Niopek Lab
@niopeklab.bsky.social
Lab account for AG Niopek at the University of Heidelberg IPMB
Protein Engineering | Allostery | CRISPR | Optogenetics | ML
Account is managed by PhD Students
https://Niopeklab.de/
Protein Engineering | Allostery | CRISPR | Optogenetics | ML
Account is managed by PhD Students
https://Niopeklab.de/
Many congratulations to first author @neuroscinikolai.bsky.social for his amazing work and to all other authors that were involved, including Anna Von Bachmann for her excellent bioinformatics skills!
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June 13, 2025 at 1:52 PM
Many congratulations to first author @neuroscinikolai.bsky.social for his amazing work and to all other authors that were involved, including Anna Von Bachmann for her excellent bioinformatics skills!
Together, POGO-PANCE and RAMPhaGE offer a versatile framework for evolving molecular switches and decoding allosteric architecture—by letting evolution sculpt the signal.
June 13, 2025 at 1:38 PM
Together, POGO-PANCE and RAMPhaGE offer a versatile framework for evolving molecular switches and decoding allosteric architecture—by letting evolution sculpt the signal.
Using RAMPhaGE, we diversified the AraC–LOV2 linker and applied POGO-PANCE evolution, uncovering a single-residue deletion/substitution that markedly improved switching likely by stabilizing a continuous α-helix at the sensor-effector junction, yielding near-digital on/off behavior.
June 13, 2025 at 1:38 PM
Using RAMPhaGE, we diversified the AraC–LOV2 linker and applied POGO-PANCE evolution, uncovering a single-residue deletion/substitution that markedly improved switching likely by stabilizing a continuous α-helix at the sensor-effector junction, yielding near-digital on/off behavior.
To go beyond point mutations, we also built RAMPhaGE: a retron-recombineering platform for targeted phage genome editing. RAMPhaGE enables targeted and cummulative substitutions, insertions, and deletions—supporting tunable library design and high-efficiency in vivo diversification.
June 13, 2025 at 1:35 PM
To go beyond point mutations, we also built RAMPhaGE: a retron-recombineering platform for targeted phage genome editing. RAMPhaGE enables targeted and cummulative substitutions, insertions, and deletions—supporting tunable library design and high-efficiency in vivo diversification.
Long-read sequencing across POGO-PANCE cycles revealed mutational trajectories and co-evolving networks spanning both AraC and LOV; We observed allosteric communication emerging in real time, structured by alternating selection and mapped as mutational hotspots.
June 13, 2025 at 1:35 PM
Long-read sequencing across POGO-PANCE cycles revealed mutational trajectories and co-evolving networks spanning both AraC and LOV; We observed allosteric communication emerging in real time, structured by alternating selection and mapped as mutational hotspots.
To overcome this, we developed POGO-PANCE—a system that evolves protein switches by mimicking nature. By alternating positive and negative selection aligned with the presence or absence of an inducer, we yielded Optogenetic AraC-AsLOV2 variants with >1000-fold dark/light expression changes.
June 13, 2025 at 1:35 PM
To overcome this, we developed POGO-PANCE—a system that evolves protein switches by mimicking nature. By alternating positive and negative selection aligned with the presence or absence of an inducer, we yielded Optogenetic AraC-AsLOV2 variants with >1000-fold dark/light expression changes.
The principles underlying allostery remain elusive; engineering synthetic allostery is an even greater challenge. While tools like ProDomino can identify permissive allosteric insertion sites in proteins, achieving efficient switching output often still requires further optimization.
June 13, 2025 at 1:32 PM
The principles underlying allostery remain elusive; engineering synthetic allostery is an even greater challenge. While tools like ProDomino can identify permissive allosteric insertion sites in proteins, achieving efficient switching output often still requires further optimization.
Congratulations to all authors, especially 1st author @pmuench.bsky.social as well as @neuroscinikolai.bsky.social and Matteo Fiumara for their important contributions!
Many thanks to @graeffjohannes.bsky.social for the productive and fun collaboration.
Many thanks to @graeffjohannes.bsky.social for the productive and fun collaboration.
December 16, 2024 at 12:55 PM
Congratulations to all authors, especially 1st author @pmuench.bsky.social as well as @neuroscinikolai.bsky.social and Matteo Fiumara for their important contributions!
Many thanks to @graeffjohannes.bsky.social for the productive and fun collaboration.
Many thanks to @graeffjohannes.bsky.social for the productive and fun collaboration.
Many congratulations to first author @bene837.bsky.social for his amazing work and to all other authors that were involved into the extensive experimental validation, especially @pegish.bsky.social and Sabine Aschenbrenner.
December 5, 2024 at 10:01 AM
Many congratulations to first author @bene837.bsky.social for his amazing work and to all other authors that were involved into the extensive experimental validation, especially @pegish.bsky.social and Sabine Aschenbrenner.
Especially the chemically regulated Cas12a variants showed potent editing and extremely strong response to the inducer. Importantly, all our reported protein switches were generated without any downstream optimization.
December 5, 2024 at 10:00 AM
Especially the chemically regulated Cas12a variants showed potent editing and extremely strong response to the inducer. Importantly, all our reported protein switches were generated without any downstream optimization.
Using ProDomino, we created potent optogenetic variants of the puromycin and chloramphenicol antibiotic resistances. Moreover, we engineered blue light-responsive Cas9-VPR transcriptional activators and light- or cortisol-dependent variants of MbCas12a.
December 5, 2024 at 10:00 AM
Using ProDomino, we created potent optogenetic variants of the puromycin and chloramphenicol antibiotic resistances. Moreover, we engineered blue light-responsive Cas9-VPR transcriptional activators and light- or cortisol-dependent variants of MbCas12a.
This approach, together with ESM-2-based embeddings and a masking strategy enabled us to train a model that showed high success rates in the subsequent wetlab validation.
December 5, 2024 at 10:00 AM
This approach, together with ESM-2-based embeddings and a masking strategy enabled us to train a model that showed high success rates in the subsequent wetlab validation.
A main limitation is the absence of sufficiently large experimental datasets that could be used to train ML models. For our new model ProDomino (protein domain insertion optimizer), we leveraged intradomain insertions in natural proteins identified based on CATH/Interpro annotations.
December 5, 2024 at 10:00 AM
A main limitation is the absence of sufficiently large experimental datasets that could be used to train ML models. For our new model ProDomino (protein domain insertion optimizer), we leveraged intradomain insertions in natural proteins identified based on CATH/Interpro annotations.
Allosteric protein switches are usually created by inserting a receptor domain into an effector protein. However, the identification of suitable insertion sites remained challenging and nearly impossible to predict.
December 5, 2024 at 9:59 AM
Allosteric protein switches are usually created by inserting a receptor domain into an effector protein. However, the identification of suitable insertion sites remained challenging and nearly impossible to predict.
Deep congrats to co-first authors @lucabrenker.bsky.social , Sabine Aschenbrenner, and Felix Bubeck as well as all other authors.
November 26, 2024 at 12:09 PM
Deep congrats to co-first authors @lucabrenker.bsky.social , Sabine Aschenbrenner, and Felix Bubeck as well as all other authors.
On the fly, we also created circularly permuted variants of human receptor domains that should be well-suited for allosteric protein control beyond the anti-CRISPR space.
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November 26, 2024 at 11:34 AM
On the fly, we also created circularly permuted variants of human receptor domains that should be well-suited for allosteric protein control beyond the anti-CRISPR space.
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Deep congrats to co-first authors Luca Brenker, Sabine Aschenbrenner, and Felix Bubeck as well as all other authors.
November 26, 2024 at 11:33 AM
Deep congrats to co-first authors Luca Brenker, Sabine Aschenbrenner, and Felix Bubeck as well as all other authors.
On the fly, we also created circularly permuted variants of human receptor domains that should be well-suited for allosteric protein control beyond the anti-CRISPR space.
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November 26, 2024 at 11:33 AM
On the fly, we also created circularly permuted variants of human receptor domains that should be well-suited for allosteric protein control beyond the anti-CRISPR space.
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Congrats to co-first authors Tobias Stadelmann, Daniel Heid and @mjendrusch.bsky.social as well as everyone involved.
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November 26, 2024 at 11:31 AM
Congrats to co-first authors Tobias Stadelmann, Daniel Heid and @mjendrusch.bsky.social as well as everyone involved.
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Moreover, we find that AcrIIA5 can actually inhibit Cas9 DNA binding in E. coli to some extent, a property which can be enhanced by certain mutations within or close to its internal IDR.
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November 26, 2024 at 11:30 AM
Moreover, we find that AcrIIA5 can actually inhibit Cas9 DNA binding in E. coli to some extent, a property which can be enhanced by certain mutations within or close to its internal IDR.
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