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Updates Biochemistry : Anastassis (Tassos) Perrakis group

Veni grant for Yoshitaka Hiruma

Yoshitaka Hiruma, postdoc in the group of Anastassis Perrakis, will receive a Veni grant from the Netherlands Organisation for Scientific Research (Dutch abbreviation: NWO). He will use the grant of 250.000 Euro to further study the role of the Mps1 protein during cell division.

Errors during cell division can cause all kinds of problems, including cancer. The division process consists of a number of separate phases. Between these phases there exist several checkpoints, molecular mechanisms that the cell uses to check whether it is safe to progress to the next phase. One such checkpoint is between the metaphase and anaphase. During the metaphase, the chromosomes are lined up and connected to the spindle apparatus. It is very important that all chromosomes are properly connected to the spindle microtubules, so that they will be neatly pulled apart and divided over the two daughter cells. Recently, Hiruma was the first author of a Science paper in which he and his colleagues describe how cells use the Mps1 protein to check whether all chromosomes are properly connected.

The majority of solid tumors contain cells with an aberrant number of chromosomes, pointing to problems in the process described above. Hiruma now wants to study the Mps1 protein on the level of specific molecular and atomic interactions . Understanding the structures of the transient complexes that Mps1 makes during cell division,  could hopefully lead to the development of inhibitors of Mps1 interactions, that might in the future be developed as new anti-cancer drugs.

Yoshitaka, Hiruma.jpgYoshitaka HirumaPostdoctoral Fellow

European Union invests 10 million Euro in research on the structure and function of complex proteins

Aim of this initiative called iNEXT, is to determine new structures and functions of proteins and their complexes, by giving researchers integrated access to structural biology technologies such as NMR, electron microscopy and X-ray technologies. The project contributes to European goals for health and green economy, as fundamental knowledge of biological processes is important, for example, for
the development of novel drugs and safe and sustainable food production methods.

Groundbreaking research

iNEXT will provide access to the most advanced facilities for structural biology in Europe. The collaborating facilities include advanced X-ray synchrotron sources in Grenoble, Hamburg, Oxford, Lund and Paris, high-field NMR facilities in Utrecht, Frankfurt, Florence, Brno, Lyon and Grenoble, imaging facilities in Oxford, Brno, Heidelberg, Leiden and Madrid and advanced biophysical characterization in Amsterdam. Together, these facilities will make it possible for European scientists to perform ground breaking protein research with technologies to which they otherwise would not have had access.

Starting September 2015

iNEXT ( is coordinated from the Netherlands by prof. Rolf Boelens (Utrecht University) with dr. Anastassis Perrakis (Netherlands Cancer Institute) as deputy coordinator. The program is
setup in coordination with the European ESFRI projects Instruct, ESS, EU-OPENSCREEN and Euro-BioImaging. Researchers across Europe will be able to apply for access to the advanced facilities of iNEXT through a peer-review process. Starting September 1, 2015, the facilities will be available and
proposals for access can be submitted.

Vidi Grant for Robbie Joosten - juni 2014

NKI researcher dr. Robbie Joosten has received a Vidi grant from the Netherlands Organization for Scientific Research (NWO). With the grant money of 800.000 Euros, he can develop his own research line.

Joosten works on the 3D structure of proteins. Comprehensive knowledge of protein structure is essential for understanding molecular mechanisms of diseases. Within cancer research, high quality protein structures can be used to explain the effect of disease-causing mutations and provide structural scaffolds for drug design. Protein structures are determined experimentally, mostly through X-ray crystallography. And with great success: in May 2014 the 100,000th structure was made publicly available through the Protein Data Bank (PDB).

However, the quality of the protein structure models is limited by the quality of the available data, the tools used to make the models and the skill and experience of the scientists using these tools. Joosten focuses on improving the digital tools that are used to make the models. He and his colleagues developed the automated PDB_REDO framework. With this framework, it is possible to improve protein structure models using their original crystallographic data. PDB_REDO combines decision-making algorithms  with model building algorithms to deliver optimized structure models,  with improved fit to their X-ray data and to broader chemical knowledge. Joosten and his colleagues applied PDB_REDO to all published X-ray structures, yielding the publicly available PDB_REDO data bank of optimized, consistently treated structure models [1]. Recently, they also  launched the PDB_REDO web-server that allows crystallographers to optimize their structure models before deposition to the PDB [2].

With the Vidi grant Joosten will bring PDB_REDO to a new level of sophistication that provides evolutionary context to structures. This context is key to exploit  structural insight, because conserved features, clade-specific characteristics, and  deviations from "normality" hint towards specific biology and medical relevance. To do this he will develop algorithms to detect and thoroughly validate 'unusual' features of protein structures, such as localized multiple conformations, post-translational modifications, and ligand binding. He will then use these structural features to integrate structural knowledge from all homologous structures into individual structures. This allows for the detection of important structural details, even when the data is relatively poor, and will lead to higher quality, more informative protein structures for biomedical research.

[1] See and its references.

[2] See

Joosten, Robbie.jpgRobbie JoostenResearch associate

Vacancy for an enthusiastic Biochemist!

A vacancy to work together with the group of Prof. Dr. Geert Kops in the function and structure of the BubR1 pseudo-kinase and the Mps1 kinase is available for an enthusiastic biochemist

Ph.D. degree Jens Hausmann

Jens Hausmann defended his thesis on the structure and function of Autotaxin at Leiden University!

Link to thesis Jens Hausmann

Release of the PDB_REDO server

Robbie Joosten and Anastassis Perrakis have announced the PDB_REDO web server, to help crystallographer construct more accurate models of their structures.

NeilAaronson.jpgNeil AaronsonGroup leader, Professor

PDB_REDO web server

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