Concentration‐dependent dimerization of staphylokinase variants with engineered surface charges Staphylokinase (SAK) is a promising third-generation thrombolytic protein, but its clinical potential is limited by immunogenicity and stability concerns. The conformational and colloidal stabilities....

New paper accepted in 𝗣𝗿𝗼𝘁𝗲𝗶𝗻 𝗦𝗰𝗶𝗲𝗻𝗰𝗲! 🧬 We explored how engineered surface charges and concentration-dependent dimerization shape the stability of #staphylokinase (SAK) variants.

Huge thanks to our collaborators at P. J. Safarik University! 🇸🇰

Read here: onlinelibrary.wiley.com/doi/10.1002/...

We’re proud to have hosted 𝗟𝘂𝗰𝗶𝗷𝗮 𝗕𝗿𝘁𝗮𝗻 (University of Zagreb) for a 3-month internship! 🧪✨

She worked on engineering enzymes for better bioplastic recycling using advanced in silico design. A great step forward for sustainable science! ♻️💻

Best of luck in your future research!

Theory meets practice! 🧬 MUNI students spent 4 days exploring the pharmaceutical world—from clinical research at the Cancer Institute to R&D and production at FAVEA.

Big thanks to our hosts for the real-world insights! 🎓✨

📷Pavel Vanacek

The online course was made possible with the support of:
Enantis | Masaryk University | RECETOX | St. Anne's University Hospital Brno | CLARA Center | COZYME (COST Action CA21162) | ELIXIR

The 7th Hands-on Computational Enzyme Design Course by #Loschmidt Labs & #Enantis is a wrap! 🧪✨

Participants mastered tools for mining & engineering enzymes, as well as for processing kinetic data. Good luck to our researchers as they explore the frontiers of protein design! 🚀

📷 Sergio M. Marques

We might have been exhausted after three intensive days, but we still had enough energy for a great dinner at Slunecnice Pub! Here are a few snapshots of the fun! 🥂

Day 4 of the 𝟳𝘁𝗵 𝗛𝗮𝗻𝗱𝘀-𝗼𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗘𝗻𝘇𝘆𝗺𝗲 𝗗𝗲𝘀𝗶𝗴𝗻 𝗖𝗼𝘂𝗿𝘀𝗲! 🚀

Our participants have been busy: 🔹 Designing stable proteins 🔹 Modeling protein-ligand complexes 🔹 Identifying enzyme tunnels 🔹 Using ML for biochemistry

Big thanks to guest lecturers Jan Byska and Elisabet Manaskova! 🧪💻

Loschmidt Laboratories joined #CzecHopes to inspire future scientists! 🎓

🔬 Jan Cesnek led a lab workshop on protein preparation & luminescence. 🤖 David Lacko showed how AI designs binders for the COVID-19 spike protein.

Record attendance this year! 📈

The 7th Computational Enzyme Design Course has begun! 🌍🧬

We’ve welcomed 63 experts from 20 countries—from Oxford and Princeton to Bayer and Samsung.

Supported by @MasarykUni, @Recetox, @ICRC, @COZYME & @Enantis.

#Bioinformatics #Enzymes #Biocatalysis

Field trip highlights! 🧬 MUNI students explored the world of #biotechnology at 𝗘𝗻𝗮𝗻𝘁𝗶𝘀, 𝗣𝗦𝗜, 𝗖𝗼𝗻𝘁𝗶𝗽𝗿𝗼, and 𝗕𝗶𝗼𝗩𝗲𝗻𝗱𝗼𝗿. From growth factors to diagnostics, it was an incredible look at the industry.
Thanks for having us! 🧪✨

Regioselective Sesquiterpene Hydroxylation Directed by Tunnel Remodeling in Rieske Oxygenases Selective hydroxylation of sesquiterpenes remains a major challenge in synthetic chemistry due to their chemical homogeneity and steric complexity. Here, we report the Rieske oxygenase (RO)-catalyzed hydroxylation of sesquiterpenes using cumene dioxygenase (CDO) from Pseudomonas fluorescens IP01. Wild-type CDO catalyzed the monohydroxylation of the sesquiterpene β-bisabolene, producing ring-hydroxylated β-bisabolene-5-ol and tail-hydroxylated (S)-β-bisabolene-13-ol in a 64:21 ratio, with a total product formation of 0.43 ± 0.07 mM. A single-loop deletion variant, L284del, enhanced both total product formation and selectivity toward the ring-hydroxylated product, producing 1.40 ± 0.08 mM and enabling preparative-scale isolation (17 mg, 0.08 mmol, 39% yield). Another single-loop variant, I288del, similarly increased total product formation while shifting regioselectivity from ring- to tail-hydroxylation in a 5:81 ratio, generating 1.07 ± 0.04 mM tail-hydroxylated product and enabling its preparative-scale isolation (24 mg, 0.11 mmol, 55% yield). To understand this clear switch in regioselectivity, we conducted molecular dynamics (MD) and adaptive steered MD simulations. This revealed that I288del increased the substrate tunnel openness and frequency of access, promoting a tail-first orientation of the substrate. This preorientation enhanced the probability of reactive conformations in proximity to the catalytic iron. Binding energy calculations further supported a loss of orientation bias in I288del, giving further insight into the regioselectivity shift. Additional engineering yielded the variant N279T_I288del_A321T, which enhanced the formation of the tail-hydroxylated compound to 1.58 ± 0.26 mM. Further, variant I288del enabled the conversion of α-santalene, a reaction not catalyzed by the wild-type enzyme. Our study provides mechanistic insight into how tunnel dynamics and substrate preorientation govern selectivity in RO-catalyzed C–H functionalization.

Excited to share our latest research in 𝗝𝗔𝗖𝗦 𝗔𝘂! 🧬✨ We discovered that substrate access tunnels govern the precision of Rieske oxygenases.

Great work by Jonathan Berger during his stay at Loschmidt Labs with Sérgio Marques. Congrats on the PhD, Jonathan!

🔗 pubs.acs.org/doi/10.1021/...

𝗠𝗮𝗿𝘁𝗶𝗻 𝗦𝗶𝘁𝘁𝗲 and 𝗠𝗮𝗿𝘁𝗶𝗻 𝗠𝗮𝗿𝗲𝗸 recently represented our team at the 𝗗𝗘𝗦𝗬 𝗣𝗵𝗼𝘁𝗼𝗻 𝗦𝗰𝗶𝗲𝗻𝗰𝗲 𝗨𝘀𝗲𝗿𝘀' 𝗠𝗲𝗲𝘁𝗶𝗻𝗴 and the 𝗘𝘂𝗿𝗼𝗽𝗲𝗮𝗻 𝗫𝗙𝗘𝗟 𝗨𝘀𝗲𝗿𝘀' 𝗠𝗲𝗲𝘁𝗶𝗻𝗴 in Hamburg (January 25–28, 2026).

Both researchers also participated in the 𝗠𝗫 𝗦𝗮𝘁𝗲𝗹𝗹𝗶𝘁𝗲 𝗪𝗼𝗿𝗸𝘀𝗵𝗼𝗽 to discuss the sample preparation techniques.

📸 Martin Sitte

Our first team-building event of the year was a hit! ⛸️We kicked off January on the ice at the Za Lužánkami Stadium, followed by a get-together at U Dřeváka Beer&Grill. 🍻

A special thank you to Irena Halikova and Sergio Marques for organizing such an event! 👏

📸 Linda Kasiarova & Sergio Marques

Kicking off 2026! 🚀

Our first group meeting featured inspiring reflections on 2025 and a look at the challenges ahead. We’re staying resilient and keeping our team spirit strong!

Welcome to our new postdoc, Khushboo Rani! 🤝🥂

Warmest wishes for a peaceful holiday season and a happy, healthy, and prosperous New Year 🍀.

The LL team came together to celebrate this year's successes and get into the festive spirit ahead of the Christmas season. 🎄

📸 Kaja Sedlackova

Among the 25 winners of the 𝗕𝗿𝗻𝗼 𝗣𝗵𝗗 𝗧𝗮𝗹𝗲𝗻𝘁 𝟮𝟬𝟮𝟱 𝗮𝘄𝗮𝗿𝗱 are four students from Loschmidt Laboratories: Jan Cesnek, Tim de Martines, Martin Havlasek, and Monika Rosinska! 👏🔬

Congratulations to all the winners!

More here:
www.jcmm.cz/projekt/brno...

We were delighted to welcome Dr. Zhongyue John Yang @mutexazjy.bsky.social, Assistant Professor of Chemistry at @vanderbilt.edu (USA), to Loschmidt Laboratories! 🇨🇿🇺🇸
John shared his expertise in physics-guided protein engineering during an engaging lecture for our team.

📷 Jan Mican & Jiri Damborsky

🇧🇷 Big news! Masaryk University & 𝗘𝗻𝗮𝗻𝘁𝗶𝘀 got the Brazilian #patent for FGF2-STAB!

This thermostable, genetically engineered FGF2 is key for growing cell cultures efficiently (fewer media changes). It maintains pluripotency, boosting drug discovery & cell therapies. Congrats! 🔬🇨🇿

Christmas Eve is still two weeks away, but we've already received our presents!🎁🎄🌟

Many thanks to St. Anne's University Hospital Brno for the thoughtful gifts and to Martina Damborska for taking the time to bring them to us.

We appreciate the festive cheer! 🙏

Huge congrats to 𝗗𝗮𝘃𝗶𝗱 𝗕𝗲𝗱𝗻𝗮𝗿 (JUNIOR STAR) and 𝗠𝗮𝗿𝘁𝗶𝗻 𝗠𝗮𝗿𝗲𝗸 (EXPRO)! They both received the 𝗠𝗨𝗡𝗜 𝗦𝗰𝗶𝗲𝗻𝘁𝗶𝘀𝘁 𝗔𝘄𝗮𝗿𝗱 𝟮𝟬𝟮𝟱 𝗦𝗰𝗶𝗲𝗻𝘁𝗶𝘀𝘁 𝗔𝘄𝗮𝗿𝗱 𝟮𝟬𝟮𝟱! 🏆

See the full article: is.muni.cz/go/4iufva

We are happy to announce that our 𝟳𝘁𝗵 𝗛𝗮𝗻𝗱𝘀-𝗼𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗘𝗻𝘇𝘆𝗺𝗲 𝗗𝗲𝘀𝗶𝗴𝗻 𝗖𝗼𝘂𝗿𝘀𝗲 is now full! 🚀

Congrats to our scholarship winners: Julieta Beiro 🇦🇷 and Sukriti Sacher 🇮🇳! (We received 26 applications!)

Looking forward to Feb 2026! 🔬

📢 Fully funded 𝗣𝗵𝗗 𝗣𝗼𝘀𝗶𝘁𝗶𝗼𝗻 at Loschmidt Labs in Machine learning-based tools for multiparametric enzyme optimisation!

Unique opportunity to develop and validate next-generation data-driven models for protein engineering.

Apply here: www.muni.cz/o-univerzite...

Share this opportunity! 🤝

𝗝𝗮𝗻𝗮 𝗛𝗼𝗿𝗮𝗰𝗸𝗼𝘃𝗮 and 𝗝𝗮𝗻 𝗩𝗲𝗹𝗲𝗰𝗸𝘆 celebrated their PhD achievements 🎓 with us! Their party took place at Hostinec u Tesare on Monday (December 1st).

Thanks to all who came to the party! 🎉

Photos: Jan Velecky & Monika Rosinska

Our doctoral student, 𝗠𝗮𝗿𝗶𝗸𝗮 𝗠𝗮𝗷𝗲𝗿𝗼𝘃𝗮, has been awarded the prestigious 𝗠𝗮𝗿𝘁𝗶𝗻𝗮 𝗥𝗼𝗲𝘀𝗲𝗹𝗼𝘃𝗮 𝗠𝗲𝗺𝗼𝗿𝗶𝗮𝗹 𝗙𝗲𝗹𝗹𝗼𝘄𝘀𝗵𝗶𝗽 𝟮𝟬𝟮𝟲 from @nf-iocbtech.bsky.social! 🎉
The award is designed to help Marika restart her scientific career after parental leave.
Congratulations to Marika on this achievement! 👏
📸 Tomas Bellon

🚀 Zajímá vás, jak moderní počítačový design a umělá inteligence transformují biologii? Přesně to je náplní Proteinového inženýrství! 💻🧬

Naučte se navrhovat proteiny s vylepšenými vlastnostmi a vytvářet zcela nové molekuly pro praktické aplikace v medicíně a biotechnologiích.

FireProtDB 2.0: large-scale manually curated database of the protein stability data Abstract. Thermostable proteins are crucial in numerous biomedical and biotechnological applications. However, naturally occurring proteins have evolved to

Read the full paper here: academic.oup.com/nar/advance-...

Our paper on FireProtDB 2.0 is accepted in Nucleic Acids Research! 🎉🔬
We've massively upgraded the essential database for computational protein design:
✅ 5.5 million stability experiments
✅ Now handles complex changes
✅ FAIR compliant & fully future-proofed

🔗 loschmidt.chemi.muni.cz/fireprotdb

Big congratulations to 𝗝𝗮𝗻𝗮 𝗛𝗼𝗿𝗮𝗰𝗸𝗼𝘃𝗮, 𝗣𝗵𝗗, and 𝗝𝗮𝗻 𝗩𝗲𝗹𝗲𝗰𝗸𝘆, 𝗣𝗵𝗗! 🥳🎓

They both completed the Environmental Health Sciences doctoral degree programme at RECETOX, Faculty of Science, Masaryk University.
We wish Jana and Jan every success in their future endeavors. 🔬🚀

📸 Jiri Damborsky

Great news from CLARA Days 2025! 🎉 Our post-doc, Saltuk Eyrilmez, gave a talk on "Recent progress in drug screening for apolipoprotein E"—a key protein in Alzheimer's disease pathogenesis.🧠

Saltuk: "Inspiring event & a unique opportunity to discuss my research with an interdisciplinary community."