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Project

Protein folding oscillations in the secretome

Proteins are made in microscopic factories inside cells. They come out as unstructured chains of hundreds of aminoacids but must fold into defined 3D shapes before they can become functional. 70% of them do this in the cytoplasm very fast, usually in the millisecond to second range. Another 30% of proteins undergo temporally delayed and topologically altered folding. These will only fold after they are targeted to and have inserted through or crossed membranes. Some of these proteins will form channels and pores, sensors, antibodies, bacterial toxins, metastatic proteases and hormones. These are carefully orchestrated processes usually executed with astonishing fidelity. Nevertheless, occasional mis-folding causes aggregation and diseases like Alzheimer’s. For years, the global research effort has divided these processes and studied them in isolation, e.g. folding, mainly with a few cytoplasmic model proteins, secretion through the plasma membrane and the ER. And yet the protein polymer backbone that undergoes these transitions has features that are universal. What decides the different folding and localization fates of these polypeptides and what takes them to aggregation routines? What are the individual contributions of the polypeptide polymer properties and its dynamics when it oscillates from one to another state and how are these affected by cellular factors? Here we propose a unifying effort of these protein behaviours, to address these fundamental questions and derive universal principles.Our experimental approach is three-pronged and multi-disciplinary. Firstly, advanced structural bioinformatics to monitor backbone dynamics and predict/map of folding or aggregation cascades. Secondly, exploitation of our unique collection of proteins from E.coli bacteria that cover all possible behaviours from fast folding to amyloid formation and their combination with multiple chaperones. Thirdly, application of a globally unique combination of three state-of-the art biophysical tools that is powerful in revealing dynamics and energetics of protein conformations and conformational states: hydrogen deuterium exchange mass spectrometry, single molecule FRET and force nanoscopy. Over the past 4 years we have set up these methods in our lab or through collaborations. Biophysical tools will be combined with functional in vitro and in vivo assays.Our work takes on a major challenge and it exploits the secretome to explore more deeply the 'folding /mis-folding' problem and contribute to revealing fundamental principles.
Date:1 Oct 2018 →  Today
Keywords:HDX-MS, smFRET, signal peptide, protein secretion, protein folding, force nanoscopy, chaperones, protein mis-folding/aggregation
Disciplines:Biomaterials engineering, Biological system engineering, Biomechanical engineering, Other (bio)medical engineering, Environmental engineering and biotechnology, Industrial biotechnology, Other biotechnology, bio-engineering and biosystem engineering, Immunology, Microbiology, Systems biology, Laboratory medicine