Anastassis Perrakis Oncode Institute and Division of Biochemistry Netherlands Cancer Institute Biography Publications Institution JoVE Articles Anastassis Perrakis has not added a biography. If you are Anastassis Perrakis and would like to personalize this page please email our Author Liaison for assistance. Publications Autotaxin Facilitates Selective LPA Receptor Signaling Cell Chemical Biology. Jan, 2023 | Pubmed ID: 36640760 AlphaFill: Enriching AlphaFold Models with Ligands and Cofactors Nature Methods. Feb, 2023 | Pubmed ID: 36424442 Crystal Structure of the Phospholipase A and Acyltransferase 4 (PLAAT4) Catalytic Domain Journal of Structural Biology. Dec, 2022 | Pubmed ID: 36210037 Conformational Transitions of the Spindly Adaptor Underlie Its Interaction with Dynein and Dynactin The Journal of Cell Biology. Nov, 2022 | Pubmed ID: 36107127 Author Correction: Tryptophan Depletion Results in Tryptophan-to-phenylalanine Substitutants Nature. Aug, 2022 | Pubmed ID: 35840685 A Type IV Autotaxin Inhibitor Ameliorates Acute Liver Injury and Nonalcoholic Steatohepatitis EMBO Molecular Medicine. Sep, 2022 | Pubmed ID: 35833384 Small Molecule Inhibitor Targeting CDT1/Geminin Protein Complex Promotes DNA Damage and Cell Death in Cancer Cells Frontiers in Pharmacology. 2022 | Pubmed ID: 35548337 Posttranslational Modification of Microtubules by the MATCAP Detyrosinase Science (New York, N.Y.). May, 2022 | Pubmed ID: 35482892 Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators Journal of Medicinal Chemistry. Apr, 2022 | Pubmed ID: 35440138 Tryptophan Depletion Results in Tryptophan-to-phenylalanine Substitutants Nature. Mar, 2022 | Pubmed ID: 35264796 Structure and Function of the Ecto-nucleotide Pyrophosphatase/phosphodiesterase (ENPP) Family: Tidying Up Diversity The Journal of Biological Chemistry. Feb, 2022 | Pubmed ID: 34958798 Autotaxin Impedes Anti-tumor Immunity by Suppressing Chemotaxis and Tumor Infiltration of CD8 T cells Cell Reports. Nov, 2021 | Pubmed ID: 34788605 AI Revolutions in Biology: The Joys and Perils of AlphaFold EMBO Reports. Nov, 2021 | Pubmed ID: 34668287 Imaging Autotaxin with F-Labeled Positron Emission Tomography Ligands Journal of Medicinal Chemistry. Oct, 2021 | Pubmed ID: 34662125 Target Highlights in CASP14: Analysis of Models by Structure Providers Proteins. Dec, 2021 | Pubmed ID: 34561912 New Restraints and Validation Approaches for Nucleic Acid Structures in PDB-REDO Acta Crystallographica. Section D, Structural Biology. Sep, 2021 | Pubmed ID: 34473084 CCD: Design Constructs for Protein Expression, the Easy Way Acta Crystallographica. Section D, Structural Biology. Aug, 2021 | Pubmed ID: 34342272 The G132S Mutation Enhances the Resistance of β-Lactamase Against Sulbactam Biochemistry. Jul, 2021 | Pubmed ID: 34250791 Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics Antimicrobial Agents and Chemotherapy. Jul, 2021 | Pubmed ID: 34031049 Conserved Residues Glu37 and Trp229 Play an Essential Role in Protein Folding of β-lactamase The FEBS Journal. Mar, 2021 | Pubmed ID: 33792206 LAHMA: Structure Analysis Through Local Annotation of Homology-matched Amino Acids Acta Crystallographica. Section D, Structural Biology. Jan, 2021 | Pubmed ID: 33404523 Quantitative LC-MS/MS Analysis of 5-hydroxymethyl-2'-deoxyuridine to Monitor the Biological Activity of J-binding Protein Analytical Biochemistry. Dec, 2020 | Pubmed ID: 32866463 A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry Structure (London, England : 1993). 11, 2020 | Pubmed ID: 32857966 A Community Proposal to Integrate Structural Bioinformatics Activities in ELIXIR (3D-Bioinfo Community) F1000Research. 2020 | Pubmed ID: 32566135 West-Life: A Virtual Research Environment for Structural Biology Journal of Structural Biology: X. Jan-Mar, 2019 | Pubmed ID: 32647812 A TPR Domain-containing N-terminal Module of MPS1 is Required for Its Kinetochore Localization by Aurora B The Journal of Cell Biology. Apr, 2013 | Pubmed ID: 23569217 Automatic Rebuilding and Optimization of Crystallographic Structures in the Protein Data Bank Bioinformatics (Oxford, England). Dec, 2011 | Pubmed ID: 22034521 Investigating a Macromolecular Complex: the Toolkit of Methods Journal of Structural Biology. Aug, 2011 | Pubmed ID: 21620973 Modeling and Experimental Validation of the Binary Complex of the Plectin Actin-binding Domain and the First Pair of Fibronectin Type III (FNIII) Domains of the Beta4 Integrin The Journal of Biological Chemistry. Jun, 2005 | Pubmed ID: 15817481 Inhibition of Autotaxin by Lysophosphatidic Acid and Sphingosine 1-phosphate The Journal of Biological Chemistry. Jun, 2005 | Pubmed ID: 15769751 Towards Complete Validated Models in the Next Generation of ARP/wARP Acta Crystallographica. Section D, Biological Crystallography. Dec, 2004 | Pubmed ID: 15572775 Crystal Structure of the Retinoblastoma Tumor Suppressor Protein Bound to E2F and the Molecular Basis of Its Regulation Proceedings of the National Academy of Sciences of the United States of America. Mar, 2003 | Pubmed ID: 12598654 Sequence-dependent Trafficking and Activity of GDE2, a GPI-specific Phospholipase Promoting Neuronal Differentiation Journal of Cell Science. | Pubmed ID: 31932507 The Structural Binding Mode of the Four Autotaxin Inhibitor Types That Differentially Affect Catalytic and Non-Catalytic Functions Cancers. | Pubmed ID: 31623219 The Domain Architecture of the Protozoan Protein J-DNA-binding Protein 1 Suggests Synergy Between Base J DNA Binding and Thymidine Hydroxylase Activity The Journal of Biological Chemistry. | Pubmed ID: 31292194 Crystal Structure of the Tubulin Tyrosine Carboxypeptidase Complex VASH1-SVBP Nature Structural & Molecular Biology. | Pubmed ID: 31270470 Building and Rebuilding N-glycans in Protein Structure Models Acta Crystallographica. Section D, Structural Biology. | Pubmed ID: 30988258 Interactions Between N-terminal Modules in MPS1 Enable Spindle Checkpoint Silencing Cell Reports. | Pubmed ID: 30784592 Direct Binding of Cdt2 to PCNA is Important for Targeting the CRL4 E3 Ligase Activity to Cdt1 Life Science Alliance. | Pubmed ID: 30623174 A Crystal Structure of the Human Protein Kinase Mps1 Reveals an Ordered Conformation of the Activation Loop Proteins. | Pubmed ID: 30582207 Characterization and Structure Determination of a Llama-derived Nanobody Targeting the J-base Binding Protein 1 Acta Crystallographica. Section F, Structural Biology Communications. | Pubmed ID: 30387773 Profilin Binding Couples Chloride Intracellular Channel Protein CLIC4 to RhoA-mDia2 Signaling and Filopodium Formation The Journal of Biological Chemistry. | Pubmed ID: 30381396 Homology-based Loop Modeling Yields More Complete Crystallographic Protein Structures IUCrJ. | Pubmed ID: 30224962 Lysophosphatidic Acid Produced by Autotaxin Acts As an Allosteric Modulator of Its Catalytic Efficiency The Journal of Biological Chemistry. | Pubmed ID: 30026231 Dynamic Kinetochore Size Regulation Promotes Microtubule Capture and Chromosome Biorientation in Mitosis Nature Cell Biology. | Pubmed ID: 29915359 Glycerophosphodiesterase GDE2/GDPD5 Affects Pancreas Differentiation in Zebrafish The International Journal of Biochemistry & Cell Biology. | Pubmed ID: 29203233 Homology-based Hydrogen Bond Information Improves Crystallographic Structures in the PDB Protein Science : a Publication of the Protein Society. | Pubmed ID: 29168245 Vasohibins Encode Tubulin Detyrosinating Activity Science (New York, N.Y.). | Pubmed ID: 29146869 Negative Regulation of Urokinase Receptor Activity by a GPI-specific Phospholipase C in Breast Cancer Cells ELife. | Pubmed ID: 28849762 Understanding Inhibitor Resistance in Mps1 Kinase Through Novel Biophysical Assays and Structures The Journal of Biological Chemistry. | Pubmed ID: 28726638 Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators Journal of Medicinal Chemistry. | Pubmed ID: 28165241 PLA2G16 Represents a Switch Between Entry and Clearance of Picornaviridae Nature. | Pubmed ID: 28077878 Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with a Discrete Binding Mode Journal of Medicinal Chemistry. | Pubmed ID: 27982588 Structural Basis of Reversine Selectivity in Inhibiting Mps1 More Potently Than Aurora B Kinase Proteins. | Pubmed ID: 27699881 Glycerophosphodiesterase GDE2 Promotes Neuroblastoma Differentiation Through Glypican Release and Is a Marker of Clinical Outcome Cancer Cell. | Pubmed ID: 27693046 Editorial Overview: New Constructs and Expression of Proteins Current Opinion in Structural Biology. | Pubmed ID: 27520611 Recombinant Cloning Strategies for Protein Expression Current Opinion in Structural Biology. | Pubmed ID: 27391134 Structural Snapshots of the Catalytic Cycle of the Phosphodiesterase Autotaxin Journal of Structural Biology. | Pubmed ID: 27268273 Data Mining of Macromolecular Structures Methods in Molecular Biology (Clifton, N.J.). | Pubmed ID: 27115630 Steroid Binding to Autotaxin Links Bile Salts and Lysophosphatidic Acid Signalling Nature Communications. | Pubmed ID: 27075612 The Structure of the GemC1 Coiled Coil and Its Interaction with the Geminin Family of Coiled-coil Proteins Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 26527144 CELL DIVISION CYCLE. Competition Between MPS1 and Microtubules at Kinetochores Regulates Spindle Checkpoint Signaling Science (New York, N.Y.). | Pubmed ID: 26068855 The First Step of Peptide Selection in Antigen Presentation by MHC Class I Molecules Proceedings of the National Academy of Sciences of the United States of America. | Pubmed ID: 25605945 The PDB_REDO Server for Macromolecular Structure Model Optimization IUCrJ. | Pubmed ID: 25075342 Autotaxin: Structure-function and Signaling Journal of Lipid Research. | Pubmed ID: 24548887 Timely Deposition of Macromolecular Structures is Necessary for Peer Review Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 24311569 The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer That Inhibits Geminin Function in DNA Replication Licensing The Journal of Biological Chemistry. | Pubmed ID: 24064211 The Polybasic Insertion in Autotaxin α Confers Specific Binding to Heparin and Cell Surface Heparan Sulfate Proteoglycans The Journal of Biological Chemistry. | Pubmed ID: 23150666 Structure-function Relationships of Autotaxin, a Secreted Lysophospholipase D Advances in Biological Regulation. | Pubmed ID: 23069371 Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania Cell. | Pubmed ID: 22939620 Cdt1 and Geminin in DNA Replication Initiation Sub-cellular Biochemistry. | Pubmed ID: 22918581 Binding of the J-binding Protein to DNA Containing Glucosylated HmU (base J) or 5-hmC: Evidence for a Rapid Conformational Change Upon DNA Binding Journal of the American Chemical Society. | Pubmed ID: 22775585 PDB_REDO: Constructive Validation, More Than Just Looking for Errors Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 22505269 Mechanism of USP7/HAUSP Activation by Its C-terminal Ubiquitin-like Domain and Allosteric Regulation by GMP-synthetase Molecular Cell. | Pubmed ID: 21981925 Insights into Autotaxin: How to Produce and Present a Lipid Mediator Nature Reviews. Molecular Cell Biology. | Pubmed ID: 21915140 Native Mass Spectrometry Provides Direct Evidence for DNA Mismatch-induced Regulation of Asymmetric Nucleotide Binding in Mismatch Repair Protein MutS Nucleic Acids Research. | Pubmed ID: 21737427 Structure-based Design of Novel Boronic Acid-based Inhibitors of Autotaxin Journal of Medicinal Chemistry. | Pubmed ID: 21615078 Idas, a Novel Phylogenetically Conserved Geminin-related Protein, Binds to Geminin and is Required for Cell Cycle Progression The Journal of Biological Chemistry. | Pubmed ID: 21543332 Enabling High-throughput Ligation-independent Cloning and Protein Expression for the Family of Ubiquitin Specific Proteases Journal of Structural Biology. | Pubmed ID: 21453775 The Structural Basis for Recognition of Base J Containing DNA by a Novel DNA Binding Domain in JBP1 Nucleic Acids Research. | Pubmed ID: 21415010 Structural Basis of Substrate Discrimination and Integrin Binding by Autotaxin Nature Structural & Molecular Biology. | Pubmed ID: 21240271 Mammalian Cell Expression, Purification, Crystallization and Microcrystal Data Collection of Autotaxin/ENPP2, a Secreted Mammalian Glycoprotein Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. | Pubmed ID: 20823545 Ca2+ Regulation in the Na+/Ca2+ Exchanger Features a Dual Electrostatic Switch Mechanism Proceedings of the National Academy of Sciences of the United States of America. | Pubmed ID: 19667209 Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger Journal of the American Chemical Society. | Pubmed ID: 19655751 UV-induced Ligand Exchange in MHC Class I Protein Crystals Journal of the American Chemical Society. | Pubmed ID: 19655750 Use of Acetylcholine Binding Protein in the Search for Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X-ray Analysis Journal of Medicinal Chemistry. | Pubmed ID: 19331415 "Conditional Restraints": Restraining the Free Atoms in ARP/wARP Structure (London, England : 1993). | Pubmed ID: 19217389 Insights into the DNA Cleavage Mechanism of Human LINE-1 Retrotransposon Endonuclease Proteins. | Pubmed ID: 18767160 Automated Macromolecular Model Building for X-ray Crystallography Using ARP/wARP Version 7 Nature Protocols. | Pubmed ID: 18600222 A Knowledge-driven Approach for Crystallographic Protein Model Completion Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 18391408 RNA-binding Protein Dnd1 Inhibits MicroRNA Access to Target MRNA Cell. | Pubmed ID: 18155131 ARP/wARP and Molecular Replacement: the Next Generation Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 18094467 Determinants for DNA Target Structure Selectivity of the Human LINE-1 Retrotransposon Endonuclease Nucleic Acids Research. | Pubmed ID: 17626046 The Protein That Binds to DNA Base J in Trypanosomatids Has Features of a Thymidine Hydroxylase Nucleic Acids Research. | Pubmed ID: 17389644 Assessment of Automatic Ligand Building in ARP/wARP Acta Crystallographica. Section D, Biological Crystallography. | Pubmed ID: 17164533 Structure and E3-ligase Activity of the Ring-Ring Complex of Polycomb Proteins Bmi1 and Ring1b The EMBO Journal. | Pubmed ID: 16710298 Crystal Structure of the Targeting Endonuclease of the Human LINE-1 Retrotransposon Structure (London, England : 1993). | Pubmed ID: 15274918 Structures of Escherichia Coli DNA Mismatch Repair Enzyme MutS in Complex with Different Mismatches: a Common Recognition Mode for Diverse Substrates Nucleic Acids Research. | Pubmed ID: 12907723 Ptprj is a Candidate for the Mouse Colon-cancer Susceptibility Locus Scc1 and is Frequently Deleted in Human Cancers Nature Genetics. | Pubmed ID: 12089527 Ekstrahering av modifiserte mikrotubuli fra pattedyrceller for å studere mikrotubuli-proteinkomplekser ved kryo-elektronmikroskopi Jitske Bak1, Lisa Landskron1, Thijn R. Brummelkamp1, Anastassis Perrakis1 1Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute JoVE 65126 Biochemistry iNEXT-Discovery and Instruct-ERIC: Integrating High-End Services for Translational Research in Structural Biology JoVE 63435 Editorial Nano-differensialskanning fluorimetri for screening i fragmentbasert blyoppdagelse Misbha Ud Din Ahmad1, Alexander Fish1, Jeroen Molenaar1, Sridhar Sreeramulu2, Christian Richter2, Nadide Altincekic2, Harald Schwalbe2, Hans Wienk1, Anastassis Perrakis1 1Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute, 2Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University JoVE 62469 Biochemistry
Ekstrahering av modifiserte mikrotubuli fra pattedyrceller for å studere mikrotubuli-proteinkomplekser ved kryo-elektronmikroskopi Jitske Bak1, Lisa Landskron1, Thijn R. Brummelkamp1, Anastassis Perrakis1 1Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute JoVE 65126 Biochemistry
iNEXT-Discovery and Instruct-ERIC: Integrating High-End Services for Translational Research in Structural Biology JoVE 63435 Editorial
Nano-differensialskanning fluorimetri for screening i fragmentbasert blyoppdagelse Misbha Ud Din Ahmad1, Alexander Fish1, Jeroen Molenaar1, Sridhar Sreeramulu2, Christian Richter2, Nadide Altincekic2, Harald Schwalbe2, Hans Wienk1, Anastassis Perrakis1 1Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute, 2Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University JoVE 62469 Biochemistry
