Johannes Schöneberg

    Dr. Johannes Schöneberg, postdoc

Membrane  | Optical Tweezing |  FRET   |  ReaDDy  |  Reaction-Diffusion 

ESCRT | ClathrinRhodopsin 

Publications | Git  |  CV  


    Enjoy browsing my science!

4D Big Data Lattice Light-sheet Imaging

Figure 1: I combine my CS, biophysics and microscopy background with advanced 4D lattice light-sheet imaging.

Scope Engineering

Optical Tweezing of Membrane Nanotubes

Figure 2: Optical Tweezing of Membrane Nanotubes means to use an optical trap to pull a small membrane nanotube from e.g. a giant unilamellar vesicle (GUV). These nanotubes allow studying protein-membrane biophysics on tubular, highly curved membranes. They resemble vesicle necks found e.g. in normal topology budding (e.g. Clathrin mediated endocytosis) and reverse topology budding (ESCRT system). Left: The Confleezers 1.0 that combines confocal microscopy with optical tweezing. Right: Membrane nanotubes pulled from model membranes using micromanipulators (top) and the trap of the Confleezers (bottom).

SNX9 BAR domain mediated membrane constriction and fission

Figure 3: The BAR domain protein SNX9 (green) gets recruited by the lipid PI(3,4)P2 to the neck of a nascent vesicle bud. It bridges between  the formation of the clathrin coat (red) and the eventual neck scission event catalyzed by dynamin (blue). See more on our theoretical and experimental work on the process here:

J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, V Haucke, F Noé, (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications 8, 15873 doi: 10.1038/ncomms15873. (*equal contribution). 

Reverse-topology membrane scission by the ESCRT proteins
Figure 4: Have a look at Janet's illustrations for different models of ESCRT function in the review:

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteinsNature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).

smFRET-based Structure Determination of Intrinsically Flexible Proteins

Figure 5: As a first step in structure determination, an exhaustive ensemble of the conformation space is generated by molecular simulations. A: We start with a protein structure proposal that consists of a rigid domains (red, orange, grey) and flexible linkers (blue).  B: Coarse-grained replica exchange Monte Carlo simulations then explore the conformational space of the protein structure. This ensemble is the starting point for structure selection by using the experimentally derived smFRET distance distributions.

Rhodopsin - G-Protein Activation Cascade on the Disk Membrane

Figure 6We can see the stars because highly efficient photodetector molecules, rhodopsins (purple), become activated (yellow, white arrows) by capturing the star's photons. Activated rhodopsins can now in turn activate G-proteins (blue) triggering the downstream reactions of the photo-activation cascade. Using breakthrough cryo-EM tomography we were able to determine that rhodopsin is highly organized on disk membranes as tracks. 
Using ReaDDy, we could determine how this arrangement could be highly beneficial for the photoactivation cascade: We simulated free diffusing rhodopsin (left, grey trace), rhodopsin arranged in tracks but no R-G-pre-complexes (middle, black trace), rhodopsin arranged in tracks with R-G-pre-complexes (green) (right, red trace). The tracks + preCplx condition leads to rhodopsin tracks acting as kinetic traps and to biphasic kinetics (red curve). See our work in Structure 2015Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics.
Previously, before we discovered the highly organized arrangement of rhodopsin, using ReaDDy, we were able to simulate a model of the R-G photo-activation cascade, assuming uniform distribution and free diffusion of rhodopsin molecules. Note the highly crowded environment due to the high rhodopsin density. See our work in the Biophysical Journal 2014: Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes.


ReaDDy Logo Movie on Population Growth

ReaDDy is a particle-based reaction-diffusion simulation software. It features

  1. simulation in and on arbitrary geometries (i.e. 3D, 2D, spherical,...),
  2. spatial confinement (walls, boxes, tubes, ...),
  3. excluded volume of particles (crowding effects) and
  4. particle-particle interaction potentials (repulsion, attraction, clustering, ...).
ReaDDy's modular architecture separates between a 'particle dynamics'-core and a reaction engine. This allows to exchange the core by different dynamics implementations (there are currently a Brownian Dynamics and a Monte Carlo Core available) and third party particle codes. ReaDDy is open source under BSD-3clause. See more under, contribute under gitHub/readdy and read the paper under Schöneberg and Noé, PLOS ONE, 2013. Also check out the newest ReaDDy developments here.
Figure 7: The ReaDDy logo and part of ReaDDy's software architecture is depicted. The architecture shows the feature of exchangeable paticle dynamics core implementations.

ReaDDy Summer Schools 

One-week hands-on experiences to learn and develop in ReaDDy:

Tutorial on Software during Nice Winter School 2014

We were giving a tutorial on our software and methods during the winter school 'Modeling Large Molecular Assemblies' in December 2014 in Nice.

Particle-Based Reaction-Diffusion Simulations

I did research different reaction-diffusion systems, including

  • The Rod cell photoactivation cascade
  • Ribosome-tRNA interaction
  • Synaptic Exocytosis
  • Synaptic Endocytosis
The following picture provides an overview of applications and levels of modeling detail.

Figure 8: The figure shows three application examples of particle-based reaction-diffusion simulations. Left: Snapshots of a predator-prey simulation in the topology of the ReaDDy logo (full movie). Center: Simulation of synaptic exocytosis. Synaptic vesicles (yellow) can fuse with the membrane (grey disk) when thy bind a SNARE complex (red). SNARE complexes form from Syx (blue) and Snap-25 (grey) when they collide with a certain probability. Syx and Snap-25 are given attraction potentials and form clusters with themselves. A calcium channel is depicted (green) that emits Ca2+ ions (small green particles. Right: Fine-grain use of ReaDDy. The system depicted in Center in a finer molecular representation. Syx molecules consist of a membrane anchor (blue), an extended linker (red) and a terminal domain (dark gray). Synaptobrevin (orange+yellow) and synaptotagmin (dark green+grey+light green) are constructed in a similar way. Harmonic spring potentials provide the shape of the particle groups.

Spatial Predator Prey Simulation

More movies here.

Constraint-Based Molecular Dynamics  /   Structure Prediction

Figure 9: MHC peptide structure prediction and enhanced sampling. A: An MHC class I molecules is depicted (blue). The peptide binding pocket is clearly visible (in between the two alpha-helices). A peptide that is bound to MHC is depicted in orange. B: Enhanced sampling results for peptide conformations within the MHC binding pocket (pocket is omitted form the visualization). The peptide backbone is depicted in cyan, the peptide side chains in red. Note the tighter binding on the termini of the peptide (left and right) and the higher degree of flexibility towards the center. C: Certain peptides have been found to occur in two distinct bound conformations (arginine residues (red) once sticking out (top) and once buried in the groove (bottom)). The sampling algorithm's performance is demonstrated by starting from one conformation (red eg. pointing upwards) and trying to sample the other (green eg. pointing down).

In order to decode the language of the immune system (to facilitate vaccine generation) , I did research on peptide binding to MHC class I proteins (stronger binding peptides correlate with a stronger immune response). I wrote a software that

1) determined peptide conformations in the binding pocket of MHC-class I proteins based on the MD substitute CONCOORD,

2) calculated the binding energy between peptide and binding pocket and

3) ranked different peptides according to their binding energy.

Scientific Image Analysis

I write sophisticated image analysis tools in Python and ImageJ/Fiji. 


UC Berkeley

2017 - today

Postdoc in 4D big data lattice lightsheet microscopy and 3D cell biology, Betzig Lab & Drubin Lab 

2015 - 2017

Postdoc in experimental molecular membrane biochemistry and biophysics, Hurley Lab & Bustamante Lab 

Max Planck Institute of Biophysics

2014 - 2017

Postdoc in theoretical molecular membrane biochemistry and biophysics, Hummer Lab

Max Planck Institute for Molecular Genetics Berlin / Free University Berlin

2009 - 2014

PhD Biophysics
IMPRS PhD Student
Computational Molecular BiologyProf. Frank Noé
Thesis: 'Reaction-diffusion dynamics in biologial systems - theory, computation, modeling and simulation. Application to the visual cascade and the synaptic vesicle cycle.'


MSc Bioinformatics
Completion in one year (instead of two as listed in the curriculum).
Thesis: 'Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution'
Advisor: Frank Noé

2008 - 2009

Fast Track program for outstanding young researchers
(Skip masters degree and advance to PhD with the BSc immediately. The Fast Track program included 1 year of courses before an exam would grant immediate advance to the PhD. I chose to do the 2 year MSc curriculum in that year. I successfully passed the Fast Track and additionally got the MSc.)

Saarland University

2005 - 2008

BSc Bioinformatics
Thesis: 'MHC:peptide structure prediction' with fast constraint based MD-Simulation substitute
Advisor: Rainer Böckmann

Awards and Honors 

BIDS data science Fellowship, 2018

Siebel Scholars Stem Cell Fellowship, 2018

Elected Chair of the 2019 GRS Gordon Research Seminar on 'Molecular Membrane Biology', 2017

Tiburtius Prize for best PhD thesis of the universities of Berlin (Anerkennungspreis), 2015

Marie Skłodowska-Curie postdoctoral fellowship, European Union, 2015

Poster Award, 4th International caesar Conference, Bonn, 2014

Steering committee member Junges Wissenschaftsforum Dahlem, FU-Berlin, 2013

Chosen student, Excellence Initiative Proposal , FU-Berlin, 2012

Best Poster Award, IMPRS-CBSC, MPI-Molgen Berlin 2009

IMPRS-CBSC fellowship for doctoral studies, MPI-Molgen Berlin, 2009

Fast Track fellowship, IMPRS-CBSC, MPI-Molgen Berlin, 2008

Konrad Adenauer fellowship for undergraduate studies, 2006

German Federal Cultural Foundation grant, 2006

Barmer Award for best high school diploma in biology, 2005

Scheffel Award for best high school diploma in German, 2005

Young Leaders Academy, 2004

Saarland Academy for highly gifted people, 2003

Organized Scientific Events

            2014, 8th Dec                         Practical on Molecular Structure Determination
                                                             During the winter school on 'Modeling Large Molecular Assemblies' in Nice
                                                             40 intnl. participants.


           2014, 28th Jul - 1st Aug         ReaDDy Summer School 2014
                                                             "Reaction Diffusion Dynamics in Biological Systems".
                                                             Lectures in the morning, practical sessions in the afternoon.
                                                             15 local, 5 intnl. participants.
                                                             topics: Diffusion, crowding, particle-based reaction-diffusion simulation, Monte Carlo sampling,
                                                             ReaDDy software

           2012, 26th Sep                       Workshop
                                                            "Simulation and modeling of signal transduction at cell membranes"
                                                            Lectures in the morning, practical session with the ReaDDy software in the afternoon.
                                                            13 local participants.

Scientific Contributions

Poster              09/2018       Beyond the Cell Atlas, UCSF/BioHub, CA, USA

Invited Talk     09/2018       Astronomy meets MicroscopyUCSC Silicon Valley Campus, CA, USA

Invited Talk     07/2018       Datascience Pedagogy and PractiseBIDS, CA, USA

Invited Talk     04/2018       Siebel Stem Cell Conference, Asilomar Conference Center, CA, USA

Contrib. Talk   04/2018       ASBMB Annual Meeting, San Diego, CA, USA

Invited Talk     04/2018       Siebel Stem Cell Fellows Meeting, Berkeley, CA, USA

Invited Talk     03/2018       BIDS Data Science Luncheon, Berkeley, CA, USA

Invited Talk     03/2018       UCSF 3D Data Club, San Francisco, CA, USA

Contrib. Talk   02/2018       BPS 2018, Annual Meeting of the Biophysical Society, San Francisco, CA, USA

Poster              01/2018       Siebel Stem Cell Institutes Meeting Stanford, Palo Alto, CA, USA

Invited Talk     12/2017       Scheuring Lab, Weill Cornell Medicine, New York City, NY, USA

Invited Talk     12/2017       Janelia Research Campus, Ashburn, VA, USA

Contrib. Talk   12/2017       ASCB Annual Meeting, Philadelphia PA, USA

Invited Talk     10/2017       Berkeley Biophysics, Marconi Conference Center, CA, USA

Poster + Session Leader              07/2017         GRS + GRC ‘Molecular membrane biology’, Andover NH, USA

Invited Talk     06/2017         Cellular Biophysics, Experiment meets Theory Conference, Berkeley, CA, USA

Invited Talk     06/2017         Bay Area Meeting on Organelle Biology, UC Berkeley, CA, USA

Invited Talk     01/2017        BBS Division Conference, Asilomar Conference Center, CA, USA

Poster              10/2015        Berkeley Biophysics, Marconi Conference Center, CA, USA

Poster              12/2014        International Ringberg Conference, Schloss Ringberg, Germany         

Invited Talk      06/2014        McCammon Lab, San Diego, CA

Invited Talk      06/2014        Hurley Lab, San Diego, CA

Invited Talk      05/2014        Lipowsky Lab, Potsdam, Germany

Invited Talk      04/2014        Hummer Lab, Frankfurt, Germany

Poster               03/2014        4th International caesar Conference "Sensory Systems – from molecule to function", Bonn, Germany

Poster               03/2014        Membranes and Modules Conference 2014, Berlin, Germany                   

Invited Talk      02/2014        Dittrich Lab, Jena, Germany

Poster               10/2013        Macromolecular Crowding Effects in Cell Biology, Orléans, France 

Contrib. Talk + ReaDDy Tutorial    10/2013        BDBDB3: Biological Diffusion and Brownian Dynamics Brainstorm 3, Heidelberg, Germany

Contrib. Talk    06/2013        European Meeting on Phototransduction, Delmenhorst, Germany

Contrib. Talk    04/2013        Computer Simulation and Theory of Macromolecules, Huenfeld, Germany

Contrib. Talk + ReaDDy Tutorial    10/2012        Cecam Workshop Signaling Pathways, Paris, France

Contrib. Talk    06/2012        International conference on molecular crowding, Askona, Switzerland

Poster               04/2012        Workshop Computer Simulation and Theory of Macromolecules, Huenfeld, Germany

Contrib. Talk    10/2010        BDBDB2: Biological Diffusion and Brownian Dynamics Brainstorm 2, Heidelberg, Germany

Poster               10/2010        Annual Meeting of the German Biophysical Society, Bochum, Germany

Poster               03/2010        Computer Simulation and Theory of Macromolecules, Huenfeld, Germany

Poster               10/2009        International Symposium Membranes and Modules, Berlin, Germany

Poster               05/2009        Molecular Kinetics, Berlin, Germany

Poster               10/2008        Interplay between Molecular Conformations and Biological Function, Bad Kissingen, Germany


> Pubmed      > Research Gate      > Google Scholar

J SchönebergD Dambournet, T-L Liu, R Forster, D Hockemeyer, E Betzig, and D G Drubin (2018) 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids, Molecular Biology of the Cell.

M G Lin, J Schöneberg, C W Davies, X Ren, and J H Hurley (2018) The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion, Molecular Biology of the Cell, Vol. 29, No 10.

J Schöneberg, S Yan, M Righini, M Remec Pavlin, I-H Lee, L-A Carlson, A H Bahrami, D H Goldman, X Ren, G Hummer, C Bustamante, J Hurley (2018), ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. in revision, bioRxiv.

J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, V Haucke, F Noé, (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications 8, 15873 doi: 10.1038/ncomms15873. (*equal contribution). 

F Paul*, C Wehmeyer*, E T Abualrous, H Wu, M D Crabtree, J Schöneberg, J Clarke, C Freund, T R Weikl, Frank Noé, (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications. (*equal contribution). 

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteinsNature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).

Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F, (2015) Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biology,11(9):e1004407.

M Gunkel*, J Schöneberg*, W Alkhaldi, S Irsen, F Noé, U B Kaupp, A Al-Amoudi, (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kineticsStructure23(4): 628-38. (*equal contribution).

J Biedermann, A Ullrich, J Schöneberg and F Noé, (2015) ReaDDyMM: fast particle-based reaction-diffusion simulations using graphical processing units. Biophysical Journal108(3): 457-61.

J Schöneberg, A Ullrich, F Noé, (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7(11).

J Schöneberg, M Heck, KP Hofmann, F Noé, (2014) Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. Biophysical Journal, 107(5): 1042-1053.

Y Posor, M Eichhorn-Gruenig*, D Puchkov*, J Schöneberg*, A Ullrich*, A Lampe, R Müller, S Zarbakhsh, F Gulluni, E Hirsch, M Krauss, C Schultz, J Schmoranzer, F Noé and V Haucke (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 (7457): 233-237 (*equal contribution).

J Schöneberg, A Ullrich, Y Posor, V Haucke, F Noé (2013) Spatiotemporal model of a key step in endocytosis: SNX9 recruitment via phosphoinositides. arXiv:1307.4614.

J Schöneberg and F Noé (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLOS ONE, 8 (9): e74261.

Welcome  |  ReaDDy  |  Reaction-Diffusion  |  Other Science  |  CV


I currently work in the Drubin, Hockemeyer and Betzig labs. I also work in the Hurley, Bustamante and Hummer labs. At Berkeley, I'm engaged in BPEP. Before, in the Noé lab, I used to work in sfb740 and sfb958 projects. Download ReaDDy and collaborate with us on gitHub. Make sure to check out fraudinkel photography.

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