Several projects were not continued in the second funding period (2016 – 2019) or will not be continued in the third funding period (2020 – 2023).
Research Area A
Project A03: Wolfram Welte / Kay Diederichs
Biogenesis of ß-barrel proteins from Thermus thermophilus: Structure and mechanism
The correct and controlled integration of bacterial or organelle outer membrane proteins (OMPs) is prerequisite for cell viability. Proteins from the Omp85 family promote outer membrane integration of target β-barrel proteins (OMPs), yet neither the structure of an Omp85 protein nor most of the events associated with membrane assembly are known. We shall investigate the assembly of OMPs in Thermus thermophilus, expecting benefits from the thermophilic proteins. Providing structural information of TtOmp85 is central to this project. Functional mechanisms will be studied in collaboration with project A02. Omp85 family members from diatoms are investigated in collaboration with project A04.
Project A04: Peter Kroth
Biogenesis and integration of metabolite translocators into membranes surrounding complex plastids
In this project we want to study processes involved in the transport of proteins across multiple membranes of diatom plastids. For this purpose we will characterize components of the import machinery like the diatom Omp85 protein as well as integration processes of metabolite translocators into individual membranes. Furthermore, we will investigate in collaboration with B05 the possible role of preprotein glycosylation in the chloroplast ER for the function and integration of membrane proteins.
Research Area B
Project B02: Martin Scheffner
Deregulation of protein ubiquitylation by human papillomavirus E6 oncoproteins
We are studying the interaction of E6 proteins derived from different human papillomaviruses (HPVs) with the cellular E3 ubiquitin ligase E6AP. By a combination of defined ubiquitylation systems and mass spectrometry, we will identify substrates of the E6-E6AP complex and, in consequence, cellular pathways that are affected by E6 and E6AP. Furthermore, we will perform high-throughput-screens to identify small compounds that interfere with the E3 activity of the E6-E6AP complex and that can be used to functionally characterize the E6-E6AP complex in cells. Finally, cell fractionation studies will be used to identify cellular proteins that like the viral E6 proteins stimulate the E3 activity of E6AP. The results obtained will provide insight into the mechanisms by which HPVs reprogram host cells for their own need, and into the function of E6AP in normal, non-infected cells.
Project B04: Alexander Bürkle / Elisa Ferrando-May
Functional regulation of proteins by poly(ADP-ribose)
Poly(ADP-ribosyl)ation is the enzymatic posttranslational modification of proteins with poly(ADP-ribose) (PAR), a linear or multibranched polyanion of variable size that can also bind non-covalently to numerous proteins via specific PAR binding motifs. In this project we propose to investigate two PAR-interacting proteins, i.e. DEK, a chromatin protein, and XPA, a member of the nucleotide excision repair pathway, as model proteins. By characterizing in detail how PAR affects DEK and XPA activities, we aim at a better understanding of the mechanisms of PAR-dependent regulation of protein function.
Project B08: Andreas Marx / Andreas Zumbusch
Nucleotide-based activity probes: Dye-labeled ATP-analogues
The aim of this project is the development of tools for the analysis of protein activity in living cells. For this purpose, chemical synthesis of novel, fluorescently labelled ATP analogues is combined with the implementation of suitable optical live cell imaging techniques. The concept relies on the readout of changes in Förster resonance energy transfer (FRET) with high spatial and temporal resolution. The successful application of this concept has been proven in the first funding period and will be extended further in the future. For this purpose, we will collaborate extensively within the consortium, i.e., concerning ubiquitin activation (project B02), kinase (project B06) and kinesin (project B07) activities, and protein glycosylations (project B05).
Research Area C
Project C02: Iwona Adamska
Protein quality control by DEG/HtrA proteases in the plant nucleus
In this project protein quality control and signaling by DEG/HtrA proteases will be investigated in various nuclear subcompartments of Arabidopsis thaliana. DEG/HtrA proteases belong to a large family of ATP-independent serine endopeptidases with chaperone activities. We intend to study a possible role (as a protease and/or chaperone; together with project A05) of DEG7 during programmed cell death in the plant nucleoplasm and compare this role with the yeast DEG7/Nma111p ortholog involved in apoptosis. Furthermore, a role of DEG9 in early steps of ribosomal biogenesis (in collaboration with A01) will be investigated in the plant nucleolus.
Project C04: Marcel Leist
Alpha-synuclein-induced stress as trigger of mitophagy and altered mitochondrial dynamics
The project investigates the role of alpha-synuclein (ASYN) in mitochondrial turnover, with focus on posttranslational oxidative modifications (tyrosine nitration, methionine sulfoxidation) of the protein and their role in lipid binding. In close interaction with groups of projects A02 und C03, ASYN variant formation and association with mitochondria or model membranes will be studied cell-free and in neurons. Changes in mitochondrial turnover (proteolysis; mitophagy) and of their fusion/fission will be studied as functional consequences of ASYN membrane binding and chemical modification.
Project C05: Malte Drescher / Marcel Leist / Christine Peter
Local and transient structural features of the intrinsically disordered protein alpha-synuclein
The classical concept of proteostasis assumes a steady state between folding and misfolding of proteins. This picture gets considerably more complex for intrinsically disordered proteins (IDPs), since they exist in multiple conformational states. The Parkinson protein α-synuclein (ASYN) is a model system among the IDPs. A traditional view is that ASYN is disordered in solution and can adopt a variety of stable conformations upon macromolecular interaction. However, findings that ASYN assumes structured features already in solution, suggest an alternative hypothesis for its role in proteostasis that will be investigated in the present project by combining molecular simulation, spectroscopy, and biological in vitro experiments.
Project C06: Thomas Böttcher
Bacterial metabolites influencing cross-species proteostasis
Metabolites play multiple roles in the communication and coordination of bacterial cells and in the interaction with a eukaryotic host. In this project, we aim to investigate the effect of metabolites as modulators of cross-species proteostasis. We will employ activity-based probes to detect changes of enzyme activities upon exposure to foreign metabolites in proteomes of commensal bacteria and use a competitive strategy to identify bacterial metabolites as selective inhibitors of the proteasome and selected E2 and E3 ligases of a eukaryotic host.
Our goal is to investigate the effects of bacterial metabolites on proteostasis and gain a better understanding of the complex interactions of the human microbiome.
Project C07: Olga Mayans / Kay Diederichs
Molecular determinants of the catalytic and scaffolding functions of the E3 ubiquitin ligase MuRF1 in the muscle sarcomere
The muscle tissue undergoes constant remodelling to adapt its performance to mechanical demands and (patho)physiological cues. MuRF1, a muscle-specific E3 ubiquitin ligase, targets filamentous components of the muscle sarcomere in situ and constitutes a primary catabolic pathway for the turn-over of this tissue, thereby being of high biomedical relevance. Building on the combined expertise of this CRC, we will employ X-ray crystallography, biophysical, computational and biochemical methods to study the molecular targeting of filamentous proteins by MuRF1. This work will reveal the mechanistic mode of action of MuRF1 in the myofibril and the principles of its regulation. Our overarching aim is to understand how the cell deconstructs its cytoskeletal architectures by using sarcomere protein components as representative examples.