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Structure and Interaction of Biological Macromolecules

Structure and Interaction of Biological Macromolecules

Timothy Robin Skern (ORCID: )
  • Grant DOI 10.55776/W1221
  • Funding program Doctoral Programs
  • Status ended
  • Start March 1, 2009
  • End August 31, 2014
  • Funding amount € 1,936,541
  • 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 this DK-plus is to provide selected students with an in-depth, interdisciplinary training in scientific method to enable them to comprehend, rigorously analyse and provide solutions to biological problems. To achieve this aim, we have chosen the theme "Structure and Interactions of Biological Macromolecules". This theme contains questions at the heart of modern molecular and cellular biology which can be investigated by a range of powerful and varied techniques. Students will master several of the most modern techniques and to gain experience in choosing the appropriate approaches to solve biological problems in structural terms. The theoretical and practical training will emphasise the interactions of biological macromolecules for determining their function and the prerequisites necessary for interactions and subsequent outcomes. The participating faculty comprises twelve scientists with excellent publication and funding records in analysing the structures and interactions of biological macromolecules. Together, the faculty employ most of the current techniques available. Eight faculty members have substantial experience in supervising graduate students. The remaining four 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 DK-plus lies in the common theme, the supervision and the participating faculty. The students will be exposed to very different techniques and scientific approaches to examine the structures and interactions of biological macromolecules. The projects offered range from the folding of macromolecules through the importance of interactions for determining function in macromolecular complexes to the consequences of protein-protein interactions in pathogenic infectious agents. The students will have a co-supervisor from the program faculty and will be guided by a PhD committee. Lab talks, journal clubs and rotation will expose the students to different ways of thinking and environments and will permit them to master a significantly broader range of techniques than would ever be possible in a PhD outside the program. The scientific development of the students will be promoted by the inter-disciplinary approach of the faculty and the scientific environment of the Vienna Biocenter Campus. Specific lecture and seminar courses, visits to collaborating laboratories, the organisation 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, ethics, project management, gender issues and career planning will round off the students` education. The DK-plus "Structure and interactions of biological macromolecules" is geared to producing alumni disciplined in the use of the scientific method, able to analyse scientific problems with intellectual rigour and having the analytic awareness to make unexpected discoveries in the future.

Consortium
  • Dieter Blaas, Medizinische Universität Wien
    consortium member (01.03.2009 - 31.08.2014)
  • Kristina Djinovic-Carugo, Universität Wien
    consortium member (01.03.2009 - 31.08.2014)
  • Tim Clausen, Institut für Molekulare Pathologie - IMP
    consortium member (01.03.2009 - 31.08.2014)
  • Timothy Robin Skern, Medizinische Universität Wien
    consortium member (01.03.2009 - 31.08.2014)
Research institution(s)
  • Medizinische Universität Wien
  • Institut für Molekulare Pathologie - IMP
  • Universität Wien
  • IMBA – Institut für Molekulare Biotechnologie GmbH
Project participants
  • Thomas Marlovits, IMBA – Institut für Molekulare Biotechnologie GmbH , associated research partner
  • Robert Konrat, Universität Wien , associated research partner
  • Jan-Michael Peters, Institut für Molekulare Pathologie - IMP , associated research partner
International project participants
  • Luiz Juliano, Universidade de Sao Paulo - Brazil
  • Lewis E. Kay, University of Toronto - Canada
  • Anita Krisko, Mediterranean Institute for Life Sciences - Croatia
  • Martin Gregor, Academy of Sciences of the Czech Republic - Czechia
  • Bernhard Brutscher, UMR 5075 CNRS-CEA-UJF - France
  • Bernd Bukau, Ruprecht-Karls-Universität Heidelberg - Germany
  • Bettina Warscheid, Universität Freiburg - Germany
  • Michael Ehrmann, Universität Duisburg-Essen - Germany
  • Dieter O. Fürst, Universität Bonn - Germany
  • Gerhard Hummer, Max-Planck-Institut für Biophysik - Germany
  • Holger Stark, Technische Universität Berlin - Germany
  • Emmanuelle Charpentier, Max-Planck-Gesellschaft - Germany
  • Anthony A. Hyman, Max-Planck-Gesellschaft - Germany
  • Dariush Hinderberger, Max Planck-Institut f. Polymerforschung - Germany
  • Ivo Sbalzarini, Max Planck Institut Dresden - Germany
  • Matthias Wilmanns, European Molecular Biology Laboratory Hamburg - Germany
  • Brenda A. Schulman, Max-Planck-Institut - Germany
  • Navraj Pannu, Universiteit Leiden - Netherlands
  • Bartosz Rozycki, Polish Academy of Sciences - Poland
  • Yuri Drygin, Lomonosov Moscow State University - Russia
  • Xavier Daura, University of Barcelona - Spain
  • Miquel Pons, Institute for Research in Biomedicine - Spain
  • Nuria Verdaguer, Spanish National Research Council - Spain
  • Jose Caston, Centro Nacional de Biotecnología - Spain
  • Luis Carrasco, Centro Nacional de Biotecnología - Spain
  • Philippe Hünenberger, ETH Hönggerberg - Switzerland
  • Wilfred F. Van Gunsteren, ETH Zürich - Switzerland
  • Farrah Kheradmand, Baylor College of Medicine - USA
  • Adrian Elcock, The University of Iowa - USA
  • Kurt Gustin, University of Arizona - USA
  • Karla Kirkegaard, University of Stanford - USA
  • Vijay Pande, University of Stanford - USA
  • Edward H. Egelman, Virginia State University - USA
  • Jorge E. Galan, Yale University - USA
  • John Vakonakis, University of Oxford
  • Mathias Gautel, King´s College London

Research Output

  • 1372 Citations
  • 38 Publications
Publications
  • 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 Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with a-actinin
    DOI 10.1126/sciadv.abg7653
    Type Journal Article
    Author Sponga A
    Journal Science Advances
    Link Publication
  • 2020
    Title Molecular basis of F-actin regulation and sarcomere assembly via myotilin
    DOI 10.1101/2020.09.25.310029
    Type Preprint
    Author Kostan J
    Pages 2020.09.25.310029
    Link Publication
  • 2020
    Title In-depth interrogation of protein thermal unfolding data with MoltenProt
    DOI 10.1002/pro.3986
    Type Journal Article
    Author Kotov V
    Journal Protein Science
    Pages 201-217
    Link Publication
  • 2019
    Title Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats
    DOI 10.1101/826180
    Type Preprint
    Author Sajko S
    Pages 826180
    Link Publication
  • 2019
    Title HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C
    DOI 10.1126/sciadv.aav8421
    Type Journal Article
    Author Collier M
    Journal Science Advances
    Link Publication
  • 2018
    Title Phosphorylation of HspB1 regulates its mechanosensitive molecular chaperone interaction with native filamin C
    DOI 10.1101/325712
    Type Preprint
    Author Collier M
    Pages 325712
    Link Publication
  • 2021
    Title FLNC-Associated Myofibrillar Myopathy
    DOI 10.1212/nxg.0000000000000590
    Type Journal Article
    Author Kley R
    Journal Neurology: Genetics
    Link Publication
  • 2021
    Title Molecular basis of F-actin regulation and sarcomere assembly via myotilin
    DOI 10.1371/journal.pbio.3001148
    Type Journal Article
    Author Kostan J
    Journal PLOS Biology
    Link Publication
  • 2020
    Title X-ray–induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner
    DOI 10.1074/jbc.ra120.014087
    Type Journal Article
    Author Pfanzagl V
    Journal Journal of Biological Chemistry
    Pages 13488-13501
    Link Publication
  • 2020
    Title Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats
    DOI 10.1371/journal.pone.0242677
    Type Journal Article
    Author Sajko S
    Journal PLOS ONE
    Link Publication
  • 2023
    Title Unlocking Predictive Power: A Machine Learning Tool Derived from In-Depth Analysis to Forecast the Impact of Missense Variants in Human Filamin C
    DOI 10.1101/2023.08.05.552086
    Type Preprint
    Author Nagy M
    Pages 2023.08.05.552086
    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
  • 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 Calcium modulates the domain flexibility and function of an a-actinin similar to the ancestral a-actinin
    DOI 10.1073/pnas.1917269117
    Type Journal Article
    Author Pinotsis N
    Journal Proceedings of the National Academy of Sciences
    Pages 22101-22112
    Link Publication
  • 2022
    Title A Potential Citrate Shunt in Erythrocytes of PKAN Patients Caused by Mutations in Pantothenate Kinase 2
    DOI 10.3390/biom12020325
    Type Journal Article
    Author Werning M
    Journal Biomolecules
    Pages 325
    Link Publication
  • 2015
    Title Structural Insights into Ca2+-Calmodulin Regulation of Plectin 1a-Integrin ß4 Interaction in Hemidesmosomes
    DOI 10.1016/j.str.2015.01.011
    Type Journal Article
    Author Song J
    Journal Structure
    Pages 558-570
    Link Publication
  • 2017
    Title Hydrophobic Collapse of the Intrinsically Disordered Transcription Factor Myc Associated Factor X
    DOI 10.1021/acs.biochem.7b00679
    Type Journal Article
    Author Kizilsavas G
    Journal Biochemistry
    Pages 5365-5372
    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
  • 2017
    Title Conformational plasticity and evolutionary analysis of the myotilin tandem Ig domains
    DOI 10.1038/s41598-017-03323-6
    Type Journal Article
    Author Puž V
    Journal Scientific Reports
    Pages 3993
    Link Publication
  • 2016
    Title Topology and structure of an engineered human cohesin complex bound to Pds5B
    DOI 10.1038/ncomms12523
    Type Journal Article
    Author Hons M
    Journal Nature Communications
    Pages 12523
    Link Publication
  • 2015
    Title 1H, 15N, 13C resonance assignment of human osteopontin
    DOI 10.1007/s12104-014-9594-7
    Type Journal Article
    Author Platzer G
    Journal Biomolecular NMR Assignments
    Pages 289-292
    Link Publication
  • 2015
    Title Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels
    DOI 10.1038/srep08769
    Type Journal Article
    Author Bezerra G
    Journal Scientific Reports
    Pages 8769
    Link Publication
  • 2011
    Title Mutations in the N-terminal Actin-Binding Domain of Filamin C Cause a Distal Myopathy
    DOI 10.1016/j.ajhg.2011.04.021
    Type Journal Article
    Author Duff R
    Journal The American Journal of Human Genetics
    Pages 729-740
    Link Publication
  • 2011
    Title Lipocalin Q83 Reveals a Dual Ligand Binding Mode with Potential Implications for the Functions of Siderocalins
    DOI 10.1021/bi201115q
    Type Journal Article
    Author Coudevylle N
    Journal Biochemistry
    Pages 9192-9199
  • 2011
    Title The Metastasis-Associated Extracellular Matrix Protein Osteopontin Forms Transient Structure in Ligand Interaction Sites
    DOI 10.1021/bi200291e
    Type Journal Article
    Author Platzer G
    Journal Biochemistry
    Pages 6113-6124
  • 2011
    Title Random Mutagenesis of the Prokaryotic Peptide Transporter YdgR Identifies Potential Periplasmic Gating Residues*
    DOI 10.1074/jbc.m111.239657
    Type Journal Article
    Author Malle E
    Journal Journal of Biological Chemistry
    Pages 23121-23131
    Link Publication
  • 2013
    Title Cooperative Unfolding of Compact Conformations of the Intrinsically Disordered Protein Osteopontin
    DOI 10.1021/bi400502c
    Type Journal Article
    Author Kurzbach D
    Journal Biochemistry
    Pages 5167-5175
    Link Publication
  • 2013
    Title Electron microscopy structure of human APC/CCDH1–EMI1 reveals multimodal mechanism of E3 ligase shutdown
    DOI 10.1038/nsmb.2593
    Type Journal Article
    Author Frye J
    Journal Nature Structural & Molecular Biology
    Pages 827-835
    Link Publication
  • 2010
    Title The v-myc-induced Q83 Lipocalin Is a Siderocalin*
    DOI 10.1074/jbc.m110.123331
    Type Journal Article
    Author Coudevylle N
    Journal Journal of Biological Chemistry
    Pages 41646-41652
    Link Publication
  • 2010
    Title Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1
    DOI 10.1038/nsmb.1979
    Type Journal Article
    Author Buschhorn B
    Journal Nature Structural & Molecular Biology
    Pages 6-13
    Link Publication
  • 2014
    Title Characterization of a DNA exit gate in the human cohesin ring
    DOI 10.1126/science.1256904
    Type Journal Article
    Author Huis In 'T Veld P
    Journal Science
    Pages 968-972
  • 2013
    Title CtpB Assembles a Gated Protease Tunnel Regulating Cell-Cell Signaling during Spore Formation in Bacillus subtilis
    DOI 10.1016/j.cell.2013.09.050
    Type Journal Article
    Author Mastny M
    Journal Cell
    Pages 647-658
    Link Publication
  • 2013
    Title Characterization and Structure of the Vaccinia Virus NF-?B Antagonist A46 *
    DOI 10.1074/jbc.m113.512756
    Type Journal Article
    Author Fedosyuk S
    Journal Journal of Biological Chemistry
    Pages 3749-3762
    Link Publication
  • 2013
    Title Strategies for purifying variants of human rhinovirus 14 2C protein
    DOI 10.1016/j.pep.2013.11.012
    Type Journal Article
    Author Sára T
    Journal Protein Expression and Purification
    Pages 28-37
  • 2012
    Title APC15 mediates CDC20 autoubiquitylation by APC/CMCC and disassembly of the mitotic checkpoint complex
    DOI 10.1038/nsmb.2412
    Type Journal Article
    Author Uzunova K
    Journal Nature Structural & Molecular Biology
    Pages 1116-1123
    Link Publication
  • 2012
    Title 1H, 13C, and 15N backbone and side chain resonance assignments of the C-terminal DNA binding and dimerization domain of v-Myc
    DOI 10.1007/s12104-012-9437-3
    Type Journal Article
    Author Kizilsavas G
    Journal Biomolecular NMR Assignments
    Pages 321-324
    Link Publication
  • 2011
    Title Siderocalin Q83 exhibits differential slow dynamics upon ligand binding
    DOI 10.1007/s10858-011-9543-z
    Type Journal Article
    Author Coudevylle N
    Journal Journal of Biomolecular NMR
    Pages 83

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