Dr. Jocelyne Vreede

Van 't Hoff Institute for Molecular Sciences
University of Amsterdam
Science Park 904
1098 XH Amsterdam

room: C2.238
phone: (+31) 20 525 6489
j.vreedeuva.nl

Publications

  1. Cis to trans isomerization of azobenzene derivatives studied with transition path sampling and QM/MM molecular dynamics
    A. Muzdalo, P. Saalfrank, J. Vreede, M. Santer
    J. Chem. Theory. Comput. (2018), In press
  2. Mechanism of environmentally driven conformational changes that modulate H-NS DNA bridging activity
    R.A. van der Valk, J. Vreede, L. Qin, G.F. Moolenaar, A. Hofmann, N. Goosen, R.T. Dame
    eLIFE (2017), 27369
  3. Influence of Glu/Arg, Asp/Arg and Glu/Lys Salt Bridges on alpha-helical Stability and Folding Kinetics
    Meuzelaar, J. Vreede, S. Woutersen
    Biophys. J. 110 (2016), 2328
  4. The trigger factor chaperone encapsulated and stabilizes partial folds of substrate proteins
    K. Singhal, J. Vreede, A. Mashaghi, S.J. Tans, P.G. Bolhuis
    PLoS Comput. Biol. (2015), e100444
  5. Genomic looping: a key principle of chromatin organization
    R.A. van der Valk, J. Vreede, F. Cremazy, R.T. Dame
    J. Mol. Microbiol. Biotechn. 24 (2014), 344
  6. Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble
    M.A. Rohrdanz, W. Zheng, B.P. Lambeth, J. Vreede and C. Clementi
    PLoS Comput. Biol. (2014), e1003797
  7. Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield
    J. Zhu, J. Vreede, M. Hospes, J.S. Arents, J.T. Kennis, I.H. van Stokkum, K.J. Hellingwerf and M.L. Groot
    J. Phys. Chem. B (2014), In press
  8. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding
    H. Meuzelaar, M. Tros, A. Huerta-Viga, J. Vreede and S. Woutersen
    J. Phys. Chem. Lett. 5 (2014), 900
  9. Hydrophobic collapse of trigger factor monomer in solution
    K. Singhal, J. Vreede, A. Mashaghi, S. Tans and P.G. Bolhuis
    PLoS One 8 (2013), e59683
  10. A model of H-NS mediated compaction of bacterial DNA
    M. Joyeux and J. Vreede
    Biophys. J. 104 (2013), e1002913
  11. The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions
    L. Zhu, P.G. Bolhuis and J. Vreede
    PLoS Comput. Biol. 9 (2013), e1002913
  12. Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling
    M. Schor, J. Vreede and P.G. Bolhuis
    Biophys. J. 103 (2012), 1296
  13. Predicting the effect of ions on the conformation of the H-NS dimerization domain
    J. Vreede and R.Th. Dame
    Biophys. J. 103 (2012), 89
  14. Transition path sampling of protein conformational changes
    J. Juraszek, J. Vreede and P.G. Bolhuis
    Chem. Phys. 396 (2012), 30
  15. Proline 68 tunes photochemsitry yield in Photoactive Yellow Protein
    A.B. Rupenyan, J. Vreede, I.H.M. van Stokkum, M. Hospes, J.T.M. Kennis, K.J. Hellingwerf and M.L. Groot
    J. Phys. Chem. B 115 (2011), 6668
  16. Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein.
    J. Vreede, J. Juraszek and P.G. Bolhuis
    Proc. Natl. Acad. Sci. USA 107 (2010), 2397
  17. Common G102S polymorphism in chititriosidase differentially affects activity towards 4-methylumbelliferyl substrates.
    A.P. Bussink, M. Verhoek, J. Vreede, K. Ghauharali-van der Vlugt, W.E. Donker-Koopman, R.R. Sprenger, C.E. Hollak, J.M. Aerts, R.G. Boots
    FEBS J. 276 (2009), 5678
  18. In vivo mutational analysis of YtvA from Bacillus subtilis: mechanism of light activation of the general stress response.
    M. Avila-Perez, J. Vreede, Y. Tang, O. Bende, A. Losi, W. Gartner, K.J. Hellingwerf
    J. Biol. Chem. 284 (2009), 24958
  19. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.
    J. Vreede, M.G. Wolf, S.W. de Leeuw and P.G. Bolhuis
    J. Phys. Chem. B 113 (2009), 6484
  20. A single histidine residue modulates enzymatic activity in acidic mammalian chitinase.
    A.P Bussink, J. Vreede, J.M. Aerts and R.G. Boot
    FEBS Lett. 582 (2008), 931
  21. Helix formation is a bottleneck in the recovery reaction of Photoactive Yellow Protein.
    J. Vreede, K.J. Hellingwerf, and P.G. Bolhuis
    Proteins 72 (2007), 136
  22. Molecular Dynamics simulations reveal auto-inducer mediated TraR DNA binding through protein backbone fluctuations.
    J. Vreede, K.J. Hellingwerf, and W. Crielaard
    FEBS Letters 582 (2008), 805
  23. Protonation of the chromophore in the photoactive yellow protein.
    E.J.M Leenders, L. Guidoni, U. Rothlisberger, J. Vreede, P.G. Bolhuis, and E.J. Meijer
    J. Phys. Chem. B (2007), in press
  24. Predicting the signaling state of Photoactive Yellow Protein.
    J. Vreede, W. Crielaard, K.J. Hellingwerf, and P.G. Bolhuis
    Biophys J. 88 (2005), 3525
  25. Measuring and Modelling Dynamical Changes in the Structure of Photoactive Yellow Protein.
    J. Vreede, M.A. van der Horst, R. Kort, W. Crielaard, and K.J. Hellingwerf
    Phase Transitions 77 (2004), 3
  26. PAS domains: common structure, common flexibility?
    J. Vreede, M.A. van der Horst, K.J. Hellingwerf, W. Crielaard, and D.M.F. van Aalten
    J. Biol. Chem. 278, (2003), 18434
  27. Investigation of Surfactant Efficiency Using Dissipative Particle Dynamics.
    L. Rekvig, M. Kranenburg, J. Vreede, B. Hafskjold, and B. Smit
    Langmuir 19 (2003), 8195