Center for Molecular Medicine Cologne

February 04, 2021 - Thursday

11.00 - 1.30 p.m.

 

Workshop 2

Assembly, regulation and dynamics of multi-subunit complexes in cellular signaling

Organizers
Alessandro Annibaldi - CMMC-Lab. of Cell Death, Inflammation and Immunity
Débora B Trentini Schmidt  - CMMC-Lab. Protein Quality Control and Stress Response 
Simon Pöpsel  - CMMC-Lab. of Structure and Biochemistry of Epigenetic Regulators

Proteins exert their function in the context of dynamic interactions with other biomolecules, typically as part of larger, multi-subunit assemblies. Interaction partners may serve as substrates, regulatory cofactors, scaffold or partners of enzymatic cross-talk. The analysis of molecular interactions and their dynamics becomes of crucial importance to study larger scale processes at the basis of cellular signaling. Available experimental approaches, however, often reveal limitations that preclude a comprehensive and mechanistic exploration of complex functions. Changing our perspective is needed to identify larger scale implications or finer mechanistic details of observed interactions. Therefore, multi-faceted strategies, bringing together scientists with different areas of expertise, are needed to fully characterize such complexes.  

For example, the composition of many chromatin associated complexes has been known for decades, but the interplay of subunits and their role within the cell remain enigmatic. Similarly, cell death-mediating complexes have been increasingly characterized in terms of participating proteins and their roles. However, the three-dimensional architecture and mechanistic details of interactions within these death-promoting complexes have remained elusive to date.  

Our workshop is designed to explore and exchange where we encounter such boundaries in our own research, and how, through interactions and collaborations, we could facilitate breaking such barriers. We will discuss the strengths and limitations of our experimental approaches, and how collaborative efforts could help us draw a bigger or a more detailed picture of our favorite biological systems. To analyze and visualize the dynamics and molecular details of multi-subunit protein complexes we will particularly focus on

  • Cryo-EM
  • Cross-linking mass spectrometry and
  • Single Cell Imaging

Covering a number of biological processes, we aim to exchange different perspectives and approaches to identifying and assaying the dynamic action of proteins as they change the fate of a cell. 

Digital interactive  workshop via Zoom-Meeting
Alessandro Annibaldi, Débora B Trentini Schmidt and Simon Pöpsel (organizers) are pleased to welcome the on-site workshop participants (see below) and the participants who will join the workshop via Go-To-Meeting.

Participants of the roundtable discussions - digital format:

Background information:
A) General publications introducing the topic

  • Challenges and opportunities in cryo-EM single-particle analysis
    Dmitry Lyumkis (2019) J Biol Chem. 2019 Mar 29;294(13):5181-5197. https://pubmed.ncbi.nlm.nih.gov/30804214/
     
  • Characterization of the TNFR1-SC Using "Modified Tandem Affinity Purification" in Conjunction with Liquid Chromatography-Mass Spectrometry (LC-MS)
    Matthias Reichert, Amandeep Bhamra, Sebastian Kupka, Henning Walczak (2018) Methods Mol Biol. 2018;1857:161-169. https://pubmed.ncbi.nlm.nih.gov/30136240/
     
  • Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology
    Francis J O'Reilly, Juri Rappsilber (2018) Nat Struct Mol Biol Actions. 2018 Nov;25(11):1000-1008. https://pubmed.ncbi.nlm.nih.gov/30374081/
     
  • Single-particle cryo-EM-How did it get here and where will it go
    Yifan Cheng (2018) Science. 2018 Aug 31;361(6405):876-880. https://pubmed.ncbi.nlm.nih.gov/30166484/
     
  • The development of cryo-EM into a mainstream structural biology technique
    Eva Nogales (2016) Nat Methods. 2016 Jan;13(1):24-7. https://pubmed.ncbi.nlm.nih.gov/27110629/
     
  • A primer to single-particle cryo-electron microscopy
    Yifan Cheng, Nikolaus Grigorieff, Pawel A Penczek, Thomas Walz (2015) Cell. 2015 Apr 23;161(3):438-449. https://pubmed.ncbi.nlm.nih.gov/25910204/

B) Interesting publications of the organizers

  • Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3
    Ksenia Finogenova, Jacques Bonnet, Simon Poepsel, Ingmar B Schäfer, Katja Finkl, Katharina Schmid, Claudia Litz, Mike Strauss, Christian Benda, Jürg Müller (2020) Elife. 2020 Nov 19;9:e61964.
    https://pubmed.ncbi.nlm.nih.gov/33211010/
     
  • Death Receptors and Their Ligands in Inflammatory Disease and Cancer
    Alessandro Annibaldi, Henning Walczak (2020) Cold Spring Harb Perspect Biol. 2020 Sep 1;12(9):a036384.
    https://pubmed.ncbi.nlm.nih.gov/31988141/
     
  • Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes
    Simon Poepsel, Vignesh Kasinath, Eva Nogales (2018) Nat Struct Mol Biol. 2018 Feb;25(2):154-162. https://pubmed.ncbi.nlm.nih.gov/29379173/
     
  • Ubiquitin-Mediated Regulation of RIPK1 Kinase Activity Independent of IKK and MK2
    Alessandro Annibaldi, Sidonie Wicky John, Tom Vanden Berghe, Kirby N Swatek, Jianbin Ruan, Gianmaria Liccardi, Katiuscia Bianchi, Paul R Elliott, Sze Men Choi, Samya Van Coillie, John Bertin, Hao Wu, David Komander, Peter Vandenabeele, John Silke, Pascal Meier (2018) Mol Cell. 2018 Feb 15;69(4):566-580.e5. https://pubmed.ncbi.nlm.nih.gov/29452637/
     
  • MK2 Phosphorylates RIPK1 to Prevent TNF-Induced Cell Death
    Isabel Jaco, Alessandro Annibaldi, Najoua Lalaoui, Rebecca Wilson, Tencho Tenev, Lucie Laurien, Chun Kim, Kunzah Jamal, Sidonie Wicky John, Gianmaria Liccardi, Diep Chau, James M Murphy, Gabriela Brumatti, Rebecca Feltham, Manolis Pasparakis, John Silke, Pascal Meier (2017) Mol Cell. 2017 Jun 1;66(5):698-710.e5. https://pubmed.ncbi.nlm.nih.gov/28506461/

 

Overview of the Workshops

Feb. 04, 2021:

8.30 - 11.00 a.m.

WP 1  Integrative data handling for improved human health research
Katarzyna Bozek and Philipp Antczak

11.00 - 1.30 p.m.

WP 2 Assembly, regulation and dynamics of multi-subunit complexes in cellular signaling
Alessandro Annibaldi, Débora B Trentini Schmidt and Simon Pöpsel

2.00 - 4.30 p.m.

WP 3 Targeted treatment of patients through single-cell multi-OMICs Profiling
Robert Hänsel-Hertsch and Philipp Antczak