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Biochemistry: Anastassis (Tassos) Perrakis

Research interest: Macromolecular Structures

Macromolecular structures are critical for understanding the function of proteins and their complexes and to evaluate and develop new drugs. A key methodology for understanding the structure of macromolecules is X-ray crystallography. My group is interested both in analysing macromolecular structures relevant for cancer, but also in developing the tools needed to decipher these structures.

I have been involved in many methodology oriented initiatives, providing scientific developments that enable specific software tools in determining macromolecular structures better and faster.

  • The development of the ARP/wARP suite for crystallographic model building has been the focus of my team for well over a decade. With more than 5,000 academic of users, close to one hundred active commercial licenses with companies in the biotechnology and pharmaceutical area, and well over 5,000 citations in international literature, ARP/wARP is established as a major tool for routine crystallographic structure determination. Our interest and major contributions to ARP/wARP have been to develop algorithms for docking the structure fragments to know sequences, building the side chain conformations, modeling surface loops, and developing the control systems and interfaces that make ARP/wARP easy and powerful to use for every crystallographer, novice or experienced.
  • Over the last few years, my team has been the basis for the development of the PDB_REDO suite. Capitalizing on our experience in developing algorithms for model building in ARP/wARP, we developed new tools that help rebuild and re-refine models that are already in the PDB or are about to be submitted to the PDB. PDB_REDO strives to help crystallographers submit better models to the public PDB archive, but also retro-actively re-refines and re-build the models available, to make sure they all benefit from the most recent developments in the theory and the software in macromolecular crystallography. As part of this effort we make available the pdb-redo.eu for optimizing "working models" before they are submitted to the PDB.
    PDB_REDO has started a decade ago in the group of Gert Vriend at the Radboud University Medical Center at Nijmegen, as a software pipeline to remediate all PDB entries, by re-refining them with modern software. Since 2009, the original PDB_REDO developer Robbie Joosten has joined my team, and capitalising on our experience in developing algorithms for model building in ARP/wARP. We have since then developed new tools to rebuild macromolecular models and new decision and validation algorithms to improve and extend the score of this pipeline. PDB_REDO strives to help crystallographers submit better models to the public PDB archive, but also retro-actively re-refines and re-builds the models available, to make sure they all benefit from the most recent developments in the theory and the software in macromolecular crystallography. As part of this effort we make available the pdb.redo.eu for optimizing "working models" before they are submitted to the PDB.
  • To determine macromolecular structures, it is important to first make the protein of interest using recombinant DNA technologies. A crucial step is in choosing the right "boundaries" of the protein to make, and many trials are typically required. To that end, in collaboration with the NKI Protein facility we have developed a suite of cloning vectors for ligation independent cloning and the Protein CCD software to design cloning experiments for protein expression in bacteria, insect or mammalian cells.

Our scientific interests revolve around a handful of specific research questions, that concern the interplay between function and structure. Most proteins have a specific enzymatic activity that drives a chemical reaction necessary to fulfill their physiological function. Many proteins, are made by multiple domains, or interact with other proteins, to direct their enzymatic activity in space and time. A common theme in our group is to understand the spatiotemporal control that interactions with other proteins (and with small domains within the same protein) exert on the activity of the 'host' protein, at the level of the molecular structure and physiological function. We use X-ray crystallography, X-ray scattering, and a variety of biophysical methods to answer these questions.

  • Autotaxin is a secreted phosphodiesterase that produces the signaling molecule lysophosphatidic acid, LPA. We have determined the structure of Autotaxin alone and with an in-house developed inhibitor, and have explained its catalytic mechanism. Future research lines focus on deciphering the role of Autotaxin isoforms, its mode of regulation, and the role of cell-surface interactions in its activity.
  • JBP1 is the protein that bind the unusual base J in parasites, and is homologous to the TET proteins involved in myeloid leukemia. We are focusing to understand how JBP1 acts to amplify base J in specific regions in the genome of parasites, and understanding the structure of the thymidine hydroxylation function, which is homologous between JBPs and TET proteins.
  • Geminin and its homologues Idas and GemC1 are coiled coil proteins involved in DNA replication licensing, making sure that exactly only one copy of the DNA is made during that massively parallel process . We try to understand how complexes between these proteins affect the function of Geminin in proliferation - differentiation decisions in cells, especially in modulating the interaction with Cdt1, a master regulation of replication licensing.
  • Mitotic kinases like Plk1-3, Mps1, BubR1 and Bub1, regulate the mitotic check point in various ways, making sure that only one copy of each chromatid goes in each daughter cell after cell division (mitosis). We are most interested to how the regulatory domains of these kinases, PDB and TPR domains, spatiotemporally regulated the various functions of these proteins, facilitating interactions with other proteins in the cell and regulating the activity of the kinase domains.

Co-workers

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Bart van Beusekom

Ph.D. student

Experience

After graduating in chemistry from the Radboud University Nijmegen, I am now working as a PhD student on the development of methods for protein structure determination in the PDB_REDO project.

With my supervisor Robbie Joosten, I will develop automated procedures to validate and transfer structural knowledge between evolutionary related protein structure models. Such developments will allow us to focus on detecting 'unusual' features that are important factors of a protein's structure and function.

My work will provide more informative and more reliable structure models, because all available structural knowledge is used simultaneously in a systematic manner.

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Tatjana Heidebrecht

Technician

Experience

After a three year training as a research assistant at the University of Bielefeld, I took a new challenge in the laboratory of A. Perrakis, to work on the JBP1 project. The JBP1 protein binds to DNA that contains the unusual DNA base J, that is essential for survival in many protozoan pathogens. In the last years I crystallized the DNA-binding domain of JBP1 and I characterized it extensively by biophysical methods. A remaining challenge is to determine the structure of full-length JBP1 and understand its relationship with the human TET enzymes that are involved in myeloid leukemia.

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Yoshitaka Hiruma

Postdoctoral Fellow

Experience

I performed my PhD research at Leiden University, where I studied the mechanism and interactions of cytochrome P450cam with paramagnetic NMR and X-ray crystallography. At the NKI, I will use biochemical, biophysical and structural approaches to study the function of the Mps1 and BubR1 (pseudo)kinases in mitosis, in collaboration with the group of Geert Kops group in the University Medical Center in Utrecht.

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Robbie Joosten

Research associate

Experience

The PDB_REDO project (pdb-redo.eu) focuses on creating fully automated computational methods for optimizing, crystallographic structure models of proteins and nucleic acids. These methods can be applied while determining the structure of a new protein the lab, but also retro-actively to all known structure models in the Protein Data Bank. Taking full advantage of novel computational methods we provide to active crystallographers, but also to the diverse PDB user community crystallographic models with less errors and inaccuracies, helping to enhance the biological insight gained from such models in, for example, inhibitor design.

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Willem Jan Keune

Postdoctoral Fellow

Experience

I am working on the versatile protein autotaxin (ATX), the main enzyme responsible for the production of the bioactive lipid LPA. ATX and LPA are implicated in a wide range of physiological and pathological processes including the development of cancer. Having a background in lipid signaling biochemistry, I want to combine both structural and signaling studies I would like to elucidate how ATX exactly functions and understand how it may be better exploited as a drug target.

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Touw, Wouter

Wouter Touw

Postdoctoral Fellow

Experience

3D structure models provide insight on the relation between structure and biological function of macromolecules. Computers are indispensable for obtaining these structure models from experimental data. I develop computational methods that improve model quality as part of the PDB_REDO project.

In particular, I am interested in (protein-family specific) automated modelling and validation of protein-ligand complexes because an accurate description of receptor-drug interactions is important for structure-guided drug design.

Our lab is an exciting place to work because of the close interaction between computationally oriented scientists and structural biologists who perform experiments in the wet lab.

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Krista Joosten

Postdoctoral Fellow

Experience

After a PhD in theory of quantum properties in laser physics, I opted for research with a more direct link to socially relevant applications and specifically cancer research.  In the group of Anastassis Perrakis I use computer programming and modeling to improve building 3D protein models and study how to validate the quality of these models. We presently focus on combining experimental data, namely the three dimensional electron density maps that are computed from X-ray diffraction experiments of macromolecular crystals, knowledge from chemistry, and the statistical properties derived from existing models, to provide better structural models to scientists worldwide.

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Ud Din Ahmad, Misbha

Misbha Ud Din Ahmad

Postdoctoral Fellow

Experience

I have completed my PhD in protein crystallography from the University of Konstanz. During my PhD I worked on archaeal transcriptional factors and used crystallography as a tool to understand the structural basis for their DNA binding. Here at NKI, in collaboration with the group of Geert Kops at Hubrecht Institute, I work on kinetochore associated proteins. Specifically, I aim to understand the factors that regulate dynein localization at the kinetochores. I use crystallography and biophysics to understand these mechanisms.

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Research updates View All Updates

  • 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.

  • 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 (www.inext-eu.org) 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.

Key publications View All Publications

  • Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling

    Nat Commun. 2016 Apr 14;7:11248

    Keune WJ, Hausmann J, Bolier R, Tolenaars D, Kremer A, Heidebrecht T, Joosten RP, Sunkara M, Morris AJ, Matas-Rico E, Moolenaar WH, Oude et al.

    link to PubMed
  • CELL DIVISION CYCLE. Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling

    Science. 2015 Jun 12;348

    Hiruma Y, Sacristan C, Pachis ST, Adamopoulos A, Kuijt T2, Ubbink M, von Castelmur E Perrakis A, Kops GJ

    Link to Pubmed
 
 

Recent publications View All Publications

  • Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators

    (2017) J Med Chem. Mar 9;60(5):2006-2017. doi: 10.1021/acs.jmedchem.6b01743.

    Keune WJ, Potjewyd F, Heidebrecht T, Salgado-Polo F, Macdonald SJ, Chelvarajan L, Abdel Latif A, Soman S, Morris AJ, Watson AJ, Jamieson...

    Link to PubMed
  • PLA2G16 represents a switch between entry and clearance of Picornaviridae

    (2017) Nature. Jan 19;541(7637):412-416. doi: 10.1038/nature21032.

    Staring J, von Castelmur E, Blomen VA, van den Hengel LG, Brockmann M, Baggen J, Thibaut HJ, Nieuwenhuis J, Janssen H, van Kuppeveld FJ,...

    Link to PubMed
 

Contact

  • Office manager

    Mirna Ekelschot - van Diermen

  • E-mail

    m.v.diermen@nki.nl

  • Telephone Number

    +31 20 512 9127

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