A. Berçin Barlas

Postdoctoral Researcher @ibgcenter - Computational Structural Biology Lab.

[A. Berçin Barlas @aysebercinb]

🚀 Excited to share our article with @Ezgi_Karaca_ is now out in @CommsBio!

We explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked how can nearly the same proteins “see” DNA so differently? 🧬

https://t.co/jOSh6MGDXp

[Ezgi Karaca @Ezgi_Karaca_]

Only a couple of days left to introduce our brand new tool, DynaPIN that @aysebercinb developed to analyze dynamic/ensemble protein interfaces!

[BioExcel CoE @BioExcelCoE]

🎗️ reminder that our #webinar on characterising dynamic #protein interfaces with the DynaPIN #software will take place next week;

🗓️ 31 March 2026, 15:00 CET
✍️ https://t.co/NfPDGHgkYa

@Ezgi_Karaca_
#webinar #ComputerSimulation #protein #molecularmodeling

[busrasavas @busrasavas]

🚀 Excited to announce that our perspective piece with
@ezgikaraca @aysebercinb on AlphaFold distograms is now published in @febsletters!!

Here is what we did further 👇

[busrasavas @busrasavas]

364 days a year we use AlphaFold to predict protein structure…
But not on Christmas Eve! That’s when Santa does the predictions. But beware, computational structural biologists on the naughty list will only get low pLDDTs #SantaFold #bananapro

[Ezgi Karaca @Ezgi_Karaca_]

And the legacy continues ! 😊

@amjjbonvin @arneelof @LindorffLarsen #EMBOIntegMod25 ! 🍀🧿

[A. Berçin Barlas @aysebercinb]

This is the first systematic dynamic analysis of shape readout in DNMT3 enzymes, showing how small amino acid changes lead to big functional differences —and paving the way for engineering paralog-specific protein-DNA interactions.

A long journey, but rewarding! 🌱

[A. Berçin Barlas @aysebercinb]

🚀 Excited to share our article with @Ezgi_Karaca_ is now out in @CommsBio!

We explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked how can nearly the same proteins “see” DNA so differently? 🧬

https://t.co/jOSh6MGDXp

[A. Berçin Barlas @aysebercinb]

Altogether, DNMT3A uses a rigid, precise strategy, while DNMT3B is more flexible and adaptable. In other words:
✅ DNMT3A = specialist with a pre-organized catalytic loop
✅ DNMT3B = generalist with a flexible catalytic loop that supports its adaptability

[busrasavas @busrasavas]

🚨 Super excited for our new preprint on flexibility cues in AlphaFold!

Together with @Ezgi_Karaca_ and @aysebercinb, we found that distograms of AF2.3 and AF3 mirror MD sampling by predicting the extent of a novel conformational change! 🤯

For more👇

[Ezgi Karaca @Ezgi_Karaca_]

2024 has been the most challenging year of my life due to a serious health challenge in my family. During this difficult time, these incredible people have been my rock. Thank you all for your support and camaraderie. I am proud to work alongside you. This post is for you! ❤️🍀🧿

[A. Berçin Barlas @aysebercinb]

Grateful to present our work at the amazing @BioExcelCoE conference in Brno! Huge thanks to all the organizers for this event, which has expanded our horizon in the world of biomolecular simulations. 👩🏻‍💻🧬

[BioExcel CoE @BioExcelCoE]

Ayşe Barlas gave a nice talk on #moleculardynamics simulations using #GROMACS and #AMBER force field of DNA methyltransferases DNMT3A & DNMT3B in complex with different DNA sequences

[Kresten Lindorff-Larsen @LindorffLarsen]

Visualising an MD simulation with cartesian trajectory smoothing

[A. Berçin Barlas @aysebercinb]

@Ezgi_Karaca_ @jpglmrodrigues Definitely! Heartfelt thanks to @jpglmrodrigues, whose insightful feedback and critical evaluation greatly improved our manuscript! 🍀

[A. Berçin Barlas @aysebercinb]

Excited to share our latest research on de novo DNA methylation mediated by DNMT3A/B enzymes!
@Ezgi_Karaca_ ✨
Check out how a single amino acid difference drives epigenetic selectivity. For more this thread👇& https://t.co/xUYzWhKNfm

[Ezgi Karaca @Ezgi_Karaca_]

Proud of my PhD student @aysebercinb for her amazing work! 🌟 Berçin has uncovered key insights into the DNA selectivity of de novo DNA methyltransferases and supported her findings with beautiful figures❣️

Our story can be found at https://t.co/uZlj2CDrqb

[A. Berçin Barlas @aysebercinb]

@Ezgi_Karaca_ 🥹🤍💪🏼

[A. Berçin Barlas @aysebercinb]

Last but not least, wholehearted thanks to my advisor, @Ezgi_Karaca_, for her invaluable guidance, endless support and inspiring mentorship ❤️

[A. Berçin Barlas @aysebercinb]

So, we found that tiny changes at the amino acid or nucleotide level are the causes of macroscopic differences observed at the epigenetics!
Our dataset and IDF analysis scripts are at https://t.co/RWO8kaNfaA