Sachse lab

Electron cryomicroscopy of autophagy complexes

Lab members

Carsten Sachse

Carsten Sachse
I am currently a group leader at the EMBL. I got in touch with electron cryomicroscopy by studying amyloid fibrils in the groups of Marcus Fändrich (now in Ulm, Germany) and Niko Grigorieff (now at Janelia Farm, USA). For my postdoctoral period, I went to the MRC Laboratory of Molecular Biology (Cambridge, UK) to work with Richard Henderson and Roger Williams. In the last few years, we set up a group to study the mechanisms of autophagy by electron cryomicroscopy. Traditionally, I have been interested in the advancement of high-resolution single-particle EM with a particular focus on helical reconstruction. These developments have lead to our recent helical processing software package Spring.

Abul Tarafder

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Abul Tarafder. I am currently the lab manager. I completed my PhD on Rab proteins and their role in membrane trafficking at Imperial College, London. I went on to do two post-docs, at Imperial College and subsequently at the IGC, Lisbon, also in the field of membrane trafficking. Currently, I look after the day-to-day running of the lab as well as set up expression/purification strategies for the autophagy complexes we are studying.









Arvind Chand

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Arvind Chand. I am a postdoc in the lab. I am interested in structural biology, in particular single-particle cryo electron microscopy. I am working towards understanding the interaction mechanism of cargo-receptor complex in the Cvt pathway using single-particle cryo electron microscopy. I completed B.tech in Biotechnology from Vellore Institute of Technology (India) and subsequently completed MSc in Biotechnology from The Royal Institute of technology (Sweden). I carried out my PhD thesis work at University of Canterbury (New Zealand). During my time in New Zealand, I studied the interaction of mammalian autophagy proteins (LC3s and GABARAPs) with ULK1 and PLEKHM1 using X-ray crystallography, surface plasmon resonance and molecular dynamics simulation.

Simon Fromm

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Simon Fromm. I'm a PhD student and joined the lab in July 2013. My main research focus is to gain structural knowledge about TDP-43 aggregates which are implicated in several neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD). Besides that I'm also interested in methods development and try to improve various aspects of structure determination by cryo-EM. Before coming to EMBL, I got my diploma in biochemistry (comparable to a master degree) at the University of Tübingen, Germany. During my studies and for my diploma thesis I worked in the lab of Remco Sprangers (MPI Tübingen, Germany) and got a strong interest in structural biology. I applied different biophysical methods like NMR spectroscopy and ITC to study protein complexes involved in mRNA decay.

Arjen Jakobi

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Arjen Jakobi. I am a postdoc in the lab. I studied molecular sciences in Leiden (Netherlands), Erlangen (Germany) and Basel (Switzerland). With a background in molecular simulation and computational chemistry I took a turn to train in X-ray crystallography and obtained my PhD on the structural analysis of von Willebrand Factor mechanoregulation with Eric Huizinga and Piet Gros (Utrecht, Netherlands). I became interested in applying electron cryo-microscopy alongside X-ray crystallography and joined the Sachse lab as an EIPOD fellow jointly with the Wilmann’s lab at EMBL Hamburg to work on the structural characterization of selective autophagy receptors. I also have an interest in method development, in particular the improvement of atomic model refinement against high-resolution cryo-EM density maps.

Maximilian Beckers

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Maximilian Beckers. I am a PhD-student and joined the group in August 2016. With degrees both in mathematics and biochemistry my main interests are in both frequentist and bayesian statistical method development for biophysical data, especially for structure determination of macromeluclar complexes. My previous work was carried out in the group of Jens Michaelis at Ulm University where I worked in the FRETnps development team with a focus on MCMC methods and also at Boehringer Ingelheim in the Computational Chemistry group with a focus on molecular dynamics simulations and trajectory analysis.

Jan Kosinski

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Jan Kosinski. I am a postdoc shared with the Müller and Beck groups under the EIPOD programme. I work on integrative structural modeling of protein complexes. I build structural models based on EM maps, cross-links and other experimental data. I also develop new methods for modeling, and analysis of the models. Before coming to EMBL, I did my PhD in IIMCB in Warsaw, working on bioinformatics and structural modeling of DNA methyltransferases and restriction nucleases, and bioinformatics and experimental characterization of the DNA mismatch repair system. I have already done one postdoc, at Sapienza University, where I developed Modorama platform for structural modeling and characterization of proteins.

Alumni

Chiara Bertipaglia (PhD student), now Postdoc at Columbia University (US)
Jaclyn Chan (Lab technician), now in Perth (AUS)
Rodolfo Ciuffa (PhD student), now Postdoc at ETH Zürich (CH)
Ambroise Desfosses (Postdoc), now Postdoc at University of Auckland (NZ)
Audrey Guesdon (Postdoc), now in Montpellier (FR)
Marie Kirsten (Postdoc), now at Nspm Ltd (CH)
Goran Kokic (Internship 2014), now at Max Planck Institute of Biophysical Chemistry Göttingen (DE)
Tanja Kuhm (Internship 2016), now at Heidelberg University (DE)
Lena Muckenfuss (Internship 2016), now at C-Cina, Biozentrum Basel (CH)
Sofia Rybina (Lab technician), now in Heidelberg (DE)
Sarah Schneider (PhD student), now Postdoc at Imperial College London (UK)
Shirley Tremel (Master student), now PhD at MRC-LMB Cambridge (UK)
Willem Tichelaar (Postdoc), now in Heidelberg (DE)