Joshua Pajak

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What are some of your favorite molecular dynamics papers? I am compiling a reading list for a course on biomolecular simulations that I will lead next spring, and I am looking for papers that get at the "why" of performing MD sims. I have a shortlist now but the more the merrier!

What are some of your favorite molecular dynamics papers? I am compiling a reading list for a course on biomolecular simulations that I will lead next spring, and I am looking for papers that get at the "why" of performing MD sims. I have a shortlist now but the more the merrier!

POV: you are a young woman celebrating a recent academic success

We are seeking postdoctoral researchers to study viral RNA and macromolecular complexes using X-ray crystallography, cryo-EM, and biochemical methods.

Structural biology experience is required. Interested candidates should send a CV, a brief research statement, and 2–3 references to kaychoi@iu.edu.

2. We dramatically reworked both text and the figure explaining the setup and results from our MANT-ATP assay for improved clarity.

Thanks again to everyone involved in this project, and to the anonymous reviewers whose critique strengthened the final manuscript!

Onto the next one!

1. We now include a mutual information based analysis of our molecular dynamics data to predict how RFC subunits sense and respond to ATP hydrolysis. We highlight the "sensor II" arginine as a hub of allosteric communication.

My paper on nucleotide exchange in RFC is now available at PNAS! www.pnas.org/doi/10.1073/...

Should you read if you already read our preprint? Yes!

Two big updates made during peer-review include:

There are 3 PhD positions available in my lab using cryoEM to investigate phage structure!
- SWBio DTP: tinyurl.com/ytdft9bj, to apply: www.swbio.ac.uk/programme/ho...
- LSI and CSC PhD studentships and how to apply: tinyurl.com/45dze6se

On a gruelling hunt for rare associated molecules in your #cryoEM particle stack and not sure where to look?

Discover practical tips and tricks in our new case study using #CryoSPARC v4.7.1 where we find and refine a low-population interaction partner!

guide.cryosparc.com/processing-d...

Great collaboration with @guo-lab.bsky.social to determine an in situ architectural model of the Tad pilus machine. Be on the lookout soon for a preprint on the same topic by Grant Jensen and @viollierpat.bsky.social. #microsky

Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...

Next week LinkedIn will use your personal data for AI training by automatically enabling permissions.

To manually turn off go to:

Settings ➡️ Data Privacy ➡️ under
“How LinkedIn uses your data” click “Data for Generative AI improvement” ➡️ toggle off

JD Vance claims that diversity weakens unions, as people end up distrusting each other and not organizing.

Let me tell you two menswear stories related to this claim. 🧵

Human RPA is an essential telomerase processivity factor for maintaining telomeres Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical ...

Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...

Happy to share a new publication on Mechanistic Coupling of Enzyme Activities at the Replisome in JBC. We #Traklab compare and contrast strategies used across organisms to coordinate the many enzymatic processes that occur during DNA replication. Hope it is helpful. doi.org/10.1016/j.jb...

Visualizing influenza A virus assembly by in situ cryo-electron tomography - Nature Communications Influenza A virus must package eight separate genomic segments, called viral ribonucleoproteins (vRNPs). Using in situ cryo-electron tomography, the authors visualize how vRNPs are clustered on cell m...

Visualizing influenza A virus assembly by in situ cryo-electron tomography

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

A nuclease-driven mechanism of post-replicative ssDNA gap suppression. The persistence of post-replicative ssDNA gaps following PRIMPOL-mediated replication repriming is linked to chemosensitivity, and in all models reported to date the nuclease MRE11 has been implicated...

New preprint from the lab for any DNA repair or replication stress geeks out there!

www.biorxiv.org/content/10.1...

Screenshot from email that reads: Despite reporting to the contrary, we have not been asked to accept or reject the draft compact. Rather, we have been asked to provide feedback and comments as part of an ongoing dialogue, and that is our intention.

Vanderbilt has arrived, late to the chat, with this shambles of a response. While technically true, this is a clear abdication of any moral responsibility. They even work in a mention of their commitment to "institutional neutrality" later in the email.

Very sad to read about Daniel Narodistky’s passing, I’ve spent countless joy hours learning chess from his videos.

What a grand slam!! The vibes in Seattle are immaculate, I can feel it all the way across the country. Gotta love baseball

I met Prof. McIntosh at the American Cancer Society Jilers conference in Nov of last year. He was so incredibly kind to all the trainees and talked with all of us at our posters (particularly those of us doing basic science). He had a knack for telling stories. Can't wait to read his perspective :)

Locating the missing chlorophylls f in far-red photosystem I The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chloro...

Have you ever looked at the night sky and wondered if there’s a chlorophyll f in the reaction centre of Photosystem I from far-red light adapted cyanobacteria? 🦠

Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org

www.science.org/doi/10.1126/...

One of the best parts of being an academic scientist is feeling really good about a grant you just wrote. No guarantees it’ll get funded, but there’s so many good ideas in there that I’m going to pursue regardless 😎

America’s brain drain

No words

Image: A variation on Benjamin Franklin’s “Join, or Die” engraving, originally published in the Pennsylvania Gazette in 1754. Each segment of the snake has the name of a university sent Trump’s “compact”: Texas, AZ, Vanderbilt, USC, Dartmouth, UVA, Brown, Penn, MIT.

Shared courtesy of my Penn History colleague, Ben Nathans

when UNC scored on the first possession of the first game and Colin Cowherd immediately posted this, and then UNC lost by 34

🧐Checkout our preprint revealing the stepwise firing💥 mechanism of a Contractile Injection System @xujwet.bsky.social&@chipericson.bsky.social trapped the complex by structure-guided engineering🧪 in multiple intermediate states and imaged them by multimodal #cryoEM❄️🔬
www.biorxiv.org/content/10.1...

New method paper:
Bennie Lemmens et al @scilifelab.se describe 3D-SPARK, a super-resolution microscopy method that maps changes in DNA replication nanostructures in response to genetic perturbations or drugs, linking spatial cell biology with DNA synthesis dynamics
www.embopress.org/doi/full/10....

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.

Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...