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Interesting paper about how to find out whether ligands affect a receptor's conformation via induced fit or via conformational selection. www.biorxiv.org/content/10.1...

submitted 2 days ago • 1 comment

We need to organize--let’s help each other. NIH is cancelling grants, but it's not clear exactly what they're cancelling and why. Without this information, we can't respond. I've started a Google Sheet to track grant cancellations. Please add any canceled grants you know of and spread the word!

submitted 4 days ago • 5 comments

BREAKING: The University of Pittsburgh and Carnegie Mellon University has reneged on their commitment to host the @sciencewriters.org annual conference and withdrew their entire financial support. The National Association of Science Writers is now looking for a new venue, sponsors, and partners.

submitted 5 days ago • 337 comments

In Vol 43, Issue 6, 500 ns MD simulations of the Mtb cytochrome bcc-aa3 supercomplex with Telacebec reveal both binding site plasticity and persistent interactions. The binding free energy is driven largely by electrostatics. #JBSD #MDsimulations www.tandfonline.com/doi/full/10....

submitted 7 days ago • 0 comments

Vol 43:6. MD simulations suggest that antibodies can restore gp41's native 6-helix bundle in HIV-1 mutants. Mutations like Q563R or L565A disrupt secondary structure & domain interactions; binding of F240 or 3D6 re-establishes proper dynamics. #JBSD #MDSimulations www.tandfonline.com/doi/full/10....

submitted 12 days ago • 0 comments

From Vol 43 Issue 5, MD simulations comparing caprine, leporine, ovine, and equine serum albumins suggest unique structural dynamics driven by domain I differences that may influence drug binding and substitution feasibility. #JBSD #MDsimulations www.tandfonline.com/doi/full/10....

submitted 14 days ago • 1 comment

In silico analysis of DDC gene nsSNPs suggest four novel variants markedly alter protein structure and stability. MD simulations suggest these nsSNPs may have significant functional implications #JBSD www.tandfonline.com/doi/full/10....

submitted 15 days ago • 0 comments

Professor Carlos Bustamante's research deals with single-molecule force spectroscopy, a form of biophysics that uses force as a parameter to study reactions on individual molecules. Learn more about his research at the 112th annual Faculty Research Lectures on March 3, 2025.

submitted 19 days ago • 1 comment

BioPhysicists, remember to renew your membrship, and please nominate yourself or a deserving colleague for BPS Awards, BPS Fellow, or Best Dissertation! @biophysicalsoc.bsky.social

submitted 18 days ago • 0 comments

Analysis of 218 ISBs from 15 MDH structures reveals that extremophilic MDH exhibits ~30× stronger interface salt bridges than mesophilic forms. Differences in residue design and microenvironment (type-II) drive enhanced electrostatics . #JBSD #Biophysics www.tandfonline.com/doi/full/10....

submitted 18 days ago • 0 comments

Mathematical modeling of the interferon α17 gene (980 bp) suggests that higher medium viscosity stabilizes DNA by increasing the torque required for open states & unwinding. Nucleotide composition & gene boundaries further modulate these effects. #JBSD #Biophysics www.tandfonline.com/doi/full/10....

submitted 19 days ago • 0 comments

An integrated spectroscopic and MD simulation study suggests that pH modulates Staphylococcus aureus thymidine kinase structure and activity by disrupting structure and inducing aggregation at pH 5.0 while maximizing function at physiological pH. #JBSD #Biophysics www.tandfonline.com/doi/full/10....

submitted 21 days ago • 0 comments

A computational saturation mutagenesis study suggests that interfacial missense mutations in the TDP-43 CTD and α-Synuclein complex significantly destabilize the protein structure and reduce binding affinity. #JBSD www.tandfonline.com/doi/full/10....

submitted 22 days ago • 0 comments

Palmatine stabilizes G-quadruplex structures in G-rich sequences from the TRF2 promoter, as shown by FRET, CD, UV–Vis, and MD simulations. Its selective binding may inform design of ligands targeting G-quadruplexes in oncogene regulation. #JBSD #biophysics www.tandfonline.com/doi/full/10....

submitted 25 days ago • 0 comments

Vol 43 Issue 3 of #JBSD is out! We are still clearing out a backlog of articles from before we refined our aims & scope, but I'll highlight a few relevant ones. #biophysics

submitted 25 days ago • 0 comments

Next in Vol 43 Issue 3, MD simulations suggest that the S238F/W159H double mutation in IsPETase reconfigures its active site and loop dynamics—potentially boosting substrate binding and catalytic efficiency for PET depolymerization. #MDSimulations #JBSD www.tandfonline.com/doi/full/10....

submitted 26 days ago • 0 comments

Another interesting use of #MDsimulations on proton‐dependent glucose transporters proposes pH‐driven conformational dynamics. Flavonoid inhibitors bind via hydrophobic interactions in protonated states—unlike non‐inhibitors. #JBSD www.tandfonline.com/doi/full/10....

submitted 27 days ago • 0 comments

The first LIGO detection was announced on this day 9 years ago.

submitted 28 days ago • 1 comment

Happy International Day of Women and Girls in Science 🔬 On 11 February, we celebrate the important contributions of women to the STEM disciplines. On this occasion, we asked six female scientists what science means to them: home.cern/news/news/cern/international-day-women-and-girls-science-2025

submitted 29 days ago • 2 comments

🚨RED ALERT for 🧪: The Trump NIH just gashed indirect costs. This is a direct attack on universities. “Pursuant to this Supplemental Guidance, there will be a standard rate of 15% across all NIH grants for indirect costs.” 😮 Just a devastating Friday night news dump. #scicomm #academicaky

submitted 32 days ago • 22 comments

15% indirect across the board - can your university survive? grants.nih.gov/grants/guide...

submitted 32 days ago • 9 comments

Investigating the thermostable protease Protease JJ through molecular dynamics. RoseTTAFold predicts a subtilisin-like sandwich structure and MD simulations suggest stability at 60–90°C & strong interactions with BSA & β-casein #JBSD #MDsimulations www.tandfonline.com/doi/full/10.... 5/8

submitted 32 days ago • 0 comments

This article investigates glucose transporter inhibition and pH-dependent dynamics via molecular dynamics. Protonation states modulate flavonoid binding; inhibitors occupy glucose-binding sites & stabilize structures, unlike non-inhibitors. #JBSD www.tandfonline.com/doi/full/10.... 4/8

submitted 32 days ago • 0 comments

Now for predicting chromatin structure with simulations! Using an extended SBS model, they developed ChroMC, a freely available tool for chromatin modeling which suggests that non-reactive chromatin is key for accurate predictions in Drosophila #JBSD www.tandfonline.com/doi/full/10.... 3/8

submitted 32 days ago • 0 comments

Molecular dynamics simulations suggest how mutations in β-Lactamase might drive antibiotic resistance. V84I & A184V mutations in IR-TEM β-Lactamase enhance Ω-loop flexibility. This allosteric regulation may be key to inhibitor resistance. #JBSD #biophysics www.tandfonline.com/doi/full/10.... 2/8

submitted 32 days ago • 0 comments

V43 Issue 3 of #JBSD is out! We are still clearing out a backlog of articles from before we refined our aims & scope, but I'll highlight a few relevant ones. #biophysics 1/8 www.tandfonline.com/toc/tbsd20/4...

submitted 32 days ago • 0 comments

Got an email confirming that study sections are back on! Not sure what this means for many grants where we’ve watched the expiration dates change, but I’m happy to hear some things are moving forward again.

submitted 36 days ago • 7 comments

Those are all the articles I wanted to highlight in Vol 43 Issue 2 of #JBSD. Articles from more issues to come! www.tandfonline.com/loi/tbsd20 7/7

submitted 36 days ago • 0 comments

MD simulations of E. coli Hsp70 find dynamic transitions between ADP- and ATP-bound states, confirming the allosteric link between NBD & SBD. Notably, the Lid domain shows a “double-hinged” conformation with unexpected flexibility. #JBSD www.tandfonline.com/doi/full/10.... 6/7

submitted 36 days ago • 0 comments

A novel predictor for intrinsically disordered proteins harnesses random sequential amino acid profiles + CIDER; by analyzing random physicochemical properties and order-promoting residue patterns, this approach overcomes challenges in prediction #JBSD www.tandfonline.com/doi/full/10.... 5/7

submitted 36 days ago • 0 comments

Simulations of the E. coli FtsZ dimer suggest that GTP binding induces ~15° closure of helix H5 compared to GDP, modulating protofilament curvature and enhancing flexibility in the C-terminal IDR & SC2-HC2 regions. #MolecularDynamics #JBSD www.tandfonline.com/doi/full/10.... 4/7

submitted 36 days ago • 0 comments

Oops. This is actually in Vol 43 Issue 2! #JBSD 3/7

submitted 36 days ago • 0 comments

This article with MD simulations suggests that ibuprofen disrupts POPC bilayer structure—raising area per lipid, MSD, and chain order while lowering free energy barriers for water/H₂O₂ permeation. These dynamics may underlie its local cytotoxic effects. #JBSD 2/7 www.tandfonline.com/doi/full/10....

submitted 36 days ago • 0 comments

V43 Issue 2 of #JBSD is out! We are still clearing out a backlog of articles from before we refined our aims & scope, but I'll highlight a few relevant ones. 1/7

submitted 36 days ago • 0 comments

Just received this email (received 3:25 pm ET), from the NSF director, informing that DOJ has interpreted the temporary restraining order on the funding freeze as applying to “all NSF award recipients.” Again, I’ll shout it from the rooftops: lawsuits matter!!!!

submitted 37 days ago • 17 comments

If you are a PhD student and like protein disorder (or want to learn more), Birthe Kragelund @bbkrage.bsky.social and Kristian Strømgaard are organizing a PhD course on How IDPs work 🧶🧬🧪 Note the cost if you are not at a Danish university. Details: phdcourses.ku.dk/DetailKursus...

submitted 106 days ago • 1 comment

Just got a story approved to run on Monday on the crisis happening at the NSF. If you are an NSF-funded scientist and have been personally impacted by the funding pause this week, I'd love to hear from you. Reach me securely on Signal: 3162958947

submitted 39 days ago • 8 comments