Dheeraj Prakaash

4/4

Thanks to: @sykhalid.bsky.social at @oxfordbiochemistry.bsky.social

#Simulations performed on #Archer2 #HPC
#Compute resources allocated by HECBioSim.ac.uk

3/4

#Take-home-message: Our study reveals that polymyxins aggregate and form #bridges between proteins upon associating with the OM, reducing #diffusion of #proteins & #lipopolysaccharide - clarifying *why* AFM studies reveal crystalline OM structures before OM disruption upon polymyxin incubation

2/4

Our coarse-grained #simulations involve ~1400 polymyxins (a conc. mimicking experiments) interacting with a realistic #model of a protein-dense region in the #E.coli OM, whose size is directly comparable to AFM images from a previous study - DOI: 10.1038/s41467-022-33838-0

We just dropped some science! 🔬📢
Thread 🧵: 1/4

- How do #antibiotic #polymyxins physically interact with the #E.coli outer #membrane (OM)?
- How does this impact #large-scale #protein/LPS #diffusion in the OM?

..addressed in near-atomic detail @commsbio.nature.com: www.nature.com/articles/s42...

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42...

To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.

It's been a pleasure to work on this paper! Thank you for your support and kind words @sykhalid.bsky.social :)

Halloween sightings at the Uni @utah.edu and #SaltLakeCity on the way home..

The #BidoneLab with costumes and scarfaces on for the #compchem #Halloween  potluck 🎃🍲 at the Henry Eyring Center (HEC) for Theoretical Chemistry. Thanks to our colleagues at the HEC @utahchemistry.bsky.social for organizing.

Thank you, Rocco! :)

Happy to share that I have started as a #postdoc in the #BidoneLab at the Scientific Computing and Imaging Institute @uusci.bsky.social @utah.edu #SaltLakeCity, in collab with #VothGroup at UChicago @uchichemistry.bsky.social

👇🏻Pic of #beautiful #RockyMountains in #Utah from above the #clouds

🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...

Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2 - Nature Communications SPNS2 exports S1P and FTY720-P to control immune cell migration. Here, the authors use cryo-EM, immunofluorescence, in vitro binding and in vivo S1P export, and MD simulations to uncover the mechanism...

Our SPNS2 paper is published! A massive collaboration of Resolute, Oxford CMD, Nuvisan, @oxfordbiochemistry.bsky.social, CeMM, Bayer, & Univ. of Zurich

Work of many talented colleagues, including @sykhalid.bsky.social @supertifurgalab.bsky.social and numerous others

www.nature.com/articles/s41...

Happy ending (of the year): the release of our preprint, "The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior", now available on @ChemRxiv.

👉 Read the full preprint here: chemrxiv.org/engage/chemr...

and get the parameters here: github.com/Martini-Forc...

Thanks, Martin! Exciting indeed!
I figured I need a strong background in ML for future opportunities.

Happy to inform that I've been accepted into the 11-month virtual postgrad program in #AI & #ML by @caltech.edu in collab with #IBM. Excited to dive into this field & upskill myself.

Academics and scientists should have a hobby. This is a necessity. Also, I think Bragg was able to do this since for half a day his admin and staff could handle or manage things without him.

Watch the Webinar: Python Scripting for Molecular Docking This virtual course introduces life scientists to the power and flexibility of Python Scripting for Molecular Docking

Watch the Webinar: Python Scripting for Molecular Docki
This virtual course introduces life scientists to the power and flexibility of python scripting
www.rcsb.org/news/fe...

I guess we have Boltz-1 to thank for pushing all these other AF3 clones to adopt fully open-source licenses and models.

ChimeraX 1.9 has been released! Session view can now be automatically saved and restored. New ​'Find Cavities' tool identifying pockets in models. www.rbvi.ucsf.edu/chimerax/dow...

Can I be added please :)
I’m all about memb prot and lipids!

NVIDIA SC24 Special Address YouTube video by NVIDIA

Really fortunate to have had the honor of being featured as part of NVIDIA SC24 special address by Jensen Huang and Ian Buck. This summarizes a lot of the work that is ongoing in the group highlighting the role of LLMs, multi modality and generative AI.

youtu.be/eKzNKxWUeCE

Google Makes New Quantum Computing Breakthrough Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)

Google’s quantum computer chip called Willow, needed less than five minutes to perform a mathematical calculation that one of the world’s most powerful supercomputers could not complete in 10 septillion years, a length of time exceeding the age of the known universe.

www.nytimes.com/2024/12/09/t...

On the left is the structural output from the AlphaFold 3 server colored by pLDDT, which requires structural knowledge for interpretation. On the right is the AlphaBridge ring output, where the results are pre-analyzed and visually presented, making them easier to understand.

📢 Make your work FASTER and EASIER!

Use AlphaBridge to analyze your AlphaFold results and receive a clear, easy-to-understand output—even for non-experts.

➡️ Let AlphaBridge help you accelerate your workflow!

❤️ Share and try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔

➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!

🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...

I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/

But please dont share this as a mantra for success. If your success comes at the direct expense of your colleagues because they are doing all the work everyone is supposed to share in, it does not make you ‘successful’ it just makes you a horrible colleague.

Also see peer review

Rant over. For now

AlphaProteo generates novel proteins for biology and health research New AI system designs proteins that successfully bind to target molecules, with potential for advancing drug design, disease understanding and more.

New AI system designs proteins that successfully bind to target molecules, with potential for advancing drug design, disease understanding and a system for designing novel, high-strength protein binders to serve as building blocks for biological and health research.

deepmind.google/discover/blo...

Dear #comchem #glycotime folks 🍭,

I need your help!
Does anyone know a tool to build sulfated polysaccharides and get structure und topology files for GROMACS with CHARMM36 FF?🤔

Unfortunately Charmm-gui is placing sulfate groups in wrong orientations.

Please RT!
#moleculardynamics

Our paper: "OmpA controls order in the E. coli outer #membrane & shares the mechanical load" is out in
@pnas.org - led by Georgina Benn and Thomas Silhavy. Collab b/w Princeton, NYU, UCL, & @oxfordbiochemistry.bsky.social.
#Simulations by me & @sykhalid.bsky.social

doi.org/10.1073/pnas...

In a multidisciplinary study led by Georgina Benn and Tom Silhavy we show the role of OmpA in controlling the organisation of the outer membrane and in sharing the mechanical load. www.pnas.org/doi/10.1073/....