoS Computational Biology, 11(10), Article e1004444. https://doi.org/10.1371/journal.pcbi.1004444 [details]
2014
- Meuzelaar, H., Tros, M., Huerta-Viga, A., van Dijk, C. N., Vreede, J., & Woutersen, S. (2014). Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding. The Journal of Physical Chemistry Letters, 5(5), 900-904. https://doi.org/10.1021/jz500029a [details]
- Rohrdanz, M. A., Zheng, W., Lambeth, B., Vreede, J., & Clementi, C. (2014). Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble. PLoS Computational Biology, 10(10), e1003797. https://doi.org/10.1371/journal.pcbi.1003797 [details]
2013
- Joyeux, M., & Vreede, J. (2013). A Model of H-NS Mediated Compaction of Bacterial DNA. Biophysical Journal, 104(7), 1615-1622. https://doi.org/10.1016/j.bpj.2013.02.043 [details]
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013). Hydrophobic Collapse of Trigger Factor Monomer in Solution. PLoS ONE, 8(4), e59683. https://doi.org/10.1371/journal.pone.0059683 [details]
- Zhu, L., Bolhuis, P. G., & Vreede, J. (2013). The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions. PLoS Computational Biology, 9(2), Article e1002913. https://doi.org/10.1371/journal.pcbi.1002913 [details]
2012
- Juraszek, J., Vreede, J., & Bolhuis, P. G. (2012). Transition path sampling of protein conformational changes. Chemical Physics, 396, 30-44. https://doi.org/10.1016/j.chemphys.2011.04.032 [details]
- Schor, M., Vreede, J., & Bolhuis, P. G. (2012). Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling. Biophysical Journal, 103(6), 1296-1304. https://doi.org/10.1016/j.bpj.2012.07.056 [details]
- Vreede, J., & Dame, R. T. (2012). Predicting the effect of ions on the conformation of the H-NS dimerization domain. Biophysical Journal, 103(1), 89-98. https://doi.org/10.1016/j.bpj.2012.05.040 [details]
2011
- Kwakman, P. H. S., Krijgsveld, J., de Boer, L., Nguyen, L. T., Boszhard, L., Vreede, J., Dekker, H. L., Speijer, D., Drijfhout, J. W., te Velde, A. A., Crielaard, W., Vogel, H. J., Vandenbroucke-Grauls, C. M. J. E., & Zaat, S. A. J. (2011). Native thrombocidin-1 and unfolded thrombocidin-1 exert antimicrobial activity via distinct structural elements. The Journal of Biological Chemistry, 286(50), 43506-43514. https://doi.org/10.1074/jbc.M111.248641 [details]
- Rupenyan, A. B., Vreede, J., van Stokkum, I. H. M., Hospes, M., Kennis, J. T. M., Hellingwerf, K. J., & Groot, M. L. (2011). Proline 68 enhances photoisomerization yield in photoactive yellow protein. The journal of Physical Chemistry. B, 115(20), 6668-6677. https://doi.org/10.1021/jp112113s [details]
2010
- Vreede, J., Juraszek, J., & Bolhuis, P. G. (2010). Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proceedings of the National Academy of Sciences of the United States of America, 107(6), 2397-2402. https://doi.org/10.1073/pnas.0908754107 [details]
2009
- Avila-Pérez, M., Vreede, J., Tang, Y., Bende, O., Losi, A., Gärtner, W., & Hellingwerf, K. (2009). In vivo mutational analysis of YtvA from Bacillus subtilis: Mechanism of light activation of the general stress response. The Journal of Biological Chemistry, 284(37), 24958-24964. https://doi.org/10.1074/jbc.M109.033316 [details]
- Bussink, A. P., Verhoek, M., Vreede, J., Ghauharali-van der Vlugt, K., Donker-Koopman, W. E., Sprenger, R. R., Hollak, C. E., Aerts, J. F. M. G., & Boot, R. G. (2009). Common G102S polymorphism in chitotriosidase differentially affects activity towards 4-methylumbelliferyl substrates. The FEBS Journal, 276(19), 5678-5688. https://doi.org/10.1111/j.1742-4658.2009.07259.x [details]
- Vreede, J., Wolf, M. G., de Leeuw, S. W., & Bolhuis, P. G. (2009). Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems. The journal of Physical Chemistry. B, 113(18), 6484-6494. https://doi.org/10.1021/jp809641j [details]
2008
- Vreede, J., Hellingwerf, K. J., & Bolhuis, P. G. (2008). Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein. Proteins, 72(1), 136-149. https://doi.org/10.1002/prot.21902 [details]
- Vreede, J., Hellingwerf, K. J., & Crielaard, W. (2008). TraR auto-inducer enhances protein backbone fluctuations in DNA binding domain. FEBS Letters, 582(5), 805-809. https://doi.org/10.1016/j.febslet.2008.01.062 [details]
2025
- Abbondanzieri, E. A., Badrinarayanan, A. B., Barillà, D., Bell, S. D., Blombach, F., Bouet, J. Y., Bulgheresi, S., Cao, Q. A. D., Dame, R. T., Dekker, C., Demuysere, M., Espéli, O., Fogg, P. C. M., Freddolino, P. L., Ganji, M., Gerson, T. M., Grainger, D. C., Hamoen, L. W., Harju, J., ... Zhang, Z. (2025). Future Directions of the Prokaryotic Chromosome Field. Molecular Microbiology, 123(2), 89-100. https://doi.org/10.1111/mmi.15347 [details]
2017
- Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2017). Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA. Biophysical Journal, 112(3, Supplement 1), 214a. https://doi.org/10.1016/j.bpj.2016.11.1181 [details]
2015
- Zhu, J., Vreede, J., Hospes, M., Arents, J., Kennis, J. T. M., van Stokkum, I. H. M., Hellingwerf, K. J., & Groot, M. L. (2015). Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield. The journal of Physical Chemistry. B, 119(6), 2372-2383. Advance online publication. https://doi.org/10.1021/jp506785q [details]
- van Mastbergen, E. C., & Vreede, J. (2015). Modeling the binding of H-NS to DNA. Biophysical Journal, 108(2, suppl. 1), 537A-538A. https://doi.org/10.1016/j.bpj.2014.11.2948 [details]
2013
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013). A Molecular Dynamics Study of the Flexibility and Protein-Binding of the Trigger Factor Chaperone in Solution. Biophysical Journal, 104(2, Suppl. 1), 571A. https://doi.org/10.1016/j.bpj.2012.11.3172
2016
- Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2016). Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition. Biophysical Journal, 110(3, suppl. 1), 563A-564A. https://doi.org/10.1016/j.bpj.2015.11.3014 [details]
Prize / grant
- Vreede, J. (2024). Marie Curie funding. https://hims.uva.nl/content/news/2024/04/marie-curie-funding-for-jocelyne-vreede.html?origin=4zNaIwCsT1iMc%2FL4U9Sh2Q
- Vreede, J. (2024). NWO-XL Joining forces for human made molecular machines.
- Vreede, J. (2024). GRASSROOTS Implementeren tool voor visualisatie van biomoleculen zoals DNA en eiwitten voor Biomolecular modelling (BSc Scheikunde) en Biomolecular Simulation (MSc Chemistry).
- Heller, I. & Vreede, J. (2024). Joining Forces for Human-Made Molecular Machines.
- Vreede, J. & Fransen, L. (2024). ENLENS Data-Driven Optimization of Policy Strategies for Energy Transition and Sustainable Development Methodologies.
- Vreede, J. & Dubbeldam, D. (2024). GRASSROOTS Updaten computerpractica in Molecular Simulation (MSc Chemistry).
- Vreede, J. (2020). NWO grant for a public-private partnership with DSM to investigate the role of ions on the shape and aggregation of metalloproteins. https://hims.uva.nl/content/news/2020/06/the-role-of-metal-ions-on-protein-aggregation.html?origin=e9Lg9H1kRbuEFvhk7SGgCg
- Vreede, J. (2020). NWO KLEIN-2 grant for a four-year project investigating how the shape and compactness of DNA affect the expression of genes. https://hims.uva.nl/content/news/2020/03/how-does-the-accessibility-of-dna-affect-the-expression-of-genes.html?origin=e9Lg9H1kRbuEFvhk7SGgCg
- Vreede, J. (2016). Holland Research School for Molecular Chemistry fellowship.
- Vreede, J. (2016). NWO chemistry student competition.
Membership / relevant position
- Vreede, J. (2022-2023). Review board member for CECAM-Lorentz workshops, CECAM-Lorentz.
- Vreede, J. (2022-2023). Rapporteur, EuroHPC Regular Access .
- Vreede, J. (2020-2021). Member, NWO - Evaluatie commissie Veni domain Science .
- Vreede, J. (2019). NWO - CHAINS abstract selection committee .
- Vreede, J. (2019-2022). Member, NWO - Chemistry of Life werkgemeenschapscommissie .
Media appearance
- Vreede, J. (01-11-2021). Eiwitten simuleren in je tussenjaar C2W. Eiwitten simuleren in je tussenjaar. https://www.sciencelink.net/carriere-and-opleiding/eiwitten-simuleren-in-je-tussenjaar/20334.article#:~:text=pilotstudie%20kunnen%20zien.-,'…
Talk / presentation
- Vreede, J. (speaker) (11-2019). Biomolecular simulations, Universiteit Leiden, Leiden.
- Vreede, J. (speaker) (23-8-2017). Applications of Path Sampling, E-CAM/Lorentz workshop on Classical MD, Leiden.
- Vreede, J. (speaker) (18-6-2017). Hoe weet ik of iets waar is?, Nemo Kinderlezing.
- Vreede, J. (speaker) (22-9-2016). Applying national compute infrastructure: A researcher’s perspective, Support4Research Masterclass , Rotterdam.
- Vreede, J. (speaker) (29-8-2016). DNA baserolling, Lorentz workshop “Reaction Coordinates from Molecular Trajectories” , Leiden.
- Vreede, J. (speaker) (14-3-2016). Molecular simulation of biomolecules, CUI Graduate Days, Hamburg.
Others
- Vreede, J. (participant) (12-6-2016). Klokhuis vragendag 2016, Amsterdam (participating in a conference, workshop, ...).
2024
- Schwab, S., Deiss, S., van Heesch, T., Joiner, J. D., Vreede, J., Hartmann, M. D., Lupas, A. N. & Alvarez, B. (10-4-2024). Data underlying the publication: Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. 4TU.ResearchData. https://doi.org/10.4121/6c07e4bb-96f1-4ee0-88ef-6978bda27e5d.v2
- 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
2023
- Hu, Y., Schwab, S., Deiss, S., Escudeiro, P., van Heesch, T., D. Joiner, J., Vreede, J., Hartmann, M. D., Lupas, A. N., Alvarez, B., Alva, V. & Dame, R. T. (27-11-2023). Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Zenodo. https://doi.org/10.5281/zenodo.10211306
- van Heesch, T., Bolhuis, P. G. & Vreede, J. (2023). SMD Simulations of GC-analogue Sequence. Figshare. https://doi.org/10.6084/m9.figshare.22182562.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of ETS Inverse Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161295.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of ETS Anti Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161301.v1
- Bolhuis, P. G., Vreede, J. & van Heesch, T. (2023). SMD Simulations of ETS Consensus Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161280.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of High Affinity Sequence. Figshare. https://doi.org/10.6084/m9.figshare.21304482.v1
2022
- Vreede, J. (14-8-2022). EntF*-D10. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485338.v2
- Vreede, J. (14-8-2022). EntF*-D3. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485059.v2
- Vreede, J. (14-8-2022). EntF*-D7. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485206.v2
- Vreede, J. (14-8-2022). EntF*-D5. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485188.v2
- Vreede, J. (14-8-2022). EntF*-D12. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485401.v2
- Vreede, J. (14-8-2022). EntF*-D8. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485209.v2
- Vreede, J. (14-8-2022). EntF*-D1. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485035.v2
- Vreede, J. (14-8-2022). EntF*-D15. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485419.v1
- Vreede, J. (14-8-2022). EntF*-D4. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485164.v3
- Vreede, J. (14-8-2022). EntF*-D2. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485056.v2
- Vreede, J. (14-8-2022). EntF*-D14. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485416.v1
- Vreede, J. (14-8-2022). EntF*-L. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485017.v3
- Vreede, J. (14-8-2022). EntF*-D6. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485194.v2
- Vreede, J. (14-8-2022). EntF*-D11. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485395.v1
- Vreede, J. (14-8-2022). EntF*-D9. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485257.v2
- Vreede, J. (14-8-2022). EntF*-D13. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485407.v1
2021
- Vreede, J., Brul, S., Setlow, P. & Blinker, S. (11-2-2021). GerAB. Universiteit van Amsterdam. https://doi.org/10.21942/uva.13655516.v4
2020
- Vreede, J., Roet, S., Swenson, D., Hooft, F. & Bolhuis, P. (22-2-2020). Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L. Universiteit van Amsterdam. https://doi.org/10.21942/uva.11865579.v1
2019
- Vreede, J. (3-10-2019). Predicting the mechanism and rate of H-NS binding to AT-rich DNA. Universiteit van Amsterdam. https://doi.org/10.21942/uva.6960098
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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.