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Mw. dr. J. (Jocelyne) Vreede

Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Van 't Hoff Institute for Molecular Sciences
Fotograaf: Selfie

  • Science Park 904
  • Kamernummer:C2.238
  • Postbus 94157
    1090 GD Amsterdam
  • Student Projects

    There are several topics available in my group for students to work on, for a bachelor project, a master project or an extra project in the summer. 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

    Modeling the structure and formation of an H-NS DNA complex

    The Histone-like Nucleoid Structuring protein (H-NS) is a small protein that organizes chromosomal DNA in bacteria, such as E. coli, salmonella and cholera. H-NS contains two dimerization sites and a DNA binding domain and it is dimeric in solution. By forming long filaments along double stranded DNA it bridges distinct regions of DNA. External factors, such as temperature, type and concentration of ions and the presence of helper proteins, influence the nature of such nucleoprotein complexes. The aim of these research projects is to develop structural models of H-NS - DNA complexes using molecular simulation approaches.  

    Construct nucleoprotein filaments

    For H-NS the structure of several fragments have been elucidated by crystallography, NMR and molecular dynamics simulations. These fragments can be combined into a larger structure using a Metropolis Monte Carlo approach, which allows for the investigation of the effect of nucleotide sequence, protein conformation and helper proteins. The project will consist of developing the Metropolis Monte Carlo approach for the H-NS DNA system, and investigating various conditions.

    (6-9 month project)  

    Modeling the formation of coiled coil complexes

    Coiled coils are widely occurring protein interaction motifs that provide a stable scaffold for various protein functions. Comprising two to seven amphipathic α-helices wound into a supercoil, these systems rigidify protein complexes and regulate function through binding. Coiled coils stabilize multi-domain proteins and protein complexes,  and they govern protein activity by regulation through binding. The leucine zipper domain in the yeast transcription factor GCN4 dimerizes into a coiled coil, thus enabling DNA binding. Comprising two peptide chains, this complex rapidly folds into a supercoil. In a supercoil complex, the helices typically have a rise of seven residues per two turns, exhibiting a pattern of hydrophobic and hydrophilic residues, known as the heptad repeat. These residues tune the specificity of the coiled coil peptides as well as their preferred oligomeric state. A wealth of information is available on the effects of altering the heptad repeat sequence, facilitating structural prediction of supercoil complexes and de novo protein design. Nevertheless, the dynamics and mechanism of the formation and functioning of these coiled coil complexes are far from understood. In this project enhanced sampling methods such as metadynamics and transition path sampling will be used to compute the mechanisms and free energies associated with the formation of a coiled coil complex. 

    (6-9 month project)

  • Publicaties


    • 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). https://doi.org/10.3390/ijms22073793




    • Muzdalo, 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. https://doi.org/10.1021/acs.jctc.7b01120 [details]


    • 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, [e27369]. https://doi.org/10.7554/eLife.27369 [details]


    • Meuzelaar, H., Vreede, J., & Woutersen, S. (2016). Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on alpha-Helical Stability and Folding Kinetics. Biophysical Journal, 110(11), 2328-2341. https://doi.org/10.1016/j.bpj.2016.04.015



    • 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]




    • Kwakman, P. H. S., Krijgsveld, J., de Boer, L., Nguyen, L. T., Boszhard, L., Vreede, J., ... 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]


    • 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]


    • 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., ... 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]




    • Zhu, J., Vreede, J., Hospes, M., Arents, J., Kennis, J. T. M., van Stokkum, I. H. M., ... 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. https://doi.org/10.1021/jp506785q [details]


    • 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


    • 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]


    • 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.
    • 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.
    • Vreede, J. (2016). Holland Research School for Molecular Chemistry fellowship.
    • Vreede, J. (2016). NWO chemistry student competition.


    • Vreede, J. (17-06-2017). Hoe weet ik of iets waar is?. Hoe weet ik of iets waar is?.


    • Vreede, J. (speaker) (20-11-2019). Werken als scheikundig onderzoeker, METIS montessori lyceum Amsterdam.
    • 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) (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.


    • Vreede, J. (participant) (12-6-2016). Klokhuis vragendag 2016, Amsterdam (participating in a conference, workshop, ...).



    • Vreede, J., Roet, S. & Swenson, D. (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.


    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
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