iiinova — where your digital self keeps evolving

Elisabeth Bobkova @bobez.bsky.social · 30/06/2026

Said a final goodbye to my bench at the MPI for Terrestrial Microbiology today. What a feeling @mpimicrobiomarburg.bsky.social

Very clean, very empty lab space that I am leaving behind. All in pretty white and with pipettes awaiting their new master

Peeling off my "this bench belongs to Beth" sign

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

Big thanks to everyone at Erb and Hummer lab, to all collaborators for the support throughout this project and to everyone at @mpimicrobiomarburg.bsky.social 🎉 7/7

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

Overall, this establishes a modular nanopore engineering toolbox, including a “one-pot” modification and screening strategy for systematically tuning and probing diffusion in synthetic membrane systems. 6/7

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

Using this setup, we show that chemical modification of of αHL post-insertion significantly changes peptide permeability and selectivity depending on modification site and reporter structure and charge. 5/7

Panel A depicts a typical one-pot modification and peptide diffusion measurement. In brief, the pre-formed vesicles containing LgBit are combined with the MBP-dark breakage control and purified alpha-Hemolysin monomers. The solution is incubated for 30min at RT to allow for pore formation. After that the modification solution (here a fluorescent maleimide conjugate) is added to the mix and everything is incubated at 37°C for 2h to allow maximal modification of the pores post-insertion. The sample is then transferred to well-plates and the luciferase substrate together with the reporter peptide is added. The luminescence measurement is carried out in a platereader. Panel B showcases the chemical structure of the fluorophore coupled to maleimide used for pore modification. Panel C showcases the results of measurements of all 3 pore variants (wild type, 0C and 117C variants) with and without maleimide modification. The signal is normalized to the base reporter (r99), with results depicted to fused r99 constructs - neutrally charged unstructured peptide, and 2 negatively charged helices with different charge distributions. No significant changes in apparent peptide diffusion can be observed for wildtype and 0C pore variants, while a significant change in luminescence is detected between modified and unmodified pore for the 117C variant for negatively charged helices, but not for unstructured neutral reporter construct, suggesting charge and position dependent selectivity in peptide diffusion of the modified pore.

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

We show a LUV-based nanoluc assay, providing a robust and unbiased readout of peptide diffusion. We directly visualize the large contribution that vesicle breakage has on measured diffusion signal in non-stabilized synthetic membranes — a critical factor that is often underestimated in studies. 4/7

The depiction of the nanoluciferase based assay setup followed by measurements of the breakage contributions. Panel A depicts the setup of the breakage controlled nanoluciferase assay. In brief, the large unilamellar vesicles encapsulate the large bit (LgBit) of the split nanoluciferase, while the substrate, the breakage control (dark peptide fused to MBP) and the reporter peptide (small bit of the nanoluciferase) are added to the outside solution. In case the vesicles are intact, no luminescence signal is generated; in case of vesicle breakage the large bit is inactivated by the MBP-dark breakage control - no luminescence signal is generated; in case of successful pore insertion and reporter peptide diffusion inside the vesicle, a functional nanluciferase is formed, enabling substrate conversion with luminescence signal generation. Panels B and C depict example measurements with and without the addition of a breakage control. The luminescence values taken at t=30min are substantially higher for both, the buffer only and alpha-hemolysin containing system, while the breakage control containing samples show an overall lower signal. Particularly, the signal with alpha-hemolysin containing vesicles shows a 7-fold drop for the breakage-controlled sample compared to measurements without breakage control

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

We use α-Hemolysin (αHL) as a self-inserting scaffold to reduce variability in membrane insertion. By employing site-specific cysteine mutations we enable controlled chemical modification pre- and post-insertion, helping decouple pore design from batch-to-batch and folding-related effects. 3/7

ChmeraX visualizations of alpha-Hemolysin in different assembly states. Panel A showcases the monomer of aHL with the cysteine modifications at positions 0 and 117c highlighted in violet and pink respectively. Panel B shows the assembled heptamer from the side. Panel C depicts a top-view on the assembled alpha-Hemolysin pore with peptide-modifications attached to the cysteine at the pore entry (0C) position highlighted in orange. The peptides are predicted (alphafold multimer) to forma mesh at the entry of the pore

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

A key challenge in synbio is that selectively permeable synthetic membranes are difficult to build and difficult to measure reliably. Modified membrane protein insertion is often variable, and most diffusion assays suffer from low throughput, instability, or hidden biases from vesicle breakage. 2/7

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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026

Very happy to share my first preprint from my PhD 🎉 doi.org/10.64898/202... We develop an αHL-based framework to engineer and quantify selective diffusion across synthetic membranes using controlled nanopore chemistry. 1/7

doi.org

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Elisabeth Bobkova @bobez.bsky.social · 28/03/2026

Really enjoyed the 77th #MosbacherKolloquium ! Thanks to the organizers @gbmev.bsky.social for putting together such an amazing program and for giving me the chance to present my poster. To quote André Nadler: Membranes are great, science is great, and let's continue making discoveries! ;)

Beth standing in front of her Poster with a coffee looking happy and well caffeinated. The poster features her work on chemically tunable permeability of engineered alpha-Hemolysin in synthetic membranes

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Elisabeth Bobkova @bobez.bsky.social · 28/01/2026

Just realized, that I have never posted my artwork on bluesky! So here are some of my favorite pieces I got to create during my PhD for different projects from @mpimicrobiomarburg.bsky.social What a journey it has been :)

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Reposted by Elisabeth Bobkova

Max Planck Institute for Terrestrial Microbiology @mpimicrobiomarburg.bsky.social · 01/12/2025

🚨 Fully funded PhD positions in #microbiology! Join IMPRS Principles of Microbial Life in Marburg,Germany 🌱 Interdisciplinary research 🧬 World-class mentoring 🧪 State-of-the-art research infrastructure 🗓️ Apply until Jan 31, 2026 🔗 imprs-marburg.mpg.de/3197/JOIN-US #PhDposition #WomenInSTEM

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Reposted by Elisabeth Bobkova

Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025

With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵

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Elisabeth Bobkova @bobez.bsky.social · 03/09/2025

Just submitted my PhD thesis. Feeling kinda empty now...

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Reposted by Elisabeth Bobkova

Ari Satanowski @ari-satanowski.bsky.social · 04/04/2025

Excited to share a main project from my PhD, out now in @naturecomms.bsky.social! 📝 We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱 nature.com/articles/s41... Take a look! Thread below... 🧵

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Elisabeth Bobkova @bobez.bsky.social · 24/03/2025

Thrilled to have been part of the 76th Mosbacher Kolloquium! Huge thanks to @gbmev.bsky.social for organizing such an engaging conference! @anastasiagtz.bsky.so and I were excited to share our insights on differential transport across membranes, and we're truly honored to receive the poster award!

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Reposted by Elisabeth Bobkova

Helena Schulz-Mirbach @helenasm.bsky.social · 04/03/2025

Really happy to share that our work on constructing six glyoxylate / glycolate sensors covering a three order of magnitude concentration range is out now in Nature Communications ! 🔥 Read below to see how we developed the sensors and what they are good for 🥳. www.nature.com/articles/s41...

nature.com

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications

Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...

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Elisabeth Bobkova @bobez.bsky.social · 24/02/2025

Marburg. Sometimes it feels like I am working at Silent Hill. But it has its own charm ;)

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Reposted by Elisabeth Bobkova

Michael Jendrusch @mjendrusch.bsky.social · 06/02/2025

New protein ML preprint from my PhD project. We describe salad (sparse all-atom denoising), a family of efficient protein structure diffusion models and show that it works well on a bunch of protein design task previously described in the literature. Preprint: www.biorxiv.org/content/10.1... (1/N)

Five generated protein structures coloured with a gradient from purple to teal. The structures are shaped and positioned to spell out the word "salad" – the name of the software described in the mentioned preprint – in all-capital letters.

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