Only a couple of days left to introduce our brand new tool, DynaPIN that @aysebercinb.bsky.social developed (in collaboration with @sacquin-mo.bsky.social & co.) to analyze dynamic/ensemble protein interfaces!
🎗️ reminder that our #webinar on characterising dynamic #protein interfaces with the DynaPIN #software will take place next week;
🗓️ 31 March 2026, 15:00 CET
✍️ bioexcel.eu/lgmq
@ezgikaraca.bsky.social
#webinar #ComputerSimulation #protein #molecularmodeling
🚀 Excited to announce that our perspective piece with @ezgikaraca.bsky.social and @aysebercinb.bsky.social on AlphaFold distograms is now published in @febsletters.bsky.social!!
Here is what we did further 👇
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
And the legacy continues! 😊
@amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social #EMBOIntegMod25 ! 🍀🧿
This is the first systematic dynamic analysis of shape readout in DNMT3 enzymes, showing how small molecular changes can lead to big functional differences --and laying groundwork for engineering paralog-specific protein-DNA interactions.
A long journey, but rewarding! 🌱
Altogether,
✅ DNMT3A uses a rigid, precise strategy, while DNMT3B is more flexible and adaptable.
In other words,
✅ DNMT3A is a specialist with a pre-organized catalytic loop, while DNMT3B is a generalist with a flexible catalytic loop supporting its adaptability.
We found that subtle amino acid substitutions reshape DNA recognition:
⚡ DNMT3A uses Arg836 → rigid hydrogen bonding + electrostatic anchoring, favors pyrimidines (C/T).
🤸♀️ DNMT3B replaces Arg836 with Lys777 and introduces Asn779 → flexible and cooperative readout with broader substrate tolerance.
To answer this, we ran 16 μs MD sims and built a new framework: Comparative Dynamics Analysis (CDA).
CDA integrates two complementary perspectives:
➡️ Base readout: base-specific hydrogen bonds at major groove
➡️ Shape readout: DNA deformation, electrostatics, and hydrophobic contacts at minor groove
🚀 Excited to share that our article with @ezgikaraca.bsky.social is now published in Communications Biology!
In this study, 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? 🧬✨