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Integrative Structure Biology

Integrative Structure Biology

Timothy Robin Skern (ORCID: )
  • Grant DOI 10.55776/W1258
  • Funding program Doctoral Programs
  • Status ended
  • Start January 1, 2016
  • End September 30, 2021
  • Funding amount € 1,752,838
  • Project website

Disciplines

Biology (100%)

Keywords

    Macromolecular Structure And Dynamics, Macromolecular Complexes, Structure-Function Analysis, Molecular Conformation, Inter-Molecular Recognition, Protein Engineering

Abstract

The aim of the PhD Program is to provide selected students with an in-depth, interdisciplinary training in scientific methods to enable them to comprehend, rigorously analyse, and provide solutions to biological problems from a fundamentally structural perspective. This theme contains questions lying at the heart of modern molecular and cellular biology which are being investigated by a combination of powerful and varied techniques. Students will be trained to understand when to use these modern techniques and to gain experience in integrating the appropriate approaches to solve a biological problem in structural terms. The initial three month theoretical and practical training will emphasize the importance of validating structural data in its biological context as well as current topics such as the idea that macromolecules may have many conformations, which may vary depending on the location and the environment The participating faculty comprises ten scientists with excellent publication and funding records in analysing the structures and functions of biological macromolecules. Together, the faculty employs most of the current techniques available. Eight faculty members have substantial experience in supervising graduate students. The remaining three faculty are younger scientists in the early part of their careers who themselves will be guided in mentoring by the more experienced faculty. The added value of this PhD program lies in the in-depth training in structural biology and complementary techniques, empowering students with both conceptual framework and tools for understanding structure and function of biological molecules. Varied and complementary expertise of the participating faculty will ensure that students will be exposed to all the modern techniques and scientific methodology needed to discover and comprehend how macromolecules work. The proposed PhD projects all emphasize the integrated use of such approaches and the need for biological validation of the results. Students will be supported in their research by a co-supervisor from the program faculty and a PhD committee. Regular meetings with faculty and work in progress seminars will ensure expert scientific supervision, expose the students to methods and lines of reasoning from other areas of biology (structural, computational, cellular biology, biochemistry and biophysics) and provide expert feedback on presentation and other soft skills. Interdisciplinary faculty and the rich scientific environment of the Vienna Biocenter, as well as research stays abroad, will contribute to the academic development of the students. Specific lecture and seminar courses, visits to collaborating laboratories, the organization of an international workshop and participation at international meetings will further extend their scientific development. Courses in accompanying skills such as paper and grant writing, presentation techniques, research ethics, project management, patenting, gender issues and career planning will complete the students education. The PhD program Integrative Structural Biology is geared at producing alumni disciplined in the use of modern techniques to analyze macromolecules, capable of analysing scientific problems by choosing the most suitable approach, and having the creativity to make unexpected discoveries in the future

Consortium
  • Annette Rompel, Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Bojan Zagrovic, Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Clemens Plaschka, Institut für Molekulare Pathologie - IMP
    consortium member (01.01.2016 - 30.09.2021)
  • David Haselbach, Institut für Molekulare Pathologie - IMP
    consortium member (01.01.2016 - 30.09.2021)
  • Dea Slade, Medizinische Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Gang Dong, Medizinische Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Gülsün Elif Karagöz, Medizinische Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Robert Konrat, Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Sebastian Falk, Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
  • Timothy Robin Skern, Medizinische Universität Wien
    consortium member (01.01.2016 - 30.09.2021)
Research institution(s)
  • Universität Wien
  • Medizinische Universität Wien
  • Institut für Molekulare Pathologie - IMP
Project participants
  • Kristina Djinovic-Carugo, Universität Wien , associated research partner
International project participants
  • David Komander, The University of Melbourne - Australia
  • Bostjan Kobe, University of Queensland - Australia
  • Luiz Juliano, Universidade de Sao Paulo - Brazil
  • Lewis E. Kay, University of Toronto - Canada
  • Julie Forman-Kay, University of Toronto - Canada
  • Cheryl H Arrowsmith, University of Toronto - Canada
  • Richard Stefl, Brno University of Technology - Czechia
  • Didier Auboeuf, Ecole Normale Superieure de Lyon - France
  • Fabien Ferrage, Ecole Normale Supérieure - France
  • Geoffrey Bodenhausen, Ecole Normale Supérieure de Paris - France
  • Bernhard Brutscher, UMR 5075 CNRS-CEA-UJF - France
  • Derrick R. Robinson, University of Bordeaux - France
  • Melanie Bonhivers, University of Bordeaux - France
  • Florian Fröhlich, Universität Osnabrück - Germany
  • Bettina Warscheid, Universität Freiburg - Germany
  • Michael Ehrmann, Universität Duisburg-Essen - Germany
  • Dieter O. Fürst, Universität Bonn - Germany
  • Clemens Steegborn, Universität Bayreuth - Germany
  • Carsten Schultz, Ruprecht-Karls-Universität Heidelberg - Germany
  • Enrica Bordignon, Ruhr Universität Bochum - Germany
  • Stefan Raunser, Max-Planck-Gesellschaft - Germany
  • Brenda A. Schulman, Max-Planck-Institut - Germany
  • Vladimir Pena, Max-Planck-Gesellschaft - Germany
  • Samuel Wagner, Universität Tübingen - Germany
  • Ivo Sbalzarini, Max Planck Institut Dresden - Germany
  • Matthias Wilmanns, European Molecular Biology Laboratory Hamburg - Germany
  • Dmitri I. Svergun, European Molecular Biology Laboratory Hamburg - Germany
  • Ulrich Kortz, Constructor University Bremen - Germany
  • Ben Engel, Max-Planck-Institut für Biochemie - Germany
  • Philipp Selenko, Weizmann Institute of Science - Israel
  • Isabella C. Felli, Università degli Studi di Firenze - Italy
  • René F. Ketting, Royal Netherlands Academy of Arts and Sciences - Netherlands
  • Navraj Pannu, Universiteit Leiden - Netherlands
  • Wiktor Kozminski, Warsaw University - Poland
  • Manuel Aureliano, Universidade do Algarve - Portugal
  • Cynthia He, National University of Singapore - Singapore
  • Subhash G. Vasudevan, National University of Singapore - Singapore
  • Xavier Daura, University of Barcelona - Spain
  • Miquel Pons, Universitat Autònoma de Barcelona - Spain
  • Victoriano Garre, University of Murcia - Spain
  • Luis Carrasco, Centro Nacional de Biotecnología - Spain
  • Jose Caston, Centro Nacional de Biotecnología - Spain
  • Nuria Verdaguer, Spanish National Research Council - Spain
  • Gebhard F. X. Schertler, Paul-Scherrer-Institut Villigen - Switzerland
  • Erich A. Nigg, Universität Basel - Switzerland
  • Michael Shirts, University of Colorado Boulder - USA
  • Jorge E. Galan, Yale University - USA
  • Christian Tschudi, Yale University - USA
  • Edward H. Egelman, Virginia State University - USA
  • Karla Kirkegaard, University of Stanford - USA
  • Liwang Cui, University of South Florida - USA
  • Wei Guo, University of Pennsylvania - USA
  • Nicholas G. Brown, University of North Carolina at Chapel Hill - USA
  • Roberto N. De Guzman, University of Kansas - USA
  • Ron D. Vale, University of California at San Francisco - USA
  • Diego Acosta-Alvear, University of California at Santa Barbara - USA
  • David Z. Rudner, Harvard Medical School - USA
  • Karen Oegema, University of California San Diego - USA
  • Eliezer Masliah, University of California San Diego - USA
  • Randy Schekman, University of California Berkeley - USA
  • Kurt Gustin, University of Arizona - USA
  • Ziyin Li, Texas A&M University System - USA
  • Hongmin Qin, Texas A&M University - USA
  • Ke Hu, Indiana University - USA
  • David M. Glover, California Institute of Technology - USA
  • R. Holland Cheng, University of California at Davis - USA
  • David Leys, University of Manchester
  • Feixia Chu, University of New Hampshire
  • Philipp Kukura, University of Oxford
  • Katja Gehmlich, University of Oxford
  • Michael A. Geeves, University of Kent at Canterbury
  • Justin Benesch, University of Oxford
  • John Sutherland, University of Cambridge
  • Steven Cobb, Durham University
  • Chris Tate, Medical Research Council
  • Mathias Gautel, King´s College London
  • Radoslav Enchev, Francis Crick Institute
  • Graham Sandford, Durham University
  • Ho Ying Fu, City University of Hong Kong
  • Perry Eliott, University College London

Research Output

  • 337 Citations
  • 27 Publications
Publications
  • 2019
    Title 19F NMR Spectroscopy Tagging and Paramagnetic Relaxation Enhancement-Based Conformation Analysis of Intrinsically Disordered Protein Complexes
    DOI 10.1002/cbic.201900453
    Type Journal Article
    Author Somlyay M
    Journal ChemBioChem
    Pages 696-701
  • 2018
    Title 1H, 13C, 15N resonance assignment of human YAP 50–171 fragment
    DOI 10.1007/s12104-018-9805-8
    Type Journal Article
    Author Feichtinger M
    Journal Biomolecular NMR Assignments
    Pages 179-182
    Link Publication
  • 2018
    Title 19 F multiple-quantum coherence NMR spectroscopy for probing protein–ligand interactions
    DOI 10.1039/c8ra09296f
    Type Journal Article
    Author Zawadzka-Kazimierczuk A
    Journal RSC Advances
    Pages 40687-40692
    Link Publication
  • 2018
    Title NMR Characterization of Long-Range Contacts in Intrinsically Disordered Proteins from Paramagnetic Relaxation Enhancement in 13C Direct-Detection Experiments
    DOI 10.1002/cbic.201800539
    Type Journal Article
    Author Mateos B
    Journal ChemBioChem
    Pages 335-339
    Link Publication
  • 2018
    Title Exploring Protein Structure: Principles and Practice
    DOI 10.1007/978-3-319-76858-8
    Type Book
    Author Skern T
    Publisher Springer Nature
  • 2018
    Title Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility
    DOI 10.1016/j.jmb.2018.08.017
    Type Journal Article
    Author Pivovarova Y
    Journal Journal of Molecular Biology
    Pages 4209-4229
    Link Publication
  • 2023
    Title The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators
    DOI 10.1038/s41467-023-35853-1
    Type Journal Article
    Author Appel L
    Journal Nature Communications
    Pages 166
    Link Publication
  • 2021
    Title Structural and functional studies of the first tripartite protein complex at the Trypanosoma brucei flagellar pocket collar
    DOI 10.1371/journal.ppat.1009329
    Type Journal Article
    Author Isch C
    Journal PLOS Pathogens
    Link Publication
  • 2021
    Title Structural and functional studies of the first tripartite protein complex at the Trypanosoma brucei flagellar pocket collar
    DOI 10.1101/2021.01.26.428227
    Type Preprint
    Author Isch C
    Pages 2021.01.26.428227
    Link Publication
  • 2021
    Title Hyperphosphorylation of Human Osteopontin and Its Impact on Structural Dynamics and Molecular Recognition
    DOI 10.1021/acs.biochem.1c00050
    Type Journal Article
    Author Mateos B
    Journal Biochemistry
    Pages 1347-1355
    Link Publication
  • 2021
    Title Structural studies of the shortest extended synaptotagmin with only two C2 domains from Trypanosoma brucei
    DOI 10.1016/j.isci.2021.102422
    Type Journal Article
    Author Stepinac E
    Journal iScience
    Pages 102422
    Link Publication
  • 2020
    Title Development and characterization of specific anti-Usutu virus chicken-derived single chain variable fragment antibodies
    DOI 10.1002/pro.3937
    Type Journal Article
    Author Schoenenwald A
    Journal Protein Science
    Pages 2175-2188
    Link Publication
  • 2020
    Title Dissecting distinct proteolytic activities of FMDV Lpro implicates cleavage and degradation of RLR signaling proteins, not its deISGylase/DUB activity, in type I interferon suppression
    DOI 10.1371/journal.ppat.1008702
    Type Journal Article
    Author Visser L
    Journal PLOS Pathogens
    Link Publication
  • 2022
    Title The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators
    DOI 10.1101/2022.02.26.482114
    Type Preprint
    Author Appel L
    Pages 2022.02.26.482114
    Link Publication
  • 2019
    Title Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b
    DOI 10.1021/acscatal.9b00963
    Type Journal Article
    Author Milazzo L
    Journal ACS Catalysis
    Pages 6766-6782
    Link Publication
  • 2019
    Title Crystal structure of the TbBILBO1 N-terminal domain reveals a ubiquitin fold with a long rigid loop for the binding of its partner
    DOI 10.1101/738153
    Type Preprint
    Author Vidilaseris K
    Pages 738153
    Link Publication
  • 2019
    Title Crystal structure of the N-terminal domain of the trypanosome flagellar protein BILBO1 reveals a ubiquitin fold with a long structured loop for protein binding
    DOI 10.1074/jbc.ra119.010768
    Type Journal Article
    Author Vidilaseris K
    Journal Journal of Biological Chemistry
    Pages 1489-1499
    Link Publication
  • 2021
    Title Cosolute modulation of protein oligomerization reactions in the homeostatic timescale
    DOI 10.1016/j.bpj.2021.03.020
    Type Journal Article
    Author Mateos B
    Journal Biophysical Journal
    Pages 2067-2077
    Link Publication
  • 2020
    Title PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC
    DOI 10.1101/2020.02.11.943159
    Type Preprint
    Author Appel L
    Pages 2020.02.11.943159
    Link Publication
  • 2021
    Title PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC
    DOI 10.1038/s41467-021-26360-2
    Type Journal Article
    Author Appel L
    Journal Nature Communications
    Pages 6078
    Link Publication
  • 2021
    Title Defining substrate selection by rhinoviral 2A proteinase through its crystal structure with the inhibitor zVAM.fmk
    DOI 10.1016/j.virol.2021.07.008
    Type Journal Article
    Author Deutschmann-Olek K
    Journal Virology
    Pages 128-141
    Link Publication
  • 2018
    Title Biodegradation of pentafluorosulfanyl-substituted aminophenol in Pseudomonas spp.
    DOI 10.1007/s10532-018-9827-z
    Type Journal Article
    Author Saccomanno M
    Journal Biodegradation
    Pages 259-270
  • 2017
    Title A histone-mimicking interdomain linker in a multidomain protein modulates multivalent histone binding
    DOI 10.1074/jbc.m117.801464
    Type Journal Article
    Author Kostrhon S
    Journal Journal of Biological Chemistry
    Pages 17643-17657
    Link Publication
  • 2017
    Title A novel non-canonical PIP-box mediates PARG interaction with PCNA
    DOI 10.1093/nar/gkx604
    Type Journal Article
    Author Kaufmann T
    Journal Nucleic Acids Research
    Pages 9741-9759
    Link Publication
  • 2020
    Title Vaccinia Virus Immunomodulator A46: Destructive Interactions with MAL and MyD88 Shown by Negative-Stain Electron Microscopy
    DOI 10.1016/j.str.2020.09.007
    Type Journal Article
    Author Azar D
    Journal Structure
    Link Publication
  • 2020
    Title Structural and antigenic investigation of Usutu virus envelope protein domain III
    DOI 10.1016/j.virol.2020.09.002
    Type Journal Article
    Author Josephine Schoenenwald A
    Journal Virology
    Pages 46-57
    Link Publication
  • 2016
    Title Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins
    DOI 10.1371/journal.ppat.1006079
    Type Journal Article
    Author Fedosyuk S
    Journal PLOS Pathogens
    Link Publication

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