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lstelzl.bsky.social

@lstelzl.bsky.social
644 followers 585 following 9 posts

Prof Biomolecular Simulations Uni Mainz. Disordered proteins, nucleic acids and their dynamics, complexes and phase-separated condensates. Integrating simulations and experiments.

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Physics of Life Dresden @poldresden.bsky.social · 02/04/2026
👨‍🔬🧬Are you a bachelor student curious about the physics behind biological systems and living matter? The international 'Physics of Life' MSc @cmcb-tud.bsky.social is taught entirely in English, tuition-free, and trains the next generation of interdisciplinary scientists! Learn more: tud.link/ak1hjt
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Şuayb Üstün @suaybuestuen.bsky.social · 22/08/2025
Job alert 📣 Our faculty looks for a Junior Professor W1 with tt to W2 in Membrane Biology! We are looking for #ECRs working on membrane biogenesis,contact sites,composition & other aspects of membranes in 🌱 and other organisms! DM me if you need more details! jobs.ruhr-uni-bochum.de/jobposting/f...
jobs.ruhr-uni-bochum.de
W1TTW2 Professorship in Membrane Biology (m/f/d)
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SFB 1551 - Collaborative Research Centre 1551 @sfb1551.bsky.social · 14/08/2025
🎉 Congrats to @kgaurav.bsky.social, Lukas Stelzl & @reneketting.bsky.social (SFB1551) on their new Biophysical Journal paper! #MUT16 #PhaseSeparation #MutatorFoci #SmallRNA #GeneRegulation #Celegans #ProteinAssembly #RNAResearch #MultiscaleSimulations Great teamwork👏👏👏 www.cell.com/biophysj/ful....
cell.com
Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition
Phase separation of proteins plays a critical role in cellular organisation. How phase separated protein condensates underpin biological function and how condensates achieve specificity remain elusive...
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Matthieu Chavent @matthchavent.bsky.social · 11/06/2025
Very happy to release AutoMartiniM3 for Martini3 to automatize CG modelling of small molecules and fragments. Great work from M Szczuka in my lab in collab with @pauloctsouza.bsky.social and @tbereau.bsky.social teams! Give it a try: github.com/Martini-Forc... poke @cg-martini.bsky.social
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Ed Sherer @hartreefocker.bsky.social · 07/06/2025
Very excited to be recruiting for an Associate Principal Scientist: Molecular Modeling, Analytical Research & Develop. Our Digital Sciences team is seeing many requests related to influencing formulation design, especially for biologics. #chemjobs #compchem #chemsky jobs.merck.com/us/en/job/R3...
jobs.merck.com
Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job in Rahway, New Jersey, United States of America | jobs at Merck migration
Apply for Associate Principal Scientist: Molecular Modeling, Analytical Research & Development job with Merck migration in Rahway, New Jersey, United States of America. Browse and apply for the jobs a...
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Siewert-Jan Marrink @cg-martini.bsky.social · 27/05/2025
Martini workshop registration now open !!!! See cgmartini.nl for details and how to apply. Looking forward to seeing you in Groningen, Aug 11-15th.
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SFB 1551 - Collaborative Research Centre 1551 @sfb1551.bsky.social · 22/05/2025
🚨Publication alert🚨 "Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates" by Emanuele Zippo, @lstelzl.bsky.social, @dormannlab.bsky.social & Thomas Speck. Congratulations!! 📄 www.nature.com/articles/s41... #TDP43 #CK1δ #ALS #biophysics #proteincondensates
nature.com
Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates - Nature Communications
Here, the authors implement molecular dynamics simulations to model ATP-driven enzymatic reactions, revealing how the enzyme CK1δ phosphorylates condensates of the neurodegeneration linked protein TDP...
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Siewert-Jan Marrink @cg-martini.bsky.social · 28/04/2025
Pre-announcement: MARTINI tutorial workshop, August 11-15th 2025 in Groningen, The Netherlands !! Learn basic and advanced Martini from the cocktail masters themselves. Registration will open soon.
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Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025
Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social, @marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social 🔗 Preprint here tinyurl.com/3a74uanv
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Gräter lab @graeterlab.bsky.social · 04/04/2025
Job alert: Join us in Mainz as Max Planck Research Group Leader (W2) in Molecular Design ...and make your own research dreams happen on de novo design, generative models, proteins, materials ... tinyurl.com/r2xjxnuk @mpip-mainz.mpg.de
tinyurl.com
Max Planck Research Group Leader (W2) in Molecular Design
We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on b...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 25/03/2025
Our paper on prediction of phase-separation propensities of disordered proteins from sequence is now published: www.pnas.org/doi/10.1073/... The paper has been substantially updated compared to the preprint including new experimental data and using the neural network to finetune CALVADOS. 1/n
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Gabi Heller @g-heller.bsky.social · 24/03/2025
We’re looking for fellow nerds to help us make disordered proteins druggable. Love #IDPs, #MD, #NMR, #AI, #DrugDiscovery, or #MassSpec? Let’s talk. @bindresearch.org is hiring across the board: bindresearch.org/careers/ #compchem #compbio #NMRChat #TeamMassSpec #chemjobs @chemjobber.bsky.social
bindresearch.org
Careers
Careers
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Siewert-Jan Marrink @cg-martini.bsky.social · 24/03/2025
Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: www.nature.com/articles/s41...
nature.com
Martini3-IDP: improved Martini 3 force field for disordered proteins - Nature Communications
Here, the authors introduce Martini3-IDP, a refined model for disordered proteins that addresses prior over-compact structures. Validated across diverse systems, it captures IDP interactions and biomo...
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Isabella Graf @isabellagraf.bsky.social · 24/03/2025
We are organizing a conference for young researchers at the intersection between physics & biology: www.embl.org/about/info/c... @embl.org @events.embl.org @intcha.bsky.social Please consider applying/registering -- the deadline is already in one week!
embl.org
Interdisciplinary challenges in the physics of complexity and life 2025 (IntCha25)
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lstelzl.bsky.social @lstelzl.bsky.social · 22/03/2025
Traveling to San Diego for ACS. Really looking forward to the meeting ☺️.l!
Airplane
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/03/2025
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...
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Hannah Wayment-Steele @hkws.bsky.social · 20/03/2025
Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models. Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1. 📝: rb.gy/de5axp
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Vincent Voelz @voelzlab.bsky.social · 19/03/2025
New paper from the Voelz Lab in @pccp.rsc.org! Goold et al. performed many parallel expanded ensemble free energy simulations on @foldingathome.org using GROMACS (@gromacs.bsky.social) with OpenFF 2.0 (@openforcefield.org) to make blind logP predictions in SAMPL9 doi.org/10.1039/D4CP...
doi.org
Expanded ensemble predictions of toluene–water partition coefficients in the SAMPL9 log P challenge
The logarithm of the partition coefficient (log P) between water and a nonpolar solvent is useful for characterizing a small molecule's hydrophobicity. For example, the water–octanol log P is often us...
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Sjors Scheres @sjorsscheres.bsky.social · 12/03/2025
Cool stuff from our collaboration with @mxhend.bsky.social: the fold of tau filaments matters for seeding in primary cultures & in live mice: the AD fold is more seeding efficient than non-AD folds! But that's not all: phosphorylation of the fuzzy coat matters too. 🤩 www.biorxiv.org/content/10.1...
biorxiv.org
Seed structure and phosphorylation in the fuzzy coat impact tau seeding competency
Tau is a pathogenic protein in Alzheimer's (AD) and other neurodegenerative diseases. The misfolding of tau into beta-sheet rich elongated filaments is thought to be a key event in disease pathogenesi...
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rambhaskara.bsky.social @rambhaskara.bsky.social · 13/03/2025
Just dropped on bioRxiv! Our team has assembled a data-driven map of the human E3 ligome. Check out our preprint! #E3_ligome #ubiquitination #dataIntegration #metriclearning www.biorxiv.org/content/10.1...
biorxiv.org
Multi-scale classification decodes the complexity of the human E3 ligome
E3 ubiquitin ligases are key regulators of protein homeostasis, targeting specific proteins for degradation via the ubiquitin-proteasome system (UPS). They provide crucial substrate specificity, makin...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 12/03/2025
Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB authors.elsevier.com/sd/article/S... Led by @sobuelow.bsky.social and Giulio Tesei
Figure from the paper illustrating sequence–ensemble–function relationships for disordered proteins. ML prediction (black) and design (orange) approaches are highlighted on the connecting arrows. Prediction of properties/functions from sequence (or vice versa, design) can include biophysics approaches via structural ensembles, or bioinformatics approaches via other hetero- geneous sources. The lower panels show examples of properties and functions of IDRs for predictions or design targets. ML, machine learning; IDRs, intrinsically disordered proteins and regions.
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lstelzl.bsky.social @lstelzl.bsky.social · 11/03/2025
Go and work with @reidalderson.bsky.social !!!
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Jerelle Joseph @jerelleaj.bsky.social · 06/03/2025
New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽 www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Bede Portz @ysptsps.bsky.social · 07/03/2025
www.biorxiv.org/content/10.1...
biorxiv.org
Prediction of small-molecule partitioning into biomolecular condensates from simulation
Predicting small-molecule partitioning into biomolecular condensates is key to developing drugs that selectively target aberrant condensates. However, the molecular mechanisms underlying small-molecul...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 06/03/2025
CALVADOS 🤝 PEG Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs
Figure 3 from the paper showing how the phase separation propensity of WT and aromatic variants of the hnRNPA1-LCD responds linearly to PEG concentration. Panel C shows a "slab" simulation of A1-LCD with 0%, 5% and 10% PEG.
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Diego del Alamo @delalamo.xyz · 01/03/2025
We’re hiring a computational biologist in Heidelberg DE or Stevenage UK to work on a pretty ambitious project with fun people for the year www.linkedin.com/jobs/view/41...
linkedin.com
GSK hiring Computational Biologist in Stevenage, England, United Kingdom | LinkedIn
Posted 11:13:48 PM. Site Name: UK - Hertfordshire - Stevenage, Heidelberg - OfficePosted Date: Feb 28 2025We create a…See this and similar jobs on LinkedIn.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 26/02/2025
CALVADOS-RNA is now published doi.org/10.1021/acs.... This is a simple model for flexible RNA that complements and works with the CALVADOS protein model. Work led by Ikki Yasuda who visited us from Keio University. Try it yourself using our latest code for CALVADOS github.com/KULL-Centre/...
Table of Contents figure showing the CALVADOS-RNA model and a snapshot from a mixed protein-RNA condensate
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Matt Higgins @parasitematt.bsky.social · 25/02/2025
A brilliant, kind, funny colleague gone too soon. We will miss you Bela. www.merton.ox.ac.uk/news/remembe...
merton.ox.ac.uk
Remembering Professor Béla Novák 1956 - 2025
With great sadness, we announce the loss of Professor Béla Novák.
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MaRtiNA Hallegger @martinahallegger.bsky.social · 21/02/2025
Great opportunity for clinicians to gain early-career experience in a fully-funded, translational medicine programme in Oxford. If you know anyone interested, please share this link. There is a wide range of projects, including mine. Deadline Fr 14 March 2025 www.ox.ac.uk/admissions/g...
ox.ac.uk
DPhil in Biomedical and Clinical Sciences (Oxford-GSK) | University
About the courseThe DPhil in Biomedical and Clinical Sciences (Oxford-GSK) aims to address an unmet need among clinicians for training in data science and translational medicine. The course provides
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Frank Noe @franknoe.bsky.social · 19/02/2025
The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues. github.com/microsoft/bi...
github.com
GitHub - microsoft/bioemu: Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning - microsoft/bioemu
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Rosana Collepardo @rcollepardo.bsky.social · 11/02/2025
Introducing Mpipi-Recharged🔥🔥🔥 Our Mpipi coarse-grained model for biomolecular condensates now includes a pair-specific electrostatic potential that improves its predictions, including for challenging charged systems—all while still treating solvent and ions implicitly pubs.acs.org/doi/10.1021/...
pubs.acs.org
Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates
Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of thes...
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Di Jiang @dijiang319.bsky.social · 08/02/2025
🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/... Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
science.org
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
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Phil Biggin @philbiggin.bsky.social · 08/02/2025
Very nice to see the work of Matt Warren and Isak Valsson just out with Charlotte Deane, Aniket Magarkar and @garrettmm.bsky.social where we show how augementation can dramatically improve ML affinity predictions to close to FEP accuracy. rdcu.be/d88Wm
rdcu.be
Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data
Communications Chemistry - Machine learning offers great promise for fast and accurate binding affinity predictions, however, current models lack robust evaluation and fail on tasks encountered in...
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BioExcel CoE @bioexcelcoe.bsky.social · 06/02/2025
The deadline for applications to our Summer School on Biomolecular Simulations 2025 is fast approaching ❗️ 🧑‍🎓Learn from the code developers, build your network and present your work Submit your application by 14 February ➡️ bit.ly/4ihQCUI
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Roberto Covino @rocovino.bsky.social · 24/01/2025
Check out our new paper! Protein assembly in membranes is crucial yet elusive. Why steer when you can just observe? We introduce a bias-free simulation method that captures the full picture of transmembrane dimerization—free energies, mechanisms, and rates! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simula...
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BioExcel CoE @bioexcelcoe.bsky.social · 23/01/2025
The BioExcel Summer School on Biomolecular Simulations is our flagship training event. Now in its 8th year it always receives outstanding reviews: 📽️https://www.youtube.com/watch?v=ad9EKOVScMc Don't miss out on the chance to participate ➡️ bit.ly/4ihQCUI Deadline for applications is 14 February!
bit.ly
Summer School on Biomolecular Simulations 2025
Visit the post for more.
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Rosana Collepardo @rcollepardo.bsky.social · 23/01/2025
What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties? We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
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Philip Ball @philipcball.bsky.social · 21/01/2025
In the cover story of the February issue of @sciam.bsky.social I explain what biomolecular condensates are and why they are transforming cell biology. A short 🧵 (You'll need a subscription to read the article.) www.scientificamerican.com/article/myst...
scientificamerican.com
Mysterious Blobs in Cells Are Changing the Way We Understand Life
Tiny specks called biomolecular condensates are leading to a new understanding of the cell
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Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 20/01/2025
Applications are now open for UNIQ+ @ox.ac.uk (deadline Wed 19 February 2025)! We're delighted to be offering a project on Nanobody Language Modelling. Learn about deep learning and language modelling and gain experience applying these methods to nanobody sequences www.ox.ac.uk/admissions/g...
ox.ac.uk
UNIQ+ | University of Oxford
UNIQ+ Research Internships are aimed at talented undergraduates from under-represented groups, who would find continuing into postgraduate study a challenge for reasons other than their academic
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Katja Petzold @katjapetzold.bsky.social · 17/01/2025
Interested in computational NMR? Join us in beautiful Switzerland in June! Many slots for selected talks and great hiking opportunities. GRC conference 1-6th of June with GRS ( @chrisdkolloff.bsky.social and Stase) on 30.05. please share @nmr900.bsky.social www.grc.org/computationa...
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Zechner Lab @zechnerlab.bsky.social · 17/01/2025
Please share! There are two postdoc opportunities at the Molecular and Statistical Biophysics group at SISSA. Join us in beautiful Trieste! More information at msb.sissa.it/join-us/
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Alex Holehouse @alexholehouse.bsky.social · 17/01/2025
New review / perspective with @albertilab-tud.bsky.social on our thoughts on condensate speciality and recruitment, focusing on interplay between site specific and chemically specific interactions www.cell.com/molecular-ce...
cell.com
Molecular determinants of condensate composition
Biomolecular condensates are non-stochiometric assemblies that organize cellular matter in space and time. Despite much work, many questions remain regarding what determines the recruitment and exclus...
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Nature @nature.com · 16/01/2025
Nature research paper: Targeting FOXM1 condensates reduces breast tumour growth and metastasis go.nature.com/4g7BNC8
go.nature.com
Targeting FOXM1 condensates reduces breast tumour growth and metastasis - Nature
The transcription factor FOXM1 forms functional condensates, the formation of which can be targeted with a specific peptide to suppress breast cancer growth and metastasis.
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Pedro Beltrao @pedrobeltrao.bsky.social · 13/01/2025
Come join us at this year's Basel Computational Biology Conference (8 - 10 Sept). Call for abstracts for talks and posters bc2.ch/talks-poster... I will be co-chairing with @ninjani.bsky.social the computational structural biology session.
bc2.ch
Call for talks and posters
The [BC]2 Basel Computational Biology Conference is Switzerland's main event in the domain of Computational Biology and one of the major events of its kind in Europe. The conference unites scientists ...
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John Chodera @jchodera.bsky.social · 08/01/2025
Interested in building the future of open source ligand- and structure-based ML models for ADMET prediction? The ARPA-H funded OMSF (@omsf.bsky.social) OpenADMET project is hiring multiple positions to build ML models of ADMET properties and drive informative data collection! openadmet.org/jobs/
openadmet.org
OpenADMET Jobs
Seeking talented scientists for the OpenADMET Consortium
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Xuhui Huang @xuhuihuangchem.bsky.social · 04/01/2025
The @cecamevents.bsky.social Flagship Workshop is coming to Madison! Hosted at @datascience_uw(thanks!), organized by @drgregbowman.bsky.social, @bettinagkeller.bsky.social, and me (CECAM-US-CENTRAL). We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det...
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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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Teif lab @teiflab.bsky.social · 28/12/2024
Nucleosome spacing can fine-tune higher order chromatin assembly [labs of Rosana Collepardo-Guevara and Michael Rosen] www.biorxiv.org/content/10.1... ▶️phase separation is decided by trade-off between inter- and intramolecular nucleosome stacking, favoured by 10N+5 and 10N bp linkers, respectively
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/12/2024
Check out @rasmusnorrild.bsky.social's work with Alex Buell and Joe Rogers developing and using Condensate Partitioning by mRNA-Display to probe phase separation of ~100.000 sequences, and @sobuelow.bsky.social's simulations to support and analyse the experiments www.biorxiv.org/content/10.1...
Figure 1a from the paper that outlines the method. Caption: "Peptides from the N-terminal IDR of DDX4 were encoded in a DNA library for mRNA display and transcribed using purified T7 RNA polymerase. The resulting mRNA contains a ribosomal binding site (RBS), a coding sequence (CDS) for peptide of interest, and a HA-tag for purification via the translated peptide. The synthetic mRNA (pink) is ligated to a puromycin-containing PEG-linker (black) containing a DNA sequence (blue) that forms a hetero duplex with the mRNA to facilitate single stranded RNA ligation. The resulting mRNA display molecule is purified using the HA-tag and added to an excess of DDX4N1 to measure partitioning of all library members through RNA/DNA sequencing. "
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/12/2024
Since several people mentioned how this suggests that the first components in a PCA (etc) may not always be the relevant modes, I was reminded of now 15-year-old work from Hub and de Groot on ‘functional mode analysis’ to finds motions that correlate with function doi.org/10.1371/jour...
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