Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...

Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature

 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...

nature.com

If you missed the preprint, now is a good time to read the journal version of @grocklin.bsky.social et al’s fantastic paper on multiplexed HDX measurements Large-scale discovery, analysis and design of protein energy landscapes doi.org/10.1038/s415...

bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.

Large-scale discovery, analysis, and design of protein energy landscapes https://www.biorxiv.org/content/10.1101/2025.03.20.644235v1

Cool figure reporting weekly commits to Google's monorepo (from this 2016 article: dl.acm.org/doi/10.1145/...). It would be cool to see this extended to 2026!

1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).

Fun collaboration with the Herzik lab! Very cool to see #TeamTomo + STA directly capture the effects of the AWI at the single-particle level. we know it’s happening, but it’s striking to see it so clearly!

Brian Cook@bcryo.bsky.social · 5mo ago

7) Using cryoET and STA we find that aldolase particles stuck at the AWI not only adopt a single orientation, but these particles are also partially denatured at the AWI! Only when aldolase particles were pushed into bulk ice with SurfACT did they remain intact.

So initial experiments with Open AI's vibe-coding science tool Prism are going about as well as expected.

Excited to highlight our latest bioRxiv led by grad student Zoe Duong and Qian Shao. We report a chemistry-centric, chemoproteomics-enabled strategy to discover non-degradative molecular glues for transcriptional rewiring.
🔗 www.biorxiv.org/content/10.6...

Discovery of Non-Degradative Covalent Molecular Glues for Transcriptional Reprogramming

Transcriptional reprogramming through induced proximity has emerged as a powerful strategy for modulating the expression of oncogenic and tumor-suppressive genes. Inspired by transcriptional reprogram...

biorxiv.org

Very excited to share new work out today in @natchembio.nature.com on a new approach - FACES - for selectively imaging of phospholipids and other biomolecules at spatial resolutions down to individual membrane leaflets (1/n) www.nature.com/articles/s41...

Leaflet-specific phospholipid imaging using genetically encoded proximity sensors - Nature Chemical Biology

An approach combining bioorthogonal chemistry with genetically encoded fluorogen-activating proteins enables subcellular imaging of phospholipids and glycans, as well as the visualization of lipid tra...

nature.com

Thrilled to share this manuscript from my lab where we looked at how glycopolymers that compose the glycocalyx influence protein folding and protein-protein interactions via macromolecular crowding. TLDR: The Glycocalyx stabilizes protein folding and PPIs www.biorxiv.org/content/10.1...

Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions

Macromolecular crowding is ubiquitous to physiological environments, perturbing the thermodynamics and kinetics of proteins via excluded volume and nonspecific chemical interactions. While crowding ha...

biorxiv.org

Happy to share our contribution to this special issue dedicated to "Proximity-Induced Chemical Biology". We provide our take on targeted protein acetylation. Nice work Wesley and Roy! pubs.acs.org/doi/10.1021/...

Targeted Protein Acetylation Through Chemically Induced Proximity

ConspectusProtein acetylation is a pervasive and reversible post-translational modification (PTM) that impacts various protein features including stability, localization, and interactions and regulate...

pubs.acs.org

New preprint from Daniel Du @fitzpatricklab.bsky.social shows #femtosecond light pulses can lens electron beams, promising higher contrast in #cryoET and better aberration correction in #cryoEM tinyurl.com/257sw7j9 Experiments made possible by support from @cziscience.bsky.social #ImagingTheFuture

This could be a good time to mention we are looking for a new Lab Manager / Postdoc for the biochemistry lab with expertise protein expression, purification, and protein NMR. Details to follow.

Mass spec/proteomics chempostdoc in the Ferguson lab, UCSD, La Jolla, CA chemsky 🧪 ⚗️ jobrxiv.org/job/universi...

Research Scientist - Mass spectrometry - Ferguson Lab

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org

Nature research paper: Structural basis for the conformational protection of nitrogenase from O2 https://go.nature.com/4aiD344

Structural basis for the conformational protection of nitrogenase from O2 - Nature

Cryo-electron microscopy of Azotobacter vinelandii FeSII–nitrogenase reveals a core complex of molybdenum–iron proteins (MoFePs), iron proteins (FePs) and FeSII, in which FeSII mediates interactions with MoFeP and FeP to position their FeS clusters in catalytically inactive but O2-protected states.

go.nature.com

Awesome work from Sarah, @bcryo.bsky.social and friends in the Herzik Lab! It was cool to see this come together in such a short time.

Brian Cook@bcryo.bsky.social · 2y ago

1) Since I am the only Herzik lab member on @bsky.app, I get the privilege to announce our most recent publication from the Herzik/Tezcan labs. I got the wonderful opportunity to contribute on the cryoEM study of the oxygen protection mechansim employed by cells to protect Nitrogenase!

Awesome application of biorthogonal chemistry to trap non-ribosomal peptide synthetase complexes for cryo-EM, out yesterday from the Burkart Lab @ucsandiego.bsky.social www.nature.com/articles/s41...

Crosslinking intermodular condensation in non-ribosomal peptide biosynthesis - Nature

Structural studies of tyrocidine synthetase using site-selective crosslinking probes to link condensation domains with carrier protein substrates define key interactions and molecular mechanisms of no...

nature.com

What do they keep in here…