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Biochemistry: Anastassis (Tassos) Perrakis

Anastassis Perrakis.jpg

Anastassis (Tassos) Perrakis, Ph.D. professorGroup leader

About 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. My group uses X-ray crystallography but also cryo-EM and NMR together with biochemical and biophysical methods, to link the function and structure of macromolecules relevant for cancer.

Concurrently our team is involved in many methodology-oriented initiatives, providing scientific developments that enable specific software tools in determining macromolecular structures better and faster.

  • Over the past decade, my team has been the basis for the development of the PDB-REDO suite. The principle PDB_REDO developer, Robbie Joosten who joined my team in 2009, capitalized on our experience in developing algorithms for model building in ARP/wARP (a software tool for X-ray crystallography model building, featuring 5,000 academic of users, about 100 active commercial licenses with companies in the biotechnology and pharmaceutical area, and well over 5,000 citations in international literature), and 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 site offers tools for optimizing "working models" before they are submitted to the PDB and the PDB-REDO databank, while it communicated validation criteria to the databank. 
  • 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, the role of cell-surface interactions in its activity and the mechanisms that explains how differences between orthosteric and allosteric inhibitors affect clinical outcome.
  • JBP1 is the protein that binds 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.
  • Mitotic kinases like Mps1, BubR1, Bub1, and Plk1-3, 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.
  • Microtubule binding and modifying proteins, is an interested that stemmed from our work on Mps1 interactions with microtubules to regulate mitosis, and the findings of the Thijn Brummelkamp group, that found important microtubule-modifying enzymes.


Adamopoulos, Nassos

Nassos Adamopoulos

Ph.D. student


I am interested in the role of lysophosphatidic acid (LPA) in tumor progression, angiogenesis and metastasis. Former structural studies in the group, have established the role of Autotaxin in LPA production and signaling. Recently, two new membrane proteins, members of the Glycerophosphodiester phosphodiesterase (GDE) family, which can produce LPA intracellularly were identified. Using structural biology tools, I am trying to understand the molecular mechanism of GDEs and characterise that new LPA generation pathway.



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Heidelbrecht, Tatjana.jpg

Tatjana Heidebrecht



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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Krista Joosten

Postdoctoral Fellow


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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Joosten, Robbie.jpg

Robbie Joosten

Research associate


The PDB_REDO project ( 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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Salgado Polo, Fernando

Fernando Salgado Polo

Ph.D. student


I studied Biochemistry at the Complutense University of Madrid and completed my master's degree at the VU University Amsterdam. My work in Tassos Perrakis's lab focuses on two main projects:

- Characterizing the catalysis and allosteric modulation of the lysophospholipase Autotaxin (ATX), the main producer of the bioactive lipid lysophosphatidic  acid (LPA), as well as the mechanism by which ATX presents its product to the LPA receptors at the cell surface.

- Understanding the intracellular trafficking and ligand specificity of several members in the glycerophosphodiester phosphodiesterase (GDE) family, namely, GDE2 and GDE3, which recognize GPI-anchored proteins.

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Ud Din Ahmad, Misbha

Misbha Ud Din Ahmad

Postdoctoral Fellow


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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Wienk, Hans

Hans Wienk

EU Grant Support


After my chemistry Master's and membrane biochemistry PhD at Utrecht University, I was trained in applied protein NMR at the Goethe University in Frankfurt am Main. Back at Utrecht University, I developed to facility manager, responsible for the solution NMR operation and open access to external researchers to the largest high-field NMR facility of The Netherlands. Besides guiding local, national and international NMR projects from academia and industry, over the years I increasingly shifted towards administration, finances, and project management.

My current activities at the NKI are overall science administration, grant support and project management. I support the local facilities, and I am heavily involved in the preparation and execution of European and national grants.

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Research updates View All Updates

  • Solving a Molecular Scissors Mystery

    A Netherlands Cancer Institute team, co-led by Thijn Brummelkamp and Anastassis (Tassos) Perrakis, reported independently, but almost simultaneously with three more groups from all over the world, on the crystal structure and mechanism of a peculiar molecular end-tail of the microtubules that constitute the cell skeleton.

    A cell skeleton is made of cables called microtubules. These allow a cell to maintain its shape, move to different places and transport molecules through its interior. Microtubules also play a key role in cell division.

    The frequently used cancer therapeutic paclitaxel, aimed at cells that are dividing, specifically acts on microtubules and thereby affects their detyrosination. In addition, detyrosynation of tubulin has been implicated in cardiac dysfunction, correct segregation of chromosomes during mitosis, and mental retardation.

    Microtubules are continuously modified to serve different purposes within the cell. For this, their tyrosine tails are cut and put back by different enzymes. After researchers from the Netherlands Cancer Institute and Oncode Institute, in 2017, found the identity of the scissors that remove the tail, an apparent race was launched to solve the next piece of the puzzle: to determine the 3D structure of these molecular scissors.

    This month the Netherlands Cancer Institute team, co-led by Thijn Brummelkamp and Anastassis (Tassos) Perrakis, independently but almost simultaneously with three more groups from all over the world, are reporting on the crystal structure and mechanism of these peculiar molecular end-tail scissors. Tassos Perrakis: 'This means that a beautiful consensus is emerging, supported by complementary experiments which together have been constructing an exciting story.' 

    More information: Solving a Molecular Scissors Mystery

    Athanasios Adamopoulos et al., 'Crystal structure of the VASH1-SVBP complex, a 2 tubulin tyrosine carboxypeptidase', Nature Structural & Molecular Biology, 1 July 2019.

    Kevin C. Slep. 'Cytoskeletal cryptography: structure and mechanism of an eraser', Nature Structural & Molecular Biology3 July 2019 (News & Views). 

  • PhD student utilizes evolution - Thesis Bart van Beusekom

    Did you know that human DNA copy machines are almost identical to those of chimpanzees? Researcher Bart van Beusekom from the Netherlands Cancer Institute used such similarities to develop software that allows scientists to better solve new protein structures. On Monday May 27th he will defend his PhD thesis at Utrecht University.
    Life is driven by proteins as molecular machines. To properly understand these, detailed 3D protein structure models are needed, giving unique insight into biology and helping the development of new drugs. Proteins are highly dependent on their 3D folding for properly performing their functions. However, obtaining reliable protein structure models is challenging and labor-intensive. That's why researcher Bart van Beusekom and colleagues of The Netherlands Cancer Institute developed software that optimizes thousands of protein structure models to make them more complete and reduce errors. Van Beusekom: "This allows us to better understand the biology and the automation also saves scientists' valuable time. Our software is used by over 10,000 people each month."

    The methods they've created make frequent use of the concept of homology. Van Beusekom: "Homologous protein structures remain similar during evolution. For instance, the proteins that copy DNA are almost identical  in humans and chimpanzees, but even those from tomatoes have similar 3D structures. Existing data of solved homologous structures is oftentimes not used optimally when solving a new one. That's why we have developed a website showing scientists where and how a structure model is different from its homologs. Our methods are the first to systematically use all available homologous protein structure models to improve new models in several ways."

    Want to know more? Download Bart van Beusekom's thesis here.     

    Practical information about the defense can be found on Utrecht University's website.

    Improving protein structure with homology-based information and prior knowledge

    LAHMA Local Annotation of Homology Matched Amino acids

Key publications View All Publications

  • Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP

    (2019) Nat Struct Mol Biol. Jul;26(7):567-570.

    Adamopoulos A, Landskron L, Heidebrecht T, Tsakou F, Bleijerveld OB, Altelaar M, Nieuwenhuis J, Celie PHN, Brummelkamp TR, Perrakis A.

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

    (2016) Nat Commun. 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 Elferink RP, Perrakis A.

    Link to PubMed

Recent publications View All Publications

  • The domain architecture of protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity

    (2019) J Biol Chem. Aug 23;294(34):12815-12825.

    Adamopoulos A, Heidebrecht T, Roosendaal J, Touw WG, Phan IQ, Beijnen J, Perrakis A.

    Link to PubMed
  • Building and rebuilding N-glycans in protein structure models

    (2019) Acta Crystallogr D Struct Biol. Apr 1;75(Pt 4):416-425.

    van Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley P, Joosten RP.

    Link to PubMed


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    Mirna Ekelschot - van Diermen

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    +31 20 512 9127


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