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

Research Interests

Histone-like Nucleoid Structuring protein

Bacterial chromosomal DNA is organized in the nucleoid by nucleoid-associated proteins, of which the Histone-like Nucleoid Structuring protein (H-NS) is one of the most abundant. H-NS is a small protein that binds double stranded DNA by forming complex assemblies. The focus of this project is to gain understanding of the underlying molecular mechanisms of H-NS - DNA assembly using advanced simulation methods.

H-NS contains a DNA-binding domain and a dimerization domain, connected by a flexible linker region. Dimerization occurs through the formation of a helical bundle, including a coiled coil interaction motif. Using Molecular Dynamics simulations, we have shown that the conformation of the dimerization domain can be sensitive to changes in ionic strength.

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 alpha-helices wound into a supercoil, these systems rigidify protein complexes, regulate function through binding and, surprisingly, are involved in signal transduction. In this project we use advanced molecular simulation techniques to investigate the mechanisms of the formation and functioning of three coiled-coil complexes in atomistic detail. These systems are:

1) The leucine zipper domain in the yeast transcription factor GCN4. This is the classical example of a coiled coil complex, comprising two peptide chains.

2) The HAMP domain, a linker domain in prokaryotic sensor proteins. Recently, the structure of HAMP became available, enabling a computational investigation of the unknown dynamic properties underlying signal transduction in the HAMP domain.

VENI grant 2008 (Innovational Research Incentive Scheme, NWO)

Photoactive Yellow Protein

How can a light signal, very small in size en very short in time, lead to a long-lasting, organism-wide response? To investigate (part of) this question, we study the Photoactive Yellow Protein (PYP) from the bacterium Halorhodospira halophila, where it is involved in a negative phototactile response to blue light. Comprising 125 amino acids and a covalently bound chromophore, the protein folds into a alpha-beta core capped by an N-terminal domain, containing two helices. Upon absorbing a blue-light photon as a trigger, PYP undergoes a photo cycle, starting from its receptor state. Visiting several intermediate states, the chromophore twists along its double bond to a cis configuration within picoseconds. Within microseconds of the isomerization, a proton from Glu46 (protonated in the receptor state) transfers to the chromophore, leaving a negative charge on Glu46. Driven by the new negative charge in the chromophore binding pocket, the protein subsequently unfolds to expose the chromophore and Glu46 to bulk water forming the signaling state. The completion of the photo cycle, i.e. the refolding of the protein to the receptor state pG, requires several hundreds of milliseconds. We study the conformational transitions in PYP in atomic detail, using molecular simulation methods, including parallel tempering, metadynamics and transition path sampling.