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Ashok Deniz

@ashokdeniz.bsky.social
751 followers 165 following 25 posts

Professor, @scripps.edu Interested in Single-molecule Biophysics, Soft matter physics, Condensates, Protein disorder, Membranes, RNA, #smFRET, Physical Organic Chemistry scholar.google.com/citations?user=b…

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Reposted by Ashok Deniz
Jason Buenrostro @jbuenrostro.bsky.social · 24/04/2026
Can we control cells by forcing TFs to collaborate? Interested? Read our preprint! An awesome collaboration with @cgersbach.bsky.social, @igvfconsortium.bsky.social, Christian McRoberts Amador, @rachel-savage.bsky.social: www.biorxiv.org/content/10.6... 🧵
biorxiv.org
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/04/2026
New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab doi.org/10.64898/202...
Figures shows full-length fibril model after building N- and C-terminal disordered segments for each chain, yielding a fuzzy coat
surrounding the cross-β core. The figure also shows a structure representing the interaction of LL-37 peptides with the fuzzy coat (yellow peptides) and the core (pink peptides)
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Reposted by Ashok Deniz
Nature @nature.com · 20/04/2026
Nature research paper: Continuously tunable coherent pulse generation in a semiconductor laser go.nature.com/4vrshCt
go.nature.com
Continuously tunable coherent pulse generation in a semiconductor laser - Nature
A monolithic mode-locked semiconductor laser with a continuously and widely tunable repetition rate is achieved by using a microwave driving signal that induces a spatiotemporal gain modulation along the entire laser cavity.
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Reposted by Ashok Deniz
Luke Lavis @rhodamine110.bsky.social · 15/04/2026
Out in @natmethods.nature.com: More dyes. They work. Quite well. And blink. Pick the one that fits your target, your technique, and your labeling density. With too many collaborators and institutes to list, but anchored at @hhmijanelia.bsky.social www.nature.com/articles/s41...
nature.com
A series of spontaneously blinking dyes for super-resolution microscopy - Nature Methods
A series of spontaneously blinking dyes in the far-red range facilitate single-molecule localization microscopy. These dyes vary in their blinking properties and can be matched to the applications and...
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Reposted by Ashok Deniz
Xavier Trepat @xaviertrepat.bsky.social · 17/04/2026
Our latest work on shape-programmable tissues is out in @science.org. By positioning topological defects in cellular nematics, we encode frustrated 2D force fields that relax into predictable 3D shapes. Collaboration with Marino Arroyo’s lab, led by @pauguillamat.bsky.social at @ibecbarcelona.eu.
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Tomas Pascoa @tomaspascoa.bsky.social · 14/04/2026
1/ Excited to share our preprint! 🥳 Degradation of aromatic compounds, including BTEX pollutants, requires highly endergonic aromatic ring reduction. Using #cryoEM and in situ #cryoET, we show how BCRII couples electron bifurcation modules in one giant redox machine www.biorxiv.org/content/10.6...
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Diez Lab @ TU Dresden @stefandiezlab.bsky.social · 02/04/2026
🥳 Excited to share our #diatom work out in @pnas.org. In a great collaboration with @nic-poulsen.bsky.social and @ulrichschwarz.bsky.social we show that diatoms modulate the curvature of their paths by dynamic switching of their cell–substrate contact sites. doi.org/10.1073/pnas.2506122123
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Sam Lewis, Ph.D. @samlewis.bsky.social · 13/04/2026
Excited to share a new collaborative paper with Lena Koslover's team, fueled by @chanzuckerberg.bsky.social Metabolism Across Scales Program 🧪 1/ www.pnas.org/doi/10.1073/...
pnas.org
Diffusive spreading across dynamic mitochondrial network architectures | PNAS
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual orga...
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Juan C. Landoni @jclandoni.bsky.social · 03/04/2026
Our paper is now out in Science! Super excited to share our discovery that #mitochondria #pearling is the elusive mechanism driving the regular distribution and inheritance of #mtDNA nucleoids 🧬 [1/6]
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shenvi.bsky.social @shenvi.bsky.social · 19/03/2026
Congrats to Chunyu Li, Dr Xu-cheng Gan, Yu (Hannah) Irie and Dr Milo Smith for their paper appearing today in Science!
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Jordy F. Botello @jbotello.bsky.social · 10/03/2026
Some molecular machines, like ribosomes, can persist for long periods of time in cells. Could molecular aging of ribosomes shape how proteins are made? In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10) www.biorxiv.org/content/10.6...
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fitzpatricklab.bsky.social @fitzpatricklab.bsky.social · 17/02/2026
Pulsed #lasers integrated with #cryoEM: @fitzpatricklab.bsky.social postdoc Daniel Du aims to boost contrast in #cryoET zuckermaninstitute.columbia.edu/making-world-s-best-microscopes-biology-better zuckermaninstitute.columbia.edu/science-life-daniel-du elifesciences.org/reviewed-preprints/109793v1
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Emma Chory, Ph.D. @chorye.bsky.social · 04/03/2026
Evolution navigated billions of challenges to get to us to where we are today. Directed evolution compresses this to a 1D axis. Imagine if you could sample 200 dimensions at once, with data to boot 📈 First @chorylab.bsky.social PACE preprint on our new system to tackle this: bit.ly/turboprance
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Ardem Patapoutian @ardemp.bskyverified.social · 04/03/2026
New paper from the lab led by @ericmulhall.bsky.social addresses how PIEZO1 and PIEZO2 are tuned to different types mechanical forces. From nanometer-scale super-resolution microscopy to in vivo experiments, links single-molecule observations to physiological function. www.nature.com/articles/s41...
nature.com
The molecular basis of force selectivity by PIEZO2
Nature - PIEZO2 is intrinsically more rigid than PIEZO1, and disparate mechanical stimuli paradoxically evoke opposite conformational and gating responses in each channel.
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Alex Holehouse @alexholehouse.bsky.social · 19/02/2026
Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...
nature.com
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.
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Polly Fordyce @pollyfordyce.bsky.social · 02/03/2026
Have you ever wanted to do single-molecule biophysics in high-throughput? @matt-dejong.bsky.social (amazing joint grad student with @dunnlab.bsky.social) invented a way & measured >100,000 single molecules across 241 different sequences. (1/3) www.biorxiv.org/content/10.6...
biorxiv.org
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Ashok Deniz @ashokdeniz.bsky.social · 04/03/2026
Thanks so much Samrat!
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Giordano Lippi @lippilab.bsky.social · 24/02/2026
Chuffed to see our paper with @geneyeo.bsky.social finally published in @nature.com. www.nature.com/articles/s41... Very grateful to Fede, Susie, and Dave from my lab, and Sammi, Eric, and Pratibha from Gene's lab. What did we find? ⬇️ ⬇️ ⬇️
nature.com
Single-cell and isoform-specific translational profiling of the mouse brain - Nature
Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hipp...
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Reposted by Ashok Deniz
Wiseman Lab @wisemanlab.bsky.social · 18/02/2026
New preprint from @kutseikin.bsky.social showing how pharmacologic inhibition of SLC33A1 activates IRE1/XBP1s signaling. w/ @enriquesaez.bsky.social @chrisgparker.bsky.social @landerlab.bsky.social @forlilab.bsky.social & the Birsoy lab (Rockefeller) Check it out👇 www.biorxiv.org/content/10.6...
biorxiv.org
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Michael Erb @michael-erb.bsky.social · 17/02/2026
What a thrill to see this out! Our prospective, scalable, and target-centric solution for molecular glue discovery. More thoughts and details here: www.linkedin.com/posts/activi... Paper here: www.nature.com/articles/s41...
nature.com
High-throughput ligand diversification to discover chemical inducers of proximity - Nature Chemical Biology
Molecular glue degraders have consistently been discovered retrospectively, despite their increasing importance. Herein, a high-throughput approach is described that modifies existing ligands into mol...
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Alex Holehouse @alexholehouse.bsky.social · 12/02/2026
Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.
nature.com
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology
Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...
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brangwynnelab.bsky.social @brangwynnelab.bsky.social · 20/09/2025
A tremendous honor! Thrilled & humbled to receive 2025 Keio Medical Science Prize for launching LLPS #phaseseparation field (= #softmatter + #cellbio) w collaborators esp @HymanLab. & Congrats to Akiko Iwasaki @virusesimmunity.bsky.social. www.princeton.edu/news/2025/09... #KeioMedicalSciencePrize
princeton.edu
Bioengineer Clifford Brangwynne wins Keio Medical Science Prize
Japan’s Keio University awards the prize annually to honor contributions in medicine and life sciences. Brangwynne is being recognized for groundbreaking work that has opened up a new field of cell bi...
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Reposted by Ashok Deniz
SpruijtLab @spruijtlab.bsky.social · 13/01/2025
Curious how biomolecular condensates can localize ions? Using NMR, we found that condensates selectively bind and localize both chaotropic anions and kosmotropic cations. This alters the condensate composition, interface potential and RNA duplex stability inside. By @irissmokers.bsky.social
biorxiv.org
Selective ion binding and uptake shape the microenvironment of biomolecular condensates
Biomolecular condensates modulate various ion-dependent cellular processes and can regulate subcellular ion distributions by selective uptake of ions. However, the molecular grammar governing condensa...
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Reposted by Ashok Deniz
Arindam Ghosh, PhD @arindam92.bsky.social · 10/01/2025
I am super happy to share our latest article entitled "Decoding the molecular interplay of CD20 and therapeutic antibodies with fast volumetric nanoscopy", now published in Science www.science.org/doi/10.1126/... It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!
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mvstaller.bsky.social @mvstaller.bsky.social · 10/01/2025
Happy new year! Our new preprint is live! We use single molecule imaging in live cells to show that activation domains can control how transcription factors bind to chromatin. SMT 1 TF Dogma 0 www.biorxiv.org/content/10.1...
biorxiv.org
Short activation domains control chromatin association of transcription factors
Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. It is generally assumed that DBDs are solely responsible for interacting with DNA and chromatin. ...
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Reposted by Ashok Deniz
Moumita (Mo) Das @physbee.bsky.social · 11/01/2025
Happy to be on BlueSky! For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...
nature.com
Programming scheduled self-assembly of circadian materials - Nature Communications
Harnessing biomolecular systems to endow synthetic materials with life-like properties is a significant challenge. Here, the authors use the biomolecular KaiABC circadian clock proteins to control aut...
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Reposted by Ashok Deniz
Ben Engel @cellarchlab.com · 06/01/2025
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍 Preprint📜: www.biorxiv.org/content/10.1... A short thread🧵👇
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 06/01/2025
After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month. We are very grateful for his service. @jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases Details: cdn.rcsb.org/rcsb-pd...
cdn.rcsb.org
EDUCATION CORNER: Molecule of the Month: Celebrating  25 Years of Storytelling and Announcing New Beginnings
After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month series.  Janet Iwasa will be continuing the series for PDB-101.
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Ashok Deniz @ashokdeniz.bsky.social · 31/12/2024
Rayleigh-Plateau instability in mitochondria? Exciting analysis of physics of mitochondria dynamics
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Alex Holehouse @alexholehouse.bsky.social · 30/12/2024
For inspiration, here are the papers we discussed in 2023:
List of papers presented in the 2023 cellular memory and adaptation journal club. Paper titles are:

Germline P granules are liquid droplets that localize by controlled dissolution/condensation; FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties; Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity; Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability; Hsp90 as a capacitor for morphological evolution. ; Alternative evolutionary histories in the sequence space of an ancient protein; A hydrophobic ratchet entrenches molecular complexes; Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress.; A proximity-dependent biotinylation map of a human cell.; Multiple dynamin family members collaborate to drive mitochondrial division; The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice; Five intermediate complexes in transcription initiation by RNA polymerase II; RNA Polymerase II cluster dynamics predict mRNA output in living cells; Mediator and RNA polymerase II clusters associate in transcription-dependent condensates; Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.; RNA promotes the formation of spatial compartments in the nucleus; Daily Cycles of Reversible Protein Condensation in Cyanobacteria
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Ryota IINO 飯野亮太 @ryotaiino.bsky.social · 15/12/2024
Visualizing Single V-ATPase Rotation Using Janus Nanoparticles pubs.acs.org/doi/full/10....
pubs.acs.org
Visualizing Single V-ATPase Rotation Using Janus Nanoparticles
Understanding the function of rotary molecular motors, such as rotary ATPases, relies on our ability to visualize single-molecule rotation. Traditional imaging methods often involve tagging those mot...
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Keren Lasker @kerenlasker.bsky.social · 30/12/2024
1/ 🚨We’re thrilled to share our latest study: "Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟 www.biorxiv.org/content/10.1... How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
biorxiv.org
Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure
Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We stud...
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Ashok Deniz @ashokdeniz.bsky.social · 29/12/2024
Excited to share our preprint, work by Anthony Gurunian, showing that #condensates can induce localized potentials in membranes + an analytical framework, with important biological implications, collaboration with @kerenlasker biorxiv.org/cgi/content/...
biorxiv.org
Biomolecular Condensates can Induce Local Membrane Potentials
Biomolecular condensates are a ubiquitous component of cells, known for their ability to selectively partition and compartmentalize biomolecules without the need for a lipid membrane. Nevertheless, co...
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Ashok Deniz @ashokdeniz.bsky.social · 17/12/2024
Interesting porous material - rhodium metal-organic polyhedra (MOP) with tethered polymers. Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes. www.nature.com/articles/s41...
nature.com
Phase-transformable metal-organic polyhedra for membrane processing and switchable gas separation - Nature Communications
The capability of materials to interconvert between phases enables greater control over properties without additional chemical modification but can result in a sacrifice of porosity. Here, the authors...
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Ruben Gonzalez @rubenlgonzalez.bsky.social · 11/12/2024
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
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Ashok Deniz @ashokdeniz.bsky.social · 11/12/2024
Interesting biomaterial engineering!- leveraging physical and chemical properties of gallium www.nature.com/articles/s41...
nature.com
Sacrificial capillary pumps to engineer multiscalar biological forms - Nature
A patterning method using gallium-based engineered sacrificial capillary pumps for evacuation is described for generating structures in soft natural hydrogels across several length scales and enabling...
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Olivier Duss @olivierduss.bsky.social · 04/12/2024
First paper of our lab today @natureportfolio.bsky.social by Nussi! We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping! @embl.org #RNAbiology #RNASky t.co/a24Xxcxdo0
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Ashok Deniz @ashokdeniz.bsky.social · 11/12/2024
Important advance + cool method/Physics www.science.org/doi/10.1126/...
science.org
Active-reset protein sensors enable continuous in vivo monitoring of inflammation
Continuous measurement of proteins in vivo is important for real-time disease management and prevention. Implantable sensors for monitoring small molecules such as glucose have been available for more...
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Scripps Research @scripps.edu · 05/12/2024
Published in @science.org, scientists at Scripps Research have uncovered a mutation in the H5N1 “bird flu” virus that enhances its ability to bind to human cells—emphasizing the need to monitor H5N1 to prepare for potential pandemic threats. More:
scripps.edu
Scripps Research scientists identify mutation that could facilitate H5N1 “bird flu” virus infection and potential transmission in humans
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Fletcher Lab @fletcherlabucb.bsky.social · 05/12/2024
Do you find yourself curious about the eating habits of macrophages? Check out our new preprint to discover the biophysical principles that guide macrophage behavior. www.biorxiv.org/content/10.1...
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Ashok Deniz @ashokdeniz.bsky.social · 07/12/2024
Nice work! Also includes some interesting work with lipid chirality/racemic mixtures.
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Ashok Deniz @ashokdeniz.bsky.social · 05/12/2024
Neat!
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Alex Holehouse @alexholehouse.bsky.social · 10/11/2024
We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
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Samrat Mukhopadhyay @samratmukhopadhyay.bsky.social · 05/12/2024
As the chair of the Intrinsically Disordered Proteins Subgroup of @biophysicalsoc.bsky.social I'm happy to announce the exciting scientific program put together by program co-chairs Dorothee Dormann & Lukasz Joachimiak. Looking forward to seeing you in Los Angeles! www.biophysics.org/2025meeting/...
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Samrat Mukhopadhyay @samratmukhopadhyay.bsky.social · 03/12/2024
Happy to share that my former PhD student, Debapriya Das (now doing her postdoc with my postdoc advisor, Ashok Deniz, at the Scripps Research Institute, California) has been selected for a platform talk at the Biophysical Society meeting to be held in Los Angeles in Feb 2025. Congrats, Debapriya!
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Cees Dekker @ceesdekker.bsky.social · 27/11/2024
Latest #CDlab paper: Synchronization of E. coli Bacteria Moving in Coupled Microwells: onlinelibrary.wiley.com/doi/epdf/10.... E. coli bacteria swim in sync in weakly coupled neighboring microcavities! Great work led by @AleksandreJapa from from Farbod Alijani's lab, to which I also contributed
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estella newcombe @estellaan.bsky.social · 27/11/2024
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered??? www.nature.com/articles/s41...
nature.com
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
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Ashok Deniz @ashokdeniz.bsky.social · 27/11/2024
Delighted to share our new paper, exciting collaboration with Racki, Park and Grotjahn Labs @scripps.edu. Reentrant DNA shells tune polyphosphate condensate size. Congrats Jenna and Ravi, Tumara, all other authors! @natureportfolio.bsky.social #Condensates #Biophysics #SoftMatterPhysics
nature.com
Reentrant DNA shells tune polyphosphate condensate size - Nature Communications
Polyphosphate affects many cellular processes and is often found near cellular DNA. Here, the authors show that DNA forms shells around polyP-Mg2+ condensates in vitro, controlling condensate size and...
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