mw. dr. J. (Jocelyne) Vreede
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Van 't Hoff Institute for Molecular Sciences
Science Park A
Science Park 904 Kamernummer: C2.238
1090 GD Amsterdam
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. Below short summaries are given for the various topics. Contact me for more information.
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. (8 months project)
Free energy profiles of dimer conformations - An H-NS dimer contains several flexible regions, resulting in a large number of different conformations. The population of these conformations depends on external conditions. One example is the interaction between the DNA binding domains with one of the dimerization domains. Without magnesium, this interaction seems stronger than when magnesium is present. To test this hypothesis, we will use free energy methods, such as metadynamics or steered molecular dynamics, to compute free energy profiles of binding and dissociation of the DNA binding domains in H-NS to its N-terminal dimerization site. (6 months prject)
Flexibility of helix a3 - H-NS contains a long helix, labeled a3, which buckles to form two helices, depending on external conditions. In this project, the stability of helix a3 will be investigated by running molecular dynamics simulations of various helix-a3-variants at different concentrations of ions and helper proteins. (3 months project)
Folding and unfolding alpha-helices
The alpha-helix is one of the secondary structure elements in proteins and therefore an ideal model system to investigate protein folding under various conditions, such as the type and concentration of various ions, or the temperature. However, using molecular simulation to fold and unfold a helix within a reasonable time is challenging, as the transitions between the folded and unfolded states can take microseconds to seconds, which will take many, many years, even on a fast super computer. To overcome this problem, additional bias potentials can be introduced that force the system out of stable states. The construction of such bias potentials is not straightforward, as many degrees of freedom play a role in helix folding.
Protocol for helix (un)folding - Using various enhanced sampling methods, such as temperature replica exchannge, path sampling and metadynamics, the aim of this project is to develop a simulation protocol to compute free energy profiles of folding a peptide into an alpha-helix. (8 months)
Design sodium sensitive helix - Sodium sensitivity is an emerging problem for many food crops, as the sodium concentration in arable land is increasing, and food crops typically do not like high sodium concentration in the soil. The roots of sodium sensitive plants grow away from soil with high sodium concentrations, a process known as the halotropic response, indicating plants contain signaling routes triggered by sodium. However, to date, very little is known about the proteins involved in this sodium perception process. In this project, the aim is to construct a sodium-sensitive alpha-helix, by computing the free energies of helix folding for many different peptides. From these free energy profiles, basic protein design principles can be constructed for making a peptide both sensitive to monovalent cations, and selectively sensitive to sodium. (3-8 months)
Polarizable force field - A large source of error in predictions from MD simulations arises from the way electrostatic interactions between particles are described. In most conventional force fields used for protein simulations the electrostatic contribution is modeled as pairwise interactions between atoms with a fixed single point charge. It is well known that electronic polarizability is essential for higher accuracy, especially for highly charged and electronically heterogeneous systems, such as ions in water, proteins and other biomolecular systems. The Drude oscillator approach alleviates this issue significantly by explicitly including polarization via attaching an auxiliary particle carrying a charge to an atom with a harmonic spring. Mimicking induced polarization is achieved via the particle’s displacement under the influence of an electric field. The Drude oscillator approach has recently been included in various force fields [Huang2014, Lemkul2015]. Adding Drude oscillators to all non-hydrogen atoms slows down simulations, but results in more accurate predictions. In this project, the aim is to investigate the folding of an alpha-helix using a polarizable force field. (3-6 months)
The Watson-Crick to Hoogsteen transition in DNA
In DNA, bases primarily interact via hydrogen bonds in the Watson-Crick (WC) motif. In 1963 Hoogsteen found an alternative base-pairing motif, in which the purine is rotated approximately 180° relative to the WC motif. Recent experiments show that Hoogsteen (HG) base pairing occurs transiently, but non-negligibly in DNA. Using path sampling simulations, it is possible to predict the mechanism and rate of the WC to HG conversion and vice versa. These research projects aim to extend these findings to investigate the effect of the force field, nucleotide sequences and the presence of a HG binding protein on the mechanisms and rates of this transition.
- 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. DOI: 10.1021/acs.jctc.7b01120
- 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. DOI: 10.1016/j.bpj.2016.04.015
- 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), [e1004444]. DOI: 10.1371/journal.pcbi.1004444 [details]
- van Mastbergen, E. C., & Vreede, J. (2015). Modeling the binding of H-NS to DNA. Biophysical Journal, 108(2), 537A-538A. DOI: 10.1016/j.bpj.2014.11.2948 [details]
- 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. DOI: 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. DOI: 10.1371/journal.pcbi.1003797 [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. DOI: 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), e1002913. DOI: 10.1371/journal.pcbi.1002913 [details]
- Joyeux, M., & Vreede, J. (2013). A Model of H-NS Mediated Compaction of Bacterial DNA. Biophysical Journal, 104(7), 1615-1622. DOI: 10.1016/j.bpj.2013.02.043 [details]
- Juraszek, J., Vreede, J., & Bolhuis, P. G. (2012). Transition path sampling of protein conformational changes. Chemical Physics, 396, 30-44. DOI: 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. DOI: 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. DOI: 10.1016/j.bpj.2012.05.040 [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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 10.1021/jp809641j [details]
- 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. DOI: 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. DOI: 10.1016/j.febslet.2008.01.062 [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. DOI: 10.1021/jp506785q [details]
- 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) (23-8-2017). Applications of Path Sampling, E-CAM/Lorentz workshop on Classical MD, Leiden, Netherlands.
- Vreede, J. (speaker) (22-9-2016). Applying national compute infrastructure: A researcher’s perspective, Support4Research Masterclass , Rotterdam, Netherlands.
- Vreede, J. (speaker) (29-8-2016). DNA baserolling, Lorentz workshop “Reaction Coordinates from Molecular Trajectories” , Leiden, Netherlands.
- Vreede, J. (speaker) (14-3-2016). Molecular simulation of biomolecules, CUI Graduate Days, Hamburg, Germany.
- Vreede, J. (participant) (12-6-2016). Klokhuis vragendag 2016, Amsterdam, Netherlands (participating in a conference, workshop, ...).
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