Dr. Arjen Jakobi

Research Theme(s): Nanoscopy, Cell biophysics, Cell biology

Research Interests: Membrane remodeling, cryo-EM, macromolecular structure and dynamics, intracellular immunity

Biography

I am an assistant professor at the Department of Bionanoscience, which is part of the Kavli Institute of Nanoscience in Delft.

I studied molecular sciences at Leiden University and the University of Erlangen, initially focussing on the application of computational quantum chemistry methods to structure-based drug design. I became fascinated by the complexity of protein structures, and the wish to understand them prompted an interest in experimental biophysics. During my doctoral studies at the Bijvoet Center for Biomolecular Research in Utrecht I combined structural biology and single-molecule biophysics to understand the regulatory mechanism of a nanoscale mechanosensory protein involved in bleeding arrest. I then joined the European Molecular Biology Laboratory (EMBL), where I used electron cryo-microscopy (cryo-EM) to study large molecular assemblies involved in selective autophagy. This triggered my interest in understanding the mechanism by which large protein assemblies shape and disrupt biological membranes. Since starting my own group in 2018, we are focusing on understanding how cells build up autonomous immunity by using their membrane remodeling machinery to dispose of intracellular pathogens. This knowledge is highly relevant to develop new strategies for fighting off such pathogens that are otherwise difficult to target. In our group we use cryogenic electron imaging techniques to visualize these highly dynamic processes at high resolution. We think that electron imaging is uniquely posed to addressing these questions, and we develop technical tools and computational methods to help push the frontiers of cryo-EM that will make this possible. For more information regarding our research please visit http://cryoem.tudelft.nl.

   

 

Courses

High-resolution imaging (NB4020)

Physical Biology of the Cell 2 (NB2071)

Protein Structure: Theory and Tools (NB3012)

Current Projects

Highlight Publications

1. Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Johansen T, Brech A, Sachse C. Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake
Nature Communications 11: 440 (2020) | pdf | doi |      Access the recommendation on F1000Prime
Associated data:         

2. Jakobi AJ, Wilmanns M, Sachse C.
Model-based local density sharpening of cryo-EM maps.
eLife 6: e27131 (2017) | pdf | doi |      Access the recommendation on F1000Prime
Associated data:     

3. Jakobi AJ#*, Passon DM, Knoops K, Stellato F, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M#.
In cellulo X-ray Diffraction of Native Alcohol Oxidase Crystals in Yeast Cells by Serial Femtosecond Crystallography
IUCrJ 3: 88-95 (2016) #corresponding author, *equal contribution | pdf | doi |  

       Highlighted in IUCrJ Editorial Notes, DESY Photon Science Highlights
       Featured in: DESY News, Femto, Research in Germany, CUI, chemie.de

4. Hoffmann NA, Jakobi AJ, Morcillo-Moreno M, Glatt S, Sachse C, Mueller CW.
Molecular structures of unbound and transcribing RNA polymerase III.
Nature 528: 231-236 (2015) | doi |           Access the recommendation on F1000Prime

       Highlighted in Nature News and Views
       Featured in EMBL News

5. Jakobi AJ, Mashaghi A, Tans S, Huizinga EG.
Calcium modulates force sensing by the von Willebrand Factor A2 domain
Nature Communications 2: e385 (2011) | pdf | doi |    

 

Assistant Professor

Arjen Jakobi

Management Assistant

Tracey de Ruijter