Jocelyne Vreede

Dr. J. (Jocelyne) Vreede

Associate Professor, van 't Hoff Institute for Molecular Sciences

Research interests

My expertise is focused on characterizing and understanding conformational transitions in biomolecules, including proteins and DNA, using advanced molecular simulation techniques. Throughout my career I have been interested in the mechanisms underlying sensing and signal propagation in proteins. During my PhD I predicted the structure of the active, transient state of a light receptor. As a postdoc, I elucidated the mechanisms of signal transduction in a bacterial blue light receptor and chemotaxis receptors using rare event simulation methods, including path-sampling and metadynamics. As a VENI researcher I investigated conformational transitions of the Histone-like Nucleoid Structuring protein H-NS using different levels of detail. Including all atoms explicitly enabled me to discover ion-induced conformational changes causing H-NS to switch from stiffening DNA to bridging DNA. At a larger time and length scales, I developed a model for the compaction of DNA by H-NS. Recently, I have predicted the mechanisms and associated rate constants of the Watson-Crick to Hoogsteen transition in DNA, and for the interaction between H-NS and DNA. In 2023, I developed a simulation protocol, together with my PhD student Thor van Heesch, to predict dissociation free energies for protein DNA complexes, which can be generally applied to almost any protein-DNA complex.

Throughout my career I have recognized promising developments in simulation techniques and applied these to relevant biological problems, in close collaboration with various experimental groups.

During my career I have taught several courses in molecular simulation and structural elucidation of biomolecules. My expertise in these topics resulted in courses on biochemistry and thermodynamics. In 2028 I combined my knowledge of biochemistry with my experience in thermodynamics and started teaching the course How to design an alien: Life on other planets. In this course, students from different disciplines design lifeforms for exoplanets. In 2022 I became programme director of the chemistry bachelor in Amsterdam, a joint degree between the University of Amsterdam and the Free University of Amsterdam.