Krishnendu Bera
@krishnendubera.bsky.social
PostDoc @the-gold-lab.bsky.social, @exeter.ac.uk 🇬🇧 Former PostDoc @Magistratolab.bsky.social, CNR-IOM @SISSA, Italy 🇮🇹 PhD @CEITEC.eu @masarykuniversity.bsky.social, Czechia 🇨🇿 CryoEM/ET🔬🦠MD Simulation, IDP/IDR, MetaD, AI/ML👨💻 Details: https://h1.nu/1tsfv
Delighted to share that I received the Poster Prize at the 12th #CCPBioSim Annual Conference at the University of Bristol, UK! A huge thanks to the organizers, judges, colleagues, collaborators, and everyone who stopped by. #CCPBioSim #PosterPrize #CryoEM #MolecularDynamics #StructuralBiology
We’re delighted to be able to share some exciting news: We’ve climbed 19 places in the QS World University Rankings 2027, and we’re now ranked 136th globally. This achievement reflects the growing strength of our reputation as one of the world’s top universities. news.exeter.ac.uk/staff-news/e...
⭐ #NARBreakthrough! ⭐ 🔬 New study by @magistratolab.bsky.social and @pokorna.bsky.social reveals how TAT-SF1 acts as a “molecular latch,” storing strain in #U2snRNP to drive branch-helix formation. A “loaded-spring” model for #splicingfidelity. 📖 Read the article: doi.org/10.1093/nar/...
Happy to share our new paper in the Journal of Physical Chemistry Letters! 🚨📢 We show how macromolecular crowding can enhance protein stability, combining experiments with MD simulations to understand the underlying mechanism. Many thanks to all authors! 🙏 👇👇👇 pubs.acs.org/doi/10.1021/...
Mechanistic Dissection of PEG-Induced Tuning of β-Barrel Protein Stability via Chemical Denaturation
Macromolecular crowding plays a pivotal role in shaping protein stability and bridges insights from in vitro studies to the cellular environment. We investigated the stability of CRABP I through urea ...
pubs.acs.org
Are you interested in phages, cryoEM, and looking for a PhD opportunity near the beach? www.exeter.ac.uk/research/ins...
LSI PhD programme | Living Systems Institute | University of Exeter
exeter.ac.uk
It's been a long road, but thank you to everyone involved in getting this work published! @alexanderneuhaus.bsky.social and @mathewmclaren.bsky.social
Communications Biology@commsbio.nature.com · 4mo agoThermus thermophilus forms two distinct type IV pili. Cryo-electron microscopy, mutagenesis, structural predictions and simulations reveal their structures, glycan flexibility, and a hypothetical model of pilus assembly. www.nature.com/articles/s42...
Happy to share our recent work published in JPCL. We found more than 40% IDRs in human spliceosome crucial for various biological functions and are enriched in cancer-associated mutations. Thanks to all authors @BrunoPOS @LucaG @IsabellaFelli @magistratolab.bsky.social @rpierattelli.bsky.social
PastelBio@pastelbio.bsky.social · 6mo agoExploring Disordered Regions of Human Spliceosome Proteins pubs.acs.org/doi/10.... --- #proteomics #prot-paper
Please check our recent article’s blog published in Biophysical Society and the cover page! @aminagaffour.bsky.social @quantumchemical.bsky.social @idpnmrlab.bsky.social
Biophysical Journal@biophysj.bsky.social · 9mo agoRead about the cover art for the newly released issue of Biophysical Journal on the BPS Blog: www.biophysics.org/blog/flexibi...
Congratulations to @aminagaffour.bsky.social for getting our results into the Tau protein, and its subsequent binding to BIN1! It was a lot of work in the progress and I am very happy to get our research out. @idpnmrlab.bsky.social @krishnendubera.bsky.social www.sciencedirect.com/science/arti...
Reduced binding of Tau(210–240) to BIN1: Phosphate charges prefer n-Src/distal loops over RT-Src loops
Within the disordered tangles of Tau is a proline-rich region, which is selectively targeted by the SH3 domain of BIN1, a known genetic factor for Alz…
sciencedirect.com
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 10mo agoAF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
Our new work entitled 'Plasticity of the cytotoxic Nep1-like protein enables promiscuity in binding to its lipid receptor glycosylinositol phosphorylceramides' has been published on Science Advances! In collaboration with Gregor Anderlu, NIC, Slo read 👇 www.science.org/doi/10.1126/...
Plasticity of the cytotoxic Nep1-like protein enables promiscuity in binding to its lipid receptor glycosylinositol phosphorylceramides
Microbial effectors Nep1-like proteins bind to different plant sphingolipids and disrupt di- and monocot model lipid membranes.
science.org
Our new review entitled 'Decoding Spliceosome Dynamics through Computation and Experiment' has been published on Chemical Reviews @pubs.acs.org Congrats to @pokorna.bsky.social, Sebastian Fica and Jana Aupic! pubs.acs.org/doi/10.1021/...
Decoding Spliceosome Dynamics through Computation and Experiment
RNA splicing is orchestrated by a complex and exceptionally dynamic RNA–protein machine, called the spliceosome. Stepwise, large-scale structural and compositional remodeling of the spliceosome enable...
pubs.acs.org
Snapped a selfie with Michele Parrinello at his 80th birthday 🎉🎂 a true icon in the world of science.
Almost at the end of the exciting @cecamevents.bsky.social conference 'RNA Modelling across scales' at SISSA, Trieste, Italy! 🎉 Fantastic speakers and great science. Organized with @bussigio.bsky.social @marcodevivo.bsky.social #RNA
Excited to share my recent corresponding author paper in ACS Agricultural Science & Technology Thanks all co-authors. Thanks #CzechELib for open access support! Link: shorturl.at/DhpAz #AgScience #InsecticideDesign #ACS #JAgFoodChem #CEITEC_Brno #muni_cz #CzechAcademy #MasarykUni
New Insecticide Designed to Target Ecdysone Receptors of Bemisia tabaci
Bemisia tabaci is a highly destructive pest that affects many crops worldwide. Its feeding behavior on phloem sap and secretion of honeydew on leaves leads to the accumulation of mold, which impairs p...
shorturl.at
Just published our new paper on Identification of a new Small Rho GTPase Inhibitor Effective in Glioblastoma Human Cells. Check it out! www.sciencedirect.com/science/arti.... Excellent work done by @angelaparis3.bsky.social , in collaboration with University of Trieste, University of Udine, CNR-IC
Identification of a new Small Rho GTPase Inhibitor Effective in Glioblastoma Human Cells
Glioblastoma (GBM) is the most common and lethal primary brain tumour. The prognosis for GBM patients remains poor due to rapid tumour recurrence and …
sciencedirect.com
AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2 https://www.biorxiv.org/content/10.1101/2025.04.16.649219v1
📢 Our article calling for a #FAIR database for #MolecularDynamics simulation data has now been peer-reviewed and published in @naturemethods.bsky.social 📖 Read it here: rdcu.be/ef6YX 📝 Support the statement: bit.ly/3zVS3qm #MDDB #FAIRdata #collaboration
CALVADOS now has parameters for phosphorylated amino acids @asrauh.bsky.social @giuliotesei.bsky.social and Gustav Hedemark used a top-down approach in which we targeted experimental data to derive parameters or phosphorylated serine and threonine doi.org/10.1101/2025...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.A coarse-grained model for simulations of phosphorylated disordered proteins https://www.biorxiv.org/content/10.1101/2025.03.19.644261v1
Interested in understanding the molecular details of RNA–membrane association? Read our new paper just published in Nano Letters @acs.org. Excellent work done by sdimarco.bsky.social with Jana Aupic and @bussigio.bsky.social pubs.acs.org/doi/full/10.... #RNA #MembraneBiology #compchem #compbiol
All-Atom Simulations Elucidate the Molecular Mechanism Underlying RNA–Membrane Interactions
RNA–membrane interactions are starting to emerge as an important organizing force in both natural and synthetic biological systems. Notably, RNA molecules were recently discovered to be present on the...
pubs.acs.org
New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽 www.biorxiv.org/content/10.1...
Accurate prediction of thermoresponsive phase behavior of disordered proteins
Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermorespons...
biorxiv.org
Ananya Chakravarti@ananyac2000.bsky.social · last yr.Cells have evolved to adapt to changing environments to maintain homeostasis. Can we predict how temperature affects protein phase separation? 🌡️ (1/4)
CALVADOS 🤝 PEG Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.A coarse-grained model for disordered proteins under crowded conditions https://www.biorxiv.org/content/10.1101/2025.03.01.640997v1
Proud to share: "Ensemble docking for intrinsically disordered proteins" from Dartmouth undergrad Anjali Dhar 24' and grad student Tommy Sisk. We present ensemble docking strategies for IDPs that, remarkably, seem to work! www.biorxiv.org/content/10.1... Code: github.com/paulrobustel...
Very proud to announce that a member of our group, Dr. Jana Aupič, has been awarded the prestigious "EuChemS ChemBioLife Young Investigator" prize! 🏅 This honors her hard work and exceptional contribution to chemical biology. Congratulations, Jana! 🌟✨ . www.euchems.eu/divisions/ch...
News - EuChemS
WINNER ANNOUNCEMENT! “EuChemS ChemBioLife Young Investigator Award” 2024-2025 edition We are proud to announce the winner of the EuChemS ChemBioLife Young Investigator Award of the EuChemS Division...
euchems.eu
Just published in Journal of Chemical Information and Modeling our new study on the Mechanism of Rac1b: the Alternative Spliced Variant of Rac1 Small Rho GTPase. Great work by A. Parise and S. Cresca! pubs.acs.org/doi/10.1021/...
Assessing the Mechanism of Rac1b: An All-Atom Simulation Study of the Alternative Spliced Variant of Rac1 Small Rho GTPase
The Rho GTPase family plays a key role in cell migration, cytoskeletal dynamics, and intracellular signaling. Rac1 and its splice variant Rac1b, characterized by the insertion of an Extraloop, are fre...
pubs.acs.org
📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...
arxiv.org
Publication Alert 🚨 We have studied Polyethylene Glycol‐Based Refolding Kinetic Modulation of CRABP I Protein in this article. Details 👇👇 analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
Polyethylene Glycol‐Based Refolding Kinetic Modulation of CRABP I Protein
The crowder size and concentration are responsible for the impact through viscosity and excluded volume on protein structure and dynamics. Viscosity effect predominates over the excluded volume effec...
analyticalsciencejournals.onlinelibrary.wiley.com
Meet the CALVADOS RNA model Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 2y agoA coarse-grained model of disordered RNA for simulations of biomolecular condensates https://www.biorxiv.org/content/10.1101/2024.11.26.625489v1
I'm excited to share a new manuscript with Jiaqi Zhu characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs: biorxiv.org/content/10.1... Code + Ensembles: github.com/paulrobustel...
